Merge branch 'develop' into 'master'

Update to version 1.1

See merge request !5

examples/channel_flow/input.yml

@@ -48,14 +48,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen number
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: r13
-use_coeffs: True
 kn: 1.0
 xi_tilde: 1.0
 heat_source: 0

examples/knudsen_pump/create_mesh.sh

 #!/bin/bash
-python3 ../../src/geoToH5.py knudsen_pump.geo knudsen_pump4.h5 "-setnumber p 4"
\ No newline at end of file
+geoToH5 knudsen_pump.geo knudsen_pump4.h5 "-setnumber p 4"
\ No newline at end of file

examples/knudsen_pump/input.yml

@@ -49,14 +49,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen number
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: r13
-use_coeffs: True
 kn: 0.1
 xi_tilde: 1.0
 heat_source: 0

examples/lid_driven_cavity/create_mesh.sh

 #!/bin/bash
-python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
\ No newline at end of file
+geoToH5 lid.geo lid5.h5 "-setnumber p 5"
\ No newline at end of file

examples/lid_driven_cavity/input.yml

@@ -48,14 +48,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen number
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: r13
-use_coeffs: True
 kn: 0.08
 xi_tilde: 1.0
 heat_source: 0

examples/test_examples.py

@@ -14,7 +14,7 @@ class TestExamples(object):
     All tests are compared against reference errors.
     """
 
-    solver_path = "../../src/fenicsR13.py"
+    solver_path = "fenicsR13"
 
     def run_solver(self, inputfile, working_dir_):
         """
@@ -23,7 +23,7 @@ class TestExamples(object):
         Test fails if subprocess return Exception or error.
         """
         subprocess.check_call([
-            "python3", self.solver_path, inputfile
+            self.solver_path, inputfile
         ], cwd=working_dir_)
 
     # @pytest.fixture(scope="module", autouse=True)

fenicsR13/__init__.py

+# pylint: disable=invalid-name,missing-module-docstring
+
+from .fenicsR13 import *
+from .geoToH5 import *
+from .input import *
+from .meshes import *
+from .postprocessor import *
+from .solver import *
+from .tensoroperations import *

src/fenicsR13.py → fenicsR13/fenicsR13.py

@@ -15,10 +15,10 @@ import sys
 import gc
 import dolfin as df
 
-import meshes
-from input import Input
-from solver import Solver
-from postprocessor import Postprocessor
+from fenicsR13.meshes import H5Mesh
+from fenicsR13.input import Input
+from fenicsR13.solver import Solver
+from fenicsR13.postprocessor import Postprocessor
 
 def print_information():
     r"""
@@ -28,7 +28,7 @@ def print_information():
 
     .. code-block:: text
 
-        -> Version: v1.0
+        -> Version: v1.1
         -> Contact: Lambert Theisen <lambert.theisen@rwth-aachen.de>
         -> Contact: Manuel Torrilhon <mt@mathcces.rwth-aachen.de>
         -> Repository: <https://git.rwth-aachen.de/lamBOO/fenicsR13>
@@ -40,7 +40,7 @@ def print_information():
         |_|  \___|_| |_|_|\___|___/_| \_\_|____/
 
     """
-    print(r"""-> Version: v1.0
+    print(r"""-> Version: v1.1
 -> Contact: Lambert Theisen <lambert.theisen@rwth-aachen.de>
 -> Contact: Manuel Torrilhon <mt@mathcces.rwth-aachen.de>
 -> Repository: <https://git.rwth-aachen.de/lamBOO/fenicsR13>
@@ -63,10 +63,13 @@ def main():
 
     .. code-block:: bash
 
+        # Install fenicsR13
+        pip install .
+
         # Usage: <path_to_program> <input_file>
         # Goto case folder:
         cd tests/r13
-        python3 ../../src/fenicsR13.py inputs/ \
+        fenicsR13 inputs/ \
           r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml
 
     """
@@ -108,7 +111,7 @@ def main():
 
             mesh_name = mesh_names[p]
 
-            current_mesh = meshes.H5Mesh(mesh_name)
+            current_mesh = H5Mesh(mesh_name)
             solver = Solver(params, current_mesh, p)
 
             solver.assemble()

src/geoToH5.py → fenicsR13/geoToH5.py

@@ -5,13 +5,19 @@
 """
 Converter from geo-format to a mesh in h5-format.
 
