Merge branch 'master' of github.com:fluiddyn/fluidfoam

.github/workflows/build_and_pypi.yml

@@ -12,7 +12,7 @@ jobs:
       version_changed: ${{ steps.check_file_changed.outputs.files_changed }}
     steps:
       - run: pip install -U pip pipenv coverage
-      - run: pip install -U numpy==1.21.2 scipy==1.7.3 matplotlib
+      - run: pip install -U numpy scipy matplotlib
       - name: Check out repository code
         uses: actions/checkout@v2
       - run: set -o pipefail
@@ -35,19 +35,12 @@ jobs:
   Publish-Pypi:
     needs: build
     runs-on: ubuntu-latest
-    if: github.ref == 'refs/heads/master'
+    if: startsWith(github.event.ref, 'refs/tags')
     steps:
       - name: Check out repository code
         uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-#      - uses: dorny/paths-filter@v2
-#        id: changes
-#        with:
-#          filters: |
-#            src:
-#              - 'fluidfoam/_version.py'
       - name: Deploy package
-#        if: steps.changes.outputs.src == 'true'
         uses: casperdcl/deploy-pypi@v2
         with:
           password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/build_and_test.yml

@@ -12,7 +12,7 @@ jobs:
       version_changed: ${{ steps.check_file_changed.outputs.files_changed }}
     steps:
       - run: pip install -U pip pipenv coverage
-      - run: pip install -U numpy==1.21.2 scipy==1.7.3 matplotlib
+      - run: pip install -U numpy scipy matplotlib
       - name: Check out repository code
         uses: actions/checkout@v2
       - run: set -o pipefail

.readthedocs.yml

@@ -18,7 +18,7 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: doc/requirements.txt
     - method: setuptools

README.rst

@@ -26,8 +26,8 @@ What is this repository for?
 ----------------------------
 
 * Openfoam Tools
-* Version : 0.2.3
-* Supported OpenFoam Versions : 2.4.0, 4.1 to 9, v1712plus to v2112plus
+* Version : 0.2.4
+* Supported OpenFoam Versions : 2.4.0, 4.1 to 9, v1712plus to v2212plus
 * Supported Python Versions : >= 3.8
 
 Documentation and Examples

dev-requirements.txt

@@ -1,4 +1,4 @@
 numpy>=1.11
-scipy==1.7.3
+scipy>=1.7.3
 matplotlib>=1.5
 wheel

doc/index.rst

@@ -13,9 +13,9 @@ What is this repository for?
 ----------------------------
 
 * Openfoam Tools
-* Version : 0.2.3
-* Supported OpenFoam Versions : 2.4.0, 4.1 to 9, v1712plus to v2112plus
-* Supported Python Versions : >= 3.7
+* Version : 0.2.4
+* Supported OpenFoam Versions : 2.4.0, 4.1 to 9, v1712plus to v2212plus
+* Supported Python Versions : >= 3.8
 
 Deployment instructions
 -----------------------

examples/advanced/generateDFSEMdata.py

@@ -0,0 +1,49 @@
+"""
+Create and plot boundaryData for DFSEM from a 1D RANS simulation
+=======================================
+
+This example shows how to create a boundary data for turbulentDFSEM 
+inlet boundary condition. In addition, the script also plots the 
+profiles for verification. 
+"""
+
+from fluidfoam import create1dprofilDFSEM, read1dprofilDFSEM
+import os
+
+basepath = "../../output_samples//DFSEM/"
+
+case3d = "3D/"
+case1d = "1D/"
+
+sol1d = os.path.join(basepath, case1d)
+sol3d = os.path.join(basepath, case3d)
+
+boundary_name = "inlet/"
+axis = "Y"
+
+create1dprofilDFSEM(sol1d, sol3d, boundary_name, "200", axis, 
+                         "U","k","omega","turbulenceProperties:R","Y")
+# if turbulenceProperties:R does not exist type:
+# "pimpleFoam -postProcess -func R -time 200"
+# in a terminal
+
+Y, U, L, R, ny = read1dprofilDFSEM(sol3d, boundary_name, "0", axis)
+
+import matplotlib.pyplot as plt
+
+dummy, axarr = plt.subplots(1, 3, sharey=True)
+axarr[0].set_ylabel("Y (m)")
+
+axarr[0].plot(U[:], Y)
+axarr[0].set_title("U")
+axarr[0].set_xlabel("U (m/s)")
+
+axarr[1].plot(L[:], Y)
+axarr[1].set_title("L")
+axarr[1].set_xlabel("L (m)")
+
+axarr[2].plot(R[:,1], Y)
+axarr[2].set_title("R")
+axarr[2].set_xlabel(r"R ($m^2/s^2$)")
+
+plt.show()

