From f34be1cefb14652f2bcc07e5bacd68fd894157a2 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Mon, 31 Jul 2017 13:48:49 +0200
Subject: [PATCH] inhomogeneous permeability and mass flux
---
pre/BCs/inhomogeneous-mass-flux/README.md | 10 +
.../prepare-inhomogeneous-mass-flux-BC.py | 118 ++++
.../smooth_velocity_profile.csv | 506 ++++++++++++++++++
.../inhomogeneous-permeability-cell/README.md | 5 +
.../prepare-inhomogeneous-permeability.py | 103 ++++
.../smooth_permeability_profile.csv | 506 ++++++++++++++++++
6 files changed, 1248 insertions(+)
create mode 100644 pre/BCs/inhomogeneous-mass-flux/README.md
create mode 100755 pre/BCs/inhomogeneous-mass-flux/prepare-inhomogeneous-mass-flux-BC.py
create mode 100644 pre/BCs/inhomogeneous-mass-flux/smooth_velocity_profile.csv
create mode 100644 pre/inhomogeneous-fields/inhomogeneous-permeability-cell/README.md
create mode 100755 pre/inhomogeneous-fields/inhomogeneous-permeability-cell/prepare-inhomogeneous-permeability.py
create mode 100644 pre/inhomogeneous-fields/inhomogeneous-permeability-cell/smooth_permeability_profile.csv
diff --git a/pre/BCs/inhomogeneous-mass-flux/README.md b/pre/BCs/inhomogeneous-mass-flux/README.md
new file mode 100644
index 0000000..e50238c
--- /dev/null
+++ b/pre/BCs/inhomogeneous-mass-flux/README.md
@@ -0,0 +1,10 @@
+# Prepare an inhomogeneous node-based mass flux field along a slice through a mesh
+
+The superficial velocity is given as a profile in radial (i.e., x) direction in the file `smooth_velocity_profile.csv`.
+
+A slice (hard-coded) through the `--input` mesh is taken. The mass flux field is
+evaluated at every node of the slice. The slice with the mass flux field is
+written to a VTU file in `--output`.
+
+Additionally to the `mass_flux` field, there will be a field `bulk_mesh_node_ids` which is used by OGS to map the mass flux values to the right mesh nodes if used as a Neumann BC.
+
diff --git a/pre/BCs/inhomogeneous-mass-flux/prepare-inhomogeneous-mass-flux-BC.py b/pre/BCs/inhomogeneous-mass-flux/prepare-inhomogeneous-mass-flux-BC.py
new file mode 100755
index 0000000..c8e791f
--- /dev/null
+++ b/pre/BCs/inhomogeneous-mass-flux/prepare-inhomogeneous-mass-flux-BC.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env pvpython
+
+import inspect
+
+import argparse
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", type=str, required=True)
+parser.add_argument("--output", type=str, required=True)
+args = parser.parse_args()
+
+#### import the simple module from the paraview
+from paraview.simple import *
+#### disable automatic camera reset on 'Show'
+paraview.simple._DisableFirstRenderCameraReset()
+
+# create a new 'XML Unstructured Grid Reader'
+xMLUnstructuredGridReader1 = XMLUnstructuredGridReader(FileName=[args.input])
+
+
+def do_enumerate_points():
+ data = self.GetInputDataObject(0, 0)
+
+ # point_ids = vtk.vtkIdTypeArray() ## TODO why does that not work?
