Several compatibility updates to the two-scale-heat-conduction tutori…

…al (#460)

* Make Nutils micro simulation compatible with Nutils v8.5 and the latest Micro Manager

* Make run scripts consistent

* initialize micro-data and accept sim_id in constructor

* Do not pass initial data which is not relevant for adaptivity

* Formatting

---------

Co-authored-by: Mathis Kelm <[email protected]>

two-scale-heat-conduction/micro-dumux/appl/micro_sim.cpp

@@ -63,8 +63,8 @@ class MicroSimulation {
   using SolutionVector    = Dumux::GetPropType<CellProblemTypeTag, Dumux::Properties::SolutionVector>;
 
 public:
-  MicroSimulation();
-  void initialize();
+  MicroSimulation(int simulationID);
+  py::dict initialize();
 
   // solve takes python dict for macro_write data, dt, and returns python dict for macro_read data
   py::dict solve(py::dict macro_write_data, double dt);
@@ -104,7 +104,7 @@ class MicroSimulation {
 };
 
 // Constructor
-MicroSimulation::MicroSimulation()
+MicroSimulation::MicroSimulation(int simulationID)
 {
   using namespace Dumux;
 
@@ -180,9 +180,34 @@ MicroSimulation::MicroSimulation()
   _timeLoop->start();
 };
 
-// Initialize
-void MicroSimulation::initialize()
+// Initialize micro-data to be used in initial adaptivity
+py::dict MicroSimulation::initialize()
 {
+  //update Phi in the cell problem
+  _cpProblem->spatialParams().updatePhi(_phi);
+
+  // solve the cell problems
+  _cpLinearPDESolver->solve(_psi);
+
+  // calculate porosity
+  _porosity = _acProblem->calculatePorosity(_phi);
+
+  //compute the psi derivatives (required for conductivity tensor)
+  _cpProblem->computePsiDerivatives(*_cpProblem, *_cpAssembler, *_cpGridVariables, _psi);
+
+  //calculate the conductivity tensor
+  _k_00 = _cpProblem->calculateConductivityTensorComponent(0, 0);
+  _k_11 = _cpProblem->calculateConductivityTensorComponent(1, 1);
+
+  // create python dict for micro_write_data
+  py::dict micro_write_data;
+
+  // add micro_scalar_data and micro_vector_data to micro_write_data
+  micro_write_data["k_00"]     = _k_00;
+  micro_write_data["k_11"]     = _k_11;
+  micro_write_data["porosity"] = _porosity;
+
+  return micro_write_data;
 }
 
 // Solve

two-scale-heat-conduction/micro-nutils/micro.py

@@ -13,7 +13,7 @@
 
 class MicroSimulation:
 
-    def __init__(self):
+    def __init__(self, sim_id):
         """
         Constructor of MicroSimulation class.
         """
@@ -43,6 +43,7 @@ def __init__(self):
         self._initial_condition_is_set = False
         self._k_nm1 = None  # Average effective conductivity of last time step
 
+    def initialize(self):
         # Define initial namespace
         self._ns = function.Namespace()
         self._ns.x = self._geom
@@ -85,6 +86,17 @@ def __init__(self):
         self._solphi = solphi  # Save solution of phi
         self._psi_nm1 = psi  # Average porosity value of last time step
 
+        # Solve the heat cell problem
+        solu = self._solve_heat_cell_problem(self._topo, solphi)
+        k = self._get_eff_conductivity(self._topo, solu, solphi)
+
+        output_data = dict()
+        output_data["k_00"] = k[0][0]
+        output_data["k_11"] = k[1][1]
+        output_data["porosity"] = psi
+
+        return output_data
+
     def _reinitialize_namespace(self, topo):
         self._ns = None  # Clear old namespace
         self._ns = function.Namespace()
@@ -112,7 +124,7 @@ def _reinitialize_namespace(self, topo):
 
     @staticmethod
     def _analytical_phasefield(x, y, r, lam):
-        return 1. / (1. + function.exp(-4. / lam * (function.sqrt(x ** 2 + y ** 2) - r + 0.001)))
+        return 1. / (1. + np.exp(-4. / lam * (np.sqrt(x ** 2 + y ** 2) - r + 0.001)))
 
     @staticmethod
     def _get_analytical_phasefield(topo, ns, degree_phi, lam, r):
@@ -263,7 +275,7 @@ def solve(self, macro_data, dt):
 
 
 def main():
-    micro_problem = MicroSimulation()
+    micro_problem = MicroSimulation(0)
     dt = 1e-3
     micro_problem.initialize()
     concentrations = [0.5, 0.4]

two-scale-heat-conduction/micro-nutils/run.sh

@@ -10,16 +10,16 @@ pip install -r requirements.txt
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
         echo "No input argument provided. Micro Manager is launched in serial"
-	python3 run-micro-problems.py
+	python3 run_micro_manager.py
 fi
 
 while getopts ":sp" opt; do
   case ${opt} in
   s)
-    python3 run-micro-problems.py
+    python3 run_micro_manager.py
     ;;
   p)
-    mpiexec -n "$2" python3 run-micro-problems.py
+    mpiexec -n "$2" python3 run_micro_manager.py
     ;;
   *)
     usage