Use pathlib and absolute paths to allow execution from root folder of tutorial.

Author: BenjaminRodenberg

channel-transport-reaction/chemical-fenics/chemical-reaction-advection-diffusion.py

@@ -4,8 +4,9 @@
 import numpy as np
 import csv
 from mpi4py import MPI
+from pathlib import Path
 
-outfolder = 'output'
+outfolder = Path(__file__).parent / 'output'
 
 default_dt = 1.0  # time step size
 
@@ -26,7 +27,7 @@ def inside(self, x, on_boundary):
 
 # Initialize preCICE
 precice = fenicsprecice.Adapter(
-    adapter_config_filename="chemical-reaction-advection-diffusion.json")
+    adapter_config_filename=Path(__file__).parent / "chemical-reaction-advection-diffusion.json")
 precice.initialize(coupling_subdomain=CouplingDomain(), read_function_space=W)
 precice_dt = precice.get_max_time_step_size()
 
@@ -78,16 +79,16 @@ def inside(self, x, on_boundary):
 
 
 t = 0
-vtkfileA = File(outfolder + '/chemical_A.pvd')
-vtkfileB = File(outfolder + '/chemical_B.pvd')
-vtkfileC = File(outfolder + '/chemical_C.pvd')
-vtkfileFlow = File(outfolder + '/chemical_fluid_read.pvd')
+vtkfileA = File(str(outfolder / 'chemical_A.pvd'))
+vtkfileB = File(str(outfolder / 'chemical_B.pvd'))
+vtkfileC = File(str(outfolder / 'chemical_C.pvd'))
+vtkfileFlow = File(str(outfolder / 'chemical_fluid_read.pvd'))
 
 # CSV file to keep track of integrals (i.e. total amount of A, B, C)
-# with open(outfolder + '/chemical_out.csv', 'w', newline='') as csvfile:
+# with open(outfolder / 'chemical_out.csv', 'w', newline='') as csvfile:
 
 if MPI.COMM_WORLD.rank == 0:
-    csvfile = open(outfolder + '/chemical_out.csv', 'w', newline='')
+    csvfile = open(outfolder / 'chemical_out.csv', 'w', newline='')
     writer = csv.writer(csvfile, delimiter=' ', quotechar='|',
                         quoting=csv.QUOTE_MINIMAL)
 

channel-transport-reaction/fluid-fenics/fluid.py

@@ -11,8 +11,9 @@
 from mshr import *
 import fenicsprecice
 import numpy as np
+from pathlib import Path
 
-outfolder = 'output'
+outfolder = Path(__file__).parent / 'output'
 
 # time step size (preCICE handles the main loop; if this is smaller than
 # preCICE dt, we subcycle)
@@ -117,7 +118,7 @@ def inside(self, x, on_boundary):
         return True
 
 
-precice = fenicsprecice.Adapter(adapter_config_filename="fluid-config.json")
+precice = fenicsprecice.Adapter(adapter_config_filename=Path(__file__).parent / "fluid-config.json")
 precice.initialize(coupling_subdomain=CouplingDomain(), write_object=u_)
 precice_dt = precice.get_max_time_step_size()
 
@@ -127,7 +128,7 @@ def inside(self, x, on_boundary):
 # No implicit coupling supported, as this is uni-directional coupling
 # If needed, implement checkpointing
 t = 0
-vtkfile = File(outfolder + '/chemical_fluid_write.pvd')
+vtkfile = File(str(outfolder / 'chemical_fluid_write.pvd'))
 
 while precice.is_coupling_ongoing():