Obey data and mesh naming rules in the two-scale heat conduction (#699)

* Conform to naming nomenclature in the tutorials

* Remove network from precice-config.xml

Co-authored-by: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>

* Update precice-config.xml visualization

* Fix the remaining naming changes in macro-dumux, and add a changelog entry

---------

Co-authored-by: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>

Author: IshaanDesai

changelog-entries/699.md

@@ -0,0 +1 @@
+- Adhered to the participant, data, and mesh naming rules in the two-scale heat conduction case [#699](https://github.com/precice/tutorials/pull/699)

two-scale-heat-conduction/images/tutorials-two-scale-heat-conduction-precice-config.png

@@ -94,7 +94,7 @@ int main(int argc, char **argv)
   // - What rank of how many ranks this instance is
   // Configure preCICE. For now the config file is hardcoded.
   std::string       preciceConfigFilename = "../precice-config.xml";
-  const std::string meshName              = "macro-mesh";
+  const std::string meshName              = "Macro-Mesh";
   if (argc > 2)
     preciceConfigFilename = argv[argc - 1];
 
@@ -103,7 +103,7 @@ int main(int argc, char **argv)
   const auto runWithCoupling = getParam<bool>("Precice.RunWithCoupling");
 
   if (runWithCoupling) {
-    couplingParticipant.announceSolver("macro-heat", preciceConfigFilename,
+    couplingParticipant.announceSolver("Macro", preciceConfigFilename,
                                        mpiHelper.rank(), mpiHelper.size());
     // verify that dimensions match
     const int preciceDim = couplingParticipant.getMeshDimensions(meshName);
@@ -151,13 +151,12 @@ int main(int argc, char **argv)
   }
 
   // initialize the coupling data
-  const std::string readDatak00            = "k_00";
-  const std::string readDatak01            = "k_01";
-  const std::string readDatak10            = "k_10";
-  const std::string readDatak11            = "k_11";
-  const std::string readDataPorosity       = "porosity";
-  const std::string writeDataConcentration = "concentration";
-  // const std::string writeDataTemperature = "temperature";
+  const std::string readDatak00            = "K00";
+  const std::string readDatak01            = "K01";
+  const std::string readDatak10            = "K10";
+  const std::string readDatak11            = "K11";
+  const std::string readDataPorosity       = "Porosity";
+  const std::string writeDataConcentration = "Concentration";
 
   if (runWithCoupling) {
     couplingParticipant.announceQuantity(meshName, readDatak00);
@@ -166,7 +165,6 @@ int main(int argc, char **argv)
     couplingParticipant.announceQuantity(meshName, readDatak11);
     couplingParticipant.announceQuantity(meshName, readDataPorosity);
     couplingParticipant.announceQuantity(meshName, writeDataConcentration);
-    // couplingParticipant.announceQuantity(meshName, writeDataTemperature);
   }
 
   // the solution vector (initialized with zeros) NElements x 2(pressure,
@@ -214,11 +212,11 @@ int main(int argc, char **argv)
                                                            problem->name());
   IOFields::initOutputModule(vtkWriter);
   // add model specific output fields
-  vtkWriter.addField(problem->getPorosity(), "porosity");
-  vtkWriter.addField(problem->getK00(), "k00");
-  vtkWriter.addField(problem->getK01(), "k01");
-  vtkWriter.addField(problem->getK10(), "k10");
-  vtkWriter.addField(problem->getK11(), "k11");
+  vtkWriter.addField(problem->getPorosity(), "Porosity");
+  vtkWriter.addField(problem->getK00(), "K00");
+  vtkWriter.addField(problem->getK01(), "K01");
+  vtkWriter.addField(problem->getK10(), "K10");
+  vtkWriter.addField(problem->getK11(), "K11");
   problem->updateVtkOutput(x);
   vtkWriter.write(0.0);
 

two-scale-heat-conduction/macro-dumux/appl/main.cc

@@ -111,15 +111,15 @@ public:
       for (const auto &scv : scvs(fvGeometry)) {
         const auto elementIdx = scv.elementIndex();
         couplingData_[elementIdx][0] =
-            couplingParticipant_.getScalarQuantityOnFace("macro-mesh", "porosity", elementIdx);
+            couplingParticipant_.getScalarQuantityOnFace("Macro-Mesh", "Porosity", elementIdx);
         couplingData_[elementIdx][1] =
-            couplingParticipant_.getScalarQuantityOnFace("macro-mesh", "k_00", elementIdx);
+            couplingParticipant_.getScalarQuantityOnFace("Macro-Mesh", "K00", elementIdx);
         couplingData_[elementIdx][2] =
-            couplingParticipant_.getScalarQuantityOnFace("macro-mesh", "k_01", elementIdx);
+            couplingParticipant_.getScalarQuantityOnFace("Macro-Mesh", "K01", elementIdx);
         couplingData_[elementIdx][3] =
-            couplingParticipant_.getScalarQuantityOnFace("macro-mesh", "k_10", elementIdx);
+            couplingParticipant_.getScalarQuantityOnFace("Macro-Mesh", "K10", elementIdx);
         couplingData_[elementIdx][4] =
-            couplingParticipant_.getScalarQuantityOnFace("macro-mesh", "k_11", elementIdx);
+            couplingParticipant_.getScalarQuantityOnFace("Macro-Mesh", "K11", elementIdx);
       }
     }
     // Trigger exchange of coupling data between neighboring ranks, if the domain is partitioned