+ # point_ids = vtk.vtkLongArray()
+ point_ids = vtk.vtkUnsignedLongArray()
+ point_ids.SetName("bulk_mesh_node_ids")
+ point_ids.SetNumberOfComponents(1)
+ N = data.GetPoints().GetNumberOfPoints()
+ point_ids.SetNumberOfTuples(N)
+
+ for i in range(N):
+ point_ids.SetComponent(i, 0, i)
+
+ self.GetOutputDataObject(0).GetPointData().AddArray(point_ids)
+
+ ### Cell ids do not work like that:
+ # cell_ids = vtk.vtkDoubleArray()
+ # cell_ids.SetName("bulk_mesh_element_ids")
+ # cell_ids.SetNumberOfComponents(1)
+ # C = data.GetCellData().GetNumberOfTuples()
+ # cell_ids.SetNumberOfTuples(N)
+
+ # for i in range(C):
+ # cell_ids.SetComponent(i, 0, i)
+
+ # self.GetOutputDataObject(0).GetCellData().AddArray(cell_ids)
+
+
+enumerate_points = ProgrammableFilter(Input=xMLUnstructuredGridReader1)
+enumerate_points.Script = inspect.getsource(do_enumerate_points) + "\n\ndo_enumerate_points()"
+enumerate_points.RequestInformationScript = ''
+enumerate_points.RequestUpdateExtentScript = ''
+enumerate_points.PythonPath = ''
+enumerate_points.CopyArrays = 0
+
+
+# create a new 'Slice'
+slice1 = Slice(Input=enumerate_points)
+slice1.SliceType = 'Plane'
+slice1.Triangulatetheslice = 0
+slice1.SliceOffsetValues = [0.0]
+
+# init the 'Plane' selected for 'SliceType'
+slice1.SliceType.Origin = [0.0044, 0.03, 0.0]
+slice1.SliceType.Normal = [0.0, 1.0, 0.0]
+
+
+# Trick from http://www.vtk.org/Wiki/VTK/Examples/Cxx/PolyData/PolyDataToUnstructuredGrid
+# for converting slice's polydata to an unstructured grid
+appendDatasets1 = AppendDatasets(Input=slice1)
+
+
+def do_compute_mass_flux():
+ import numpy as np
+ from scipy.interpolate import interp1d
+ data = self.GetInputDataObject(0, 0)
+
+ ### compute predefined mass flux
+
+ mu = 21.90e-6 # Pa s
+ rho = 0.9333 # kg/m³
+
+ csv = "smooth_velocity_profile.csv"
+ rs, velocities = np.loadtxt(csv, unpack=True, usecols=(0,1))
+ velocity_fct = interp1d(rs, velocities)
+
+ points = data.GetPoints()
+
+ mass_flux = vtk.vtkDoubleArray()
+ mass_flux.SetName("mass_flux")
+ mass_flux.SetNumberOfComponents(1)
+ N = points.GetNumberOfPoints()
+ mass_flux.SetNumberOfTuples(N)
+
+ for i in range(N):
+ r, z, phi = points.GetPoint(i)
+ mass_flux.SetComponent(i, 0, velocity_fct(r) * rho)
+
+ self.GetOutputDataObject(0).GetPointData().AddArray(mass_flux)
+
+
+mass_flux = ProgrammableFilter(Input=appendDatasets1)
+mass_flux.Script = inspect.getsource(do_compute_mass_flux) + "\n\ndo_compute_mass_flux()"
+mass_flux.RequestInformationScript = ''
+mass_flux.RequestUpdateExtentScript = ''
+mass_flux.PythonPath = ''
+mass_flux.CopyArrays = 1
+
+# ----------------------------------------------------------------
+# finally, restore active source
+SetActiveSource(mass_flux)
+# ----------------------------------------------------------------
+
+# save data
+SaveData(args.output, proxy=mass_flux, DataMode='Binary',
+ EncodeAppendedData=1,
+ CompressorType='ZLib')
+
diff --git a/pre/BCs/inhomogeneous-mass-flux/smooth_velocity_profile.csv b/pre/BCs/inhomogeneous-mass-flux/smooth_velocity_profile.csv
new file mode 100644
index 0000000..1cd50e1
--- /dev/null
+++ b/pre/BCs/inhomogeneous-mass-flux/smooth_velocity_profile.csv
@@ -0,0 +1,506 @@
+
+# Curve 0 of 1, 501 points
+# Curve title: ""bed_center_cross_section.csv" u x_col:y_col"
+# x y type
+ 0 0.488557 i
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diff --git a/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/README.md b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/README.md
new file mode 100644
index 0000000..1a99570
--- /dev/null
+++ b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/README.md
@@ -0,0 +1,5 @@
+# Prepare an inhomogeneous cell-based permeability field
+
+The permeability is given as a profile in radial (i.e., x) direction in the file `smooth_permeability_profile.csv`.
+The permeability value is evaluated at the center coordinate of each cell of the mesh read from `--input`.