examples/advanced/plot_unstructured_simu.py

@@ -0,0 +1,147 @@
+"""
+Plot bed interface from unstructured mesh 
+=======================================
+
+This example shows how to create a pointer list of profiles from an
+unstructured mesh and to extract the bed interface elevation. The
+results are plotted as a scatter plot.
+"""
+
+###############################################################################
+
+#path where the simulation is located
+path = '../../output_samples'
+#Name of the simulation to load
+simu = '3dscour'
+#time step to load
+timeStep = '0'
+#Switch to save postprocessed data on output
+saveOutput = 1
+
+###############################################################################
+# Read the mesh and extract the pointerList
+# --------------------------------------
+#
+# import python packages
+from fluidfoam import readmesh,readfield
+import os
+import numpy as np
+#
+#---read mesh (in folder constant, if not done type writeCellCenters -time constant in a terminal)
+#
+sol = os.path.join(path, simu)
+Xb, Yb, Zb = readfield(sol, 'constant', 'C', precision=12)
+#
+#---create a list of (x,y) positions correpsonding to Zb = min(Zb)
+#
+print("Generate pointer list")
+pbed = np.where(Zb == np.amin(Zb))[0]
+
+n2d = np.size(pbed)
+nz = 0
+profileList = []
+for i in range(n2d):
+	#Extract the list of points having the same (Xb, Yb) values
+	indices = np.where(np.logical_and(Xb == Xb[pbed[i]],
+	                                  Yb == Yb[pbed[i]]))[0]
+	nz = max(nz, np.size(indices))
+	profile = list(indices)
+	#Sort the list of points by increasing Zb values (profile)
+	profileSorted = [x for _, x in sorted(zip(Zb[profile], profile))]
+	#Append the list to the profileList
+	profileList.append(profileSorted)
+
+# Convert profileList to numpy.array
+pointer = np.array(profileList)
+
+###############################################################################
+# Extract bed surface from alpha.a profiles: min{ Zb | alpha.a <= 0.57 }
+# --------------------------------------------------------------
+#
+print("Extract bed surface")
+a    = readfield(sol, timeStep, 'alpha.a')
+
+zbed = np.zeros(n2d)
+for i in range(n2d):
+	bed_surface=np.where(a[pointer[i,:]] <= 0.57)[0]
+	zbed[i] = np.min(Zb[pointer[i,bed_surface]])
+
+###############################################################################
+# Now plot the zbed elevation
+# --------------------------------------------------------------
+#
+import matplotlib.pyplot as plt
+
+D = 0.1
+zmin = np.min([np.min(zbed), -np.max(zbed)])
+zmax = np.max([-np.min(zbed), np.max(zbed)])
+zlevels = np.linspace(zmin, zmax, 51)
+
+plt.figure()
+plt.scatter(Xb[pbed]/D, Yb[pbed]/D, c=zbed, 
+            vmin=zmin, vmax=zmax, cmap = 'seismic')
+plt.colorbar()
+
+#Setting axis labels
+plt.xlabel('x/D')
+plt.ylabel('y/D')
+
+# add grid
+plt.grid()
+
+# show figure
+plt.show()
+
+
+###############################################################################
+# save NetCDF files in constant and timeStep folders
+# --------------------------------------
+#
+if saveOutput == 1:
+	from netCDF4 import Dataset
+
+	postProcFile = os.path.join(sol, 'constant/pointerpostproc.nc')
+	print ("save postprocFile in:",postProcFile)
+
+	# NetCDF file creation
+	rootgrp = Dataset(postProcFile, 'w')
+
+	# Dimensions creation
+	rootgrp.createDimension('XY', n2d)
+	rootgrp.createDimension('Z', nz)
+
+	# Variables creation
+	pb_file = rootgrp.createVariable('pbed', np.int64, 'XY')
+	x_file  = rootgrp.createVariable('x', np.float64, 'XY')
+	y_file  = rootgrp.createVariable('y', np.float64, 'XY')
+	z_file  = rootgrp.createVariable('z', np.float64, ('XY','Z'))
+	p_file  = rootgrp.createVariable('p', np.int64, ('XY','Z'))
+
+	# Writing variables
+	pb_file[:]  = pbed
+	x_file[:]   = Xb[pbed]
+	y_file[:]   = Yb[pbed]
+	z_file[:,:] = Zb[pointer[:,:]]
+	p_file[:,:] = pointer[:,:]
+
+	# File closing
+	rootgrp.close()
+
+	postProcFile2 = os.path.join(sol, timeStep, 'zbed.nc')
+	print ("save zbed file in:",postProcFile2)
+
+	# NetCDF file creation
+	rootgrp = Dataset(postProcFile2, 'w')
+
+	# Dimensions creation
+	rootgrp.createDimension('XY', n2d)
+	rootgrp.createDimension('Z', nz)
+
+	# Variables creation
+	zb_file = rootgrp.createVariable('zbed', np.float64, 'XY')
+
+	# Writing variables
+	zb_file[:]  = zbed
+
+	# File closing
+	rootgrp.close()

examples/plot_3_postprocprobe.py

@@ -18,8 +18,8 @@
 sol = '../output_samples/ascii/'
 
 # import readprobes function from fluidfoam package
-timeU, u = readprobes(sol, time_name = 'mergeTime', name = 'U')
-timeP, p = readprobes(sol, time_name = 'mergeTime', name = 'p')
+probes_locU, timeU, u = readprobes(sol, time_name = 'mergeTime', name = 'U')
+probes_locP, timeP, p = readprobes(sol, time_name = 'mergeTime', name = 'p')
 
 ###############################################################################
 # Now plots the pressure and y velocity for the first probe

fluidfoam/__init__.py

@@ -5,6 +5,7 @@
 from fluidfoam.readof import typefield, OpenFoamFile
 from fluidfoam.processing1d import create1dprofil, read1dprofil
 from fluidfoam.processing1d import create1dprofil_spe, plot1dprofil
+from fluidfoam.processing1d import create1dprofilDFSEM, read1dprofilDFSEM
 from fluidfoam.meshdesign import getgz, getdzs
 from fluidfoam.readpostpro import readforce, readprobes
 from fluidfoam.meshvisu import MeshVisu

fluidfoam/_version.py

@@ -11,4 +11,4 @@
 'a' or 'alpha' means alpha version (internal testing),
 'b' or 'beta' means beta version (external testing).
 """
-__version__ = "0.2.3"
+__version__ = "0.2.4"