two-scale-heat-conduction/macro-dumux/appl/spatialparams.hh

@@ -20,7 +20,7 @@ MaxDt = 0.004
 InitialDt = 0.01
 
 [Problem]
-Name = macro-heat
+Name = Macro
 EnableGravity = false
 Permeability = 1.0
 DefaultPorosity = 0.5

two-scale-heat-conduction/macro-dumux/params.input

@@ -41,8 +41,8 @@ def main():
     ns.uinitial = 0.5
 
     if is_coupled_case:
-        participant = precice.Participant("macro-heat", "../precice-config.xml", 0, 1)
-        mesh_name = "macro-mesh"
+        participant = precice.Participant("Macro", "../precice-config.xml", 0, 1)
+        mesh_name = "Macro-Mesh"
 
         # Define Gauss points on entire domain as coupling mesh (volume coupling from macro side)
         couplingsample = topo.sample('gauss', degree=2)  # mesh vertices are Gauss points
@@ -68,7 +68,7 @@ def main():
     if is_coupled_case:
         if participant.requires_initial_data():
             concentrations = couplingsample.eval('u' @ ns, solu=solu0)
-            participant.write_data(mesh_name, "concentration", vertex_ids, concentrations)
+            participant.write_data(mesh_name, "Concentration", vertex_ids, concentrations)
 
         participant.initialize()
         dt = solver_dt = participant.get_max_time_step_size()
@@ -107,16 +107,16 @@ def main():
             dt = min(precice_dt, solver_dt)
 
             # Read porosity and apply it to the existing solution
-            poro_data = participant.read_data(mesh_name, "porosity", vertex_ids, dt)
+            poro_data = participant.read_data(mesh_name, "Porosity", vertex_ids, dt)
             poro_coupledata = couplingsample.asfunction(poro_data)
             sqrphi = couplingsample.integral((ns.phi - poro_coupledata) ** 2)
             solphi = solver.optimize('solphi', sqrphi, droptol=1E-12)
 
             # Read conductivity and apply it to the existing solution
-            k_00_c = couplingsample.asfunction(participant.read_data(mesh_name, "k_00", vertex_ids, dt))
-            k_01_c = couplingsample.asfunction(participant.read_data(mesh_name, "k_01", vertex_ids, dt))
-            k_10_c = couplingsample.asfunction(participant.read_data(mesh_name, "k_10", vertex_ids, dt))
-            k_11_c = couplingsample.asfunction(participant.read_data(mesh_name, "k_11", vertex_ids, dt))
+            k_00_c = couplingsample.asfunction(participant.read_data(mesh_name, "K00", vertex_ids, dt))
+            k_01_c = couplingsample.asfunction(participant.read_data(mesh_name, "K01", vertex_ids, dt))
+            k_10_c = couplingsample.asfunction(participant.read_data(mesh_name, "K10", vertex_ids, dt))
+            k_11_c = couplingsample.asfunction(participant.read_data(mesh_name, "K11", vertex_ids, dt))
 
             conductivity = function.asarray([[k_00_c, k_01_c], [k_10_c, k_11_c]])
             sqrk = couplingsample.integral(((ns.k - conductivity) * (ns.k - conductivity)).sum([0, 1]))
@@ -128,7 +128,7 @@ def main():
         if is_coupled_case:
             # Collect values of field u and write them to preCICE
             concentration = couplingsample.eval('u' @ ns, solu=solu)
-            participant.write_data(mesh_name, "concentration", vertex_ids, concentration)
+            participant.write_data(mesh_name, "Concentration", vertex_ids, concentration)
 
             participant.advance(dt)
 

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

@@ -202,9 +202,9 @@ py::dict MicroSimulation::initialize()
   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;
+  micro_write_data["K00"]      = _k_00;
+  micro_write_data["K11"]      = _k_11;
+  micro_write_data["Porosity"] = _porosity;
 
   return micro_write_data;
 }
@@ -227,7 +227,7 @@ py::dict MicroSimulation::solve(py::dict macro_write_data, double dt)
   _timeLoop->setTimeStepSize(dt);
 
   // read concentration from preCICE
-  double conc = macro_write_data["concentration"].cast<double>();
+  double conc = macro_write_data["Concentration"].cast<double>();
 