+The resulting field and mesh is written to `--output`.
diff --git a/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/prepare-inhomogeneous-permeability.py b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/prepare-inhomogeneous-permeability.py
new file mode 100755
index 0000000..4d7cb61
--- /dev/null
+++ b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/prepare-inhomogeneous-permeability.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env pvpython
+
+import inspect
+
+import argparse
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", type=str, required=True)
+parser.add_argument("--output", type=str, required=True)
+args = parser.parse_args()
+
+
+# state file generated using paraview version 5.3.0
+
+# ----------------------------------------------------------------
+# setup views used in the visualization
+# ----------------------------------------------------------------
+
+#### import the simple module from the paraview
+from paraview.simple import *
+#### disable automatic camera reset on 'Show'
+paraview.simple._DisableFirstRenderCameraReset()
+
+# create a new 'XML Unstructured Grid Reader'
+xMLUnstructuredGridReader1 = XMLUnstructuredGridReader(FileName=[args.input])
+
+# create a new 'Calculator'
+coords_to_property = Calculator(Input=xMLUnstructuredGridReader1)
+coords_to_property.ResultArrayName = 'cell_centers'
+coords_to_property.Function = 'coords'
+
+# create a new 'Point Data to Cell Data'
+pointDatatoCellData2 = PointDatatoCellData(Input=coords_to_property)
+
+def compute_perm():
+ import os
+ import numpy as np
+ from scipy.interpolate import interp1d
+
+ csv = "smooth_permeability_profile.csv"
+ rs, perms = np.loadtxt(csv, unpack=True, usecols=(0,1))
+ perm_fct = interp1d(rs, perms)
+
+ data = self.GetInputDataObject(0, 0)
+ cell_centers = data.GetCellData().GetArray("cell_centers")
+
+ perm_cell = vtk.vtkDoubleArray()
+ perm_cell.SetName("K_rho_over_mu__eff")
+ perm_cell.SetNumberOfComponents(1)
+ N = cell_centers.GetNumberOfTuples()
+ perm_cell.SetNumberOfTuples(N)
+
+ mu = 21.90e-6 # Pa s
+ rho = 0.9333 # kg/m³
+
+ for i in range(N):
+ r, z, _ = cell_centers.GetTuple(i)
+ K = perm_fct(r)
+ perm_cell.SetComponent(i, 0, K * rho / mu)
+
+ self.GetOutputDataObject(0).GetCellData().AddArray(perm_cell)
+
+
+ if True:
+ # mass flux
+
+ csv = "smooth_velocity_profile.csv"
+ rs, velocities = np.loadtxt(csv, unpack=True, usecols=(0,1))
+ velocity_fct = interp1d(rs, velocities)
+
+ points = data.GetPoints()
+
+ mass_flux = vtk.vtkDoubleArray()
+ mass_flux.SetName("mass_flux_ref")
+ mass_flux.SetNumberOfComponents(2)
+ N = points.GetNumberOfPoints()
+ mass_flux.SetNumberOfTuples(N)
+
+ for i in range(N):
+ r, z, phi = points.GetPoint(i)
+ mass_flux.SetComponent(i, 0, 0)
+ mass_flux.SetComponent(i, 1, -velocity_fct(r) * rho)
+
+ self.GetOutputDataObject(0).GetPointData().AddArray(mass_flux)
+
+ self.GetOutputDataObject(0).GetCellData().RemoveArray("cell_centers")
+
+
+perm = ProgrammableFilter(Input=pointDatatoCellData2)
+perm.Script = inspect.getsource(compute_perm) + "\n\ncompute_perm()"
+perm.RequestInformationScript = ''
+perm.RequestUpdateExtentScript = ''
+perm.PythonPath = ''
+perm.CopyArrays = 0
+
+# ----------------------------------------------------------------
+# finally, restore active source
+SetActiveSource(perm)
+# ----------------------------------------------------------------
+
+# save data
+SaveData(args.output, proxy=perm, DataMode='Binary',
+ EncodeAppendedData=1,
+ CompressorType='ZLib')
diff --git a/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/smooth_permeability_profile.csv b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/smooth_permeability_profile.csv
new file mode 100644
index 0000000..8985431
--- /dev/null
+++ b/pre/inhomogeneous-fields/inhomogeneous-permeability-cell/smooth_permeability_profile.csv
@@ -0,0 +1,506 @@
+
+# Curve 0 of 1, 501 points
+# Curve title: ""bed_center_cross_section.csv" u 14:1"
+# x y type
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--
GitLab