+Installation:
+
+.. code-block:: bash
+
+    pip install .
+
 Usage:
 
 .. code-block:: bash
 
     Usage: python3 <path_to_geoToH5.py> <geo_file> <h5_file> \
             [<gmsh cli arguments>]
-    E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
+    E.g.: geoToH5 lid.geo lid5.h5 "-setnumber p 5"
 """
 
 import os
@@ -29,7 +35,7 @@ def geo_to_h5():
     if not 3 <= len(sys.argv) <= 4:
         print("""
 Usage: python3 <path_to_geoToH5.py> <geo_file> <h5_file> [<gmsh cli arguments>]
-E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
+E.g.: geoToH5 lid.geo lid5.h5 "-setnumber p 5"
         """)
         return
 
@@ -68,10 +74,3 @@ E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
     file.write(mesh, "/mesh")
     file.write(subdomains, "/subdomains")
     file.write(boundaries, "/boundaries")
-
-def main():
-    "Execute the converter."
-    geo_to_h5()
-
-if __name__ == '__main__':
-    main()

src/input.py → fenicsR13/input.py

@@ -78,14 +78,12 @@ class Input:
         # ======================
         # - nsd: Number of spatial dimensions == 2
         # - mode: Formulation mode, one of heat, stress, r13
-        # - use_coeffs: Use real R13 coefficients, False only valid in heat
         # - kn: Knudsen numberkn
         # - xi_tilde: Refaction coefficient in Maxwell accomodation model
         # - heat_source: Heat source function for mode==heat||r13
         # - mass_source: Mass source function for mode==stress||r13
         nsd: 2
         mode: r13
-        use_coeffs: True
         kn: 1.0
         xi_tilde: 1.0
         heat_source: 0
@@ -166,8 +164,12 @@ class Input:
 
     def __init__(self, yaml_file):
         """Construct the Input class."""
-        with open(yaml_file, "r") as stream:
-            self.dict = yaml.safe_load(stream)
+        try:
+            with open(yaml_file, "r") as stream:
+                self.dict = yaml.safe_load(stream)
+        except FileNotFoundError:
+            print(f"[Error] The input file {yaml_file} is not found.\n")
+            raise
 
         val = Validator()
         input_schema = {
@@ -186,10 +188,6 @@ class Input:
                 "required": True,
                 "allowed": ["heat", "stress", "r13"]
             },
-            "use_coeffs": {
-                "type": "boolean",
-                "required": True,
-            },
             "kn": {
                 "type": "float",
                 "required": True,

src/tensoroperations.py → fenicsR13/tensoroperations.py

@@ -80,7 +80,7 @@ def stf3d3(rank3_3d):
 
     .. math::
 
-        A_{\langle i j k\rangle}=A_{(i j k)}-\frac{1}{5}\left[A_{(i l)}
+        A_{\langle i j k\rangle}=A_{(i j k)}-\frac{1}{5}\left[A_{(i l l)}
         \delta_{j k}+A_{(l j l)} \delta_{i k}+A_{(l l k)} \delta_{i j}\right]
 
     A gradient :math:`\frac{\partial S_{\langle i j}}{\partial x_{k \rangle}}`

info.json

-{
-  "schemaVersion": 1,
-  "label": "tag",
-  "message": "v0.3",
-  "color": "orange"
-}

pytest.ini

 [pytest]
-testpaths = src examples/test_examples.py tests
+testpaths = fenicsR13 tests examples/test_examples.py
 addopts = --doctest-modules --cov --cov-report=term --cov-report=html

setup.py

+"Setup file"
+
+from setuptools import setup
+
+def readme(): # pylint: disable=missing-function-docstring
+    with open('README.rst') as file:
+        return file.read()
+
+setup(
+    name="fenicsR13",
+    version="1.1",
+    description="FEniCS (FEM) Solver for Non.-Eq.-Gases Based on R13 Equations",
+    long_description=readme(),
+    url="https://git.rwth-aachen.de/lamBOO/fenicsR13",
+    author="Lambert Theisen, Manuel Torrilhon",
+    author_email="lambert.theisen@rwth-aachen.de, mt@mathcces.rwth-aachen.de",
+    license="None",
+    packages=["fenicsR13"],
+    zip_safe=False,
+    entry_points={
+        "console_scripts": [
+            "fenicsR13=fenicsR13.fenicsR13:main",
+            "geoToH5=fenicsR13.geoToH5:geo_to_h5"
+        ],
+    }
+)

tests/heat/inputs/heat_01_coeffs_p1p1_stab.yml

@@ -55,14 +55,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen numberkn
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: heat
-use_coeffs: True
 kn: 0.1
 xi_tilde: 1.0
 heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)

tests/heat/inputs/heat_01_coeffs_p1p2_nostab.yml

@@ -55,14 +55,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen numberkn
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: heat
-use_coeffs: True
 kn: 0.1
 xi_tilde: 1.0
 heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)

tests/heat/inputs/heat_01_coeffs_p2p2_stab.yml

@@ -55,14 +55,12 @@ stabilization:
 # ======================
 # - nsd: Number of spatial dimensions == 2
 # - mode: Formulation mode, one of heat, stress, r13
-# - use_coeffs: Use real R13 coefficients, False only valid in mode==heat
 # - kn: Knudsen numberkn
 # - xi_tilde: Refaction coefficient in Maxwell accomodation model
 # - heat_source: Heat source function for mode==heat||r13
 # - mass_source: Mass source function for mode==stress||r13
 nsd: 2
 mode: heat
-use_coeffs: True
 kn: 0.1
 xi_tilde: 1.0
 heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)