   // input macro concentration into allen-cahn problem
   _acProblem->updateConcentration(conc);
@@ -259,12 +259,12 @@ py::dict MicroSimulation::solve(py::dict macro_write_data, double dt)
   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_10"]       = _k_10;
-  micro_write_data["k_01"]       = _k_01;
-  micro_write_data["k_11"]       = _k_11;
-  micro_write_data["porosity"]   = _porosity;
-  micro_write_data["grain_size"] = std::sqrt((1 - _porosity) / pi_);
+  micro_write_data["K00"]        = _k_00;
+  micro_write_data["K10"]        = _k_10;
+  micro_write_data["K01"]        = _k_01;
+  micro_write_data["K11"]        = _k_11;
+  micro_write_data["Porosity"]   = _porosity;
+  micro_write_data["Grain-Size"] = std::sqrt((1 - _porosity) / pi_);
 
   // write current primary variables to previous primary variables
   _acGridVariables->advanceTimeStep();

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

@@ -3,9 +3,9 @@
     "coupling_params": {
             "participant_name": "Micro-Manager",
             "precice_config_file_name": "../precice-config.xml",
-            "macro_mesh_name": "macro-mesh",
-            "write_data_names": ["k_00", "k_01", "k_10", "k_11", "porosity"],
-            "read_data_names": ["concentration"]
+            "macro_mesh_name": "Macro-Mesh",
+            "write_data_names": ["K00", "K01", "K10", "K11", "Porosity"],
+            "read_data_names": ["Concentration"]
     },
     "simulation_params": {
       "micro_dt": 0.01,
@@ -14,14 +14,14 @@
       "adaptivity": true,
       "adaptivity_settings": {
             "type": "global",
-            "data": ["k_00", "k_11", "porosity", "concentration"],
+            "data": ["K00", "K11", "Porosity", "Concentration"],
             "history_param": 0.1,
             "coarsening_constant": 0.2,
             "refining_constant": 0.05,
             "similarity_measure": "L2rel"
         }
     },
     "diagnostics": {
-      "data_from_micro_sims": ["grain_size"]
+      "data_from_micro_sims": ["Grain-Size"]
     }
 }

two-scale-heat-conduction/micro-dumux/micro-manager-config.json

@@ -3,9 +3,9 @@
     "coupling_params": {
             "participant_name": "Micro-Manager",
             "precice_config_file_name": "../precice-config.xml",
-            "macro_mesh_name": "macro-mesh",
-            "write_data_names": ["k_00", "k_01", "k_10", "k_11", "porosity"],
-            "read_data_names": ["concentration"]
+            "macro_mesh_name": "Macro-Mesh",
+            "write_data_names": ["K00", "K01", "K10", "K11", "Porosity"],
+            "read_data_names": ["Concentration"]
     },
     "simulation_params": {
       "micro_dt": 0.01,
@@ -14,14 +14,14 @@
       "adaptivity": true,
       "adaptivity_settings": {
         "type": "global",
-        "data": ["k_00", "k_11", "porosity", "concentration"],
+        "data": ["K00", "K11", "Porosity", "Concentration"],
         "history_param": 0.1,
         "coarsening_constant": 0.2,
         "refining_constant": 0.05,
         "similarity_measure": "L2rel"
       }
     },
     "diagnostics": {
-      "data_from_micro_sims": ["grain_size"]
+      "data_from_micro_sims": ["Grain-Size"]
     }
 }

two-scale-heat-conduction/micro-nutils/micro-manager-config.json

@@ -82,9 +82,9 @@ def initialize(self):
         self._solu = solu  # Save solution for output
 
         output_data = dict()
-        output_data["k_00"] = k[0][0]
-        output_data["k_11"] = k[1][1]
-        output_data["porosity"] = psi
+        output_data["K00"] = k[0][0]
+        output_data["K11"] = k[1][1]
+        output_data["Porosity"] = psi
 
         return output_data
 
@@ -237,7 +237,7 @@ def solve(self, macro_data, dt):
 
             assert ((solphi >= 0.0) & (solphi <= 1.0)).all()
 
-            solphi = self._solve_allen_cahn(topo, solphi, macro_data["concentration"], dt)
+            solphi = self._solve_allen_cahn(topo, solphi, macro_data["Concentration"], dt)
             psi = self._get_avg_porosity(topo, solphi)
 
             solu = self._solve_heat_cell_problem(topo, solphi)
@@ -255,12 +255,12 @@ def solve(self, macro_data, dt):
             psi = self._psi_nm1
 
         output_data = dict()
-        output_data["k_00"] = k[0][0]
-        output_data["k_01"] = k[0][1]
-        output_data["k_10"] = k[1][0]
-        output_data["k_11"] = k[1][1]
-        output_data["porosity"] = psi
-        output_data["grain_size"] = math.sqrt((1 - psi) / math.pi)
+        output_data["K00"] = k[0][0]
+        output_data["K01"] = k[0][1]
+        output_data["K10"] = k[1][0]
+        output_data["K11"] = k[1][1]
+        output_data["Porosity"] = psi
+        output_data["Grain-Size"] = math.sqrt((1 - psi) / math.pi)
 
         return output_data
 
@@ -275,7 +275,7 @@ def main():
     concentration = dict()
 
     for conc in concentrations:
-        concentration["concentration"] = conc
+        concentration["Concentration"] = conc
 
         micro_sim_output = micro_problem.solve(concentration, dt)