Add test case that shows syntax

.gitignore

@@ -1 +1,4 @@
 .DS_Store
+spack*
+compile_commands.json
+.cache

app/exawind/exawind.cpp

@@ -89,9 +89,9 @@ int main(int argc, char** argv)
 #endif
     std::ofstream out;
 
-    const auto nalu_node = node["nalu_wind_inp"];
+    YAML::Node nalu_node = node["nalu_wind_inp"];
     // make sure it is a list for now
-    assert(nalu_node.IsSequence);
+    assert(nalu_node.IsSequence());
     const int num_nwsolvers = nalu_node.size();
     if (num_nwind_ranks < num_nwsolvers) {
         throw std::runtime_error(
@@ -184,28 +184,29 @@ int main(int argc, char** argv)
                                   ? node["nonlinear_iterations"].as<int>()
                                   : 1;
 
-    const auto yaml_replace_all = node["nalu_replace_all"];
+    const YAML::Node yaml_replace_all = node["nalu_replace_all"];
     for (int i = 0; i < num_nwsolvers; i++) {
         if (nalu_comms.at(i) != MPI_COMM_NULL) {
             YAML::Node yaml_replace_instance;
             std::string nalu_inpfile, logfile;
-            if (nalu_node[i].IsMap()) {
-                yaml_replace_instance = nalu_node["replace"];
-                nalu_inpfile = nalu_node["input_file"].as<std::string>();
+            YAML::Node this_instance = nalu_node[i];
+            if (this_instance.IsMap()) {
+                yaml_replace_instance = this_instance["replace"];
+                nalu_inpfile = this_instance["base_input_file"].as<std::string>();
                 // deal with the logfile name
-                if (nalu_node["logfile"]) {
-                    logfile = nalu_node["logfile"].as<std::string>();
+                if (this_instance["logfile"]) {
+                    logfile = this_instance["logfile"].as<std::string>();
                 } else {
-                    logfile = exawind::NaluWind::logfile_from_input_file_name(
-                        nalu_inpfile, i);
+                    logfile = exawind::NaluWind::change_file_name_suffix(
+                        nalu_inpfile, ".log", i);
                 }
             } else {
-                nalu_inpfile = nalu_node[i].as<std::string>();
-                logfile = exawind::NaluWind::logfile_from_input_file_name(
-                    nalu_inpfile);
+                nalu_inpfile = this_instance.as<std::string>();
+                logfile = exawind::NaluWind::change_file_name_suffix(
+                    nalu_inpfile, ".log");
             }
 
-            auto nalu_yaml = YAML::Load(nalu_inpfile);
+            YAML::Node nalu_yaml = YAML::LoadFile(nalu_inpfile);
             // replace in order so instance can overwrite all
             if (yaml_replace_all) {
                 YEDIT::find_and_replace(nalu_yaml, yaml_replace_all);
@@ -214,6 +215,15 @@ int main(int argc, char** argv)
                 YEDIT::find_and_replace(nalu_yaml, yaml_replace_instance);
             }
 
+            if (this_instance["write_final_yaml_to_disk"]) {
+                auto new_ifile_name =
+                    exawind::NaluWind::change_file_name_suffix(
+                        logfile, ".yaml");
+                std::ofstream fout(new_ifile_name);
+                fout << nalu_yaml;
+                fout.close();
+            }
+
             sim.register_solver<exawind::NaluWind>(
                 i + 1, nalu_comms.at(i), nalu_yaml, logfile, nalu_vars);
         }

src/NaluWind.h

@@ -28,16 +28,15 @@ class NaluWind : public ExawindSolver
     static void initialize();
     static void finalize();
     static std::string
-    logfile_from_input_file_name(std::string inpfile, int index = -1)
+    change_file_name_suffix(std::string inpfile, std::string suffix, int index = -1)
     {
         int extloc = inpfile.rfind(".");
         std::string logfile = inpfile;
-        std::string tail = ".log";
         if (index >= 0) {
-            tail = "_" + std::to_string(index) + tail;
+            suffix = "_" + std::to_string(index) + suffix;
         }
         if (extloc != std::string::npos) {
-            logfile = inpfile.substr(0, extloc) + tail;
+            logfile = inpfile.substr(0, extloc) + suffix;
         }
         return logfile;
     }

src/yaml-editor.hpp

@@ -2,74 +2,83 @@
 #include <stdexcept>
 #include <iostream>
 
-namespace YEDIT{
+namespace YEDIT {
 
-class YamlNodeMatchException : public std::exception{
+class YamlNodeMatchException : public std::exception
+{
 public:
-  YamlNodeMatchException(std::string currentNode, std::string accumulatedPath = ""):
-    std::exception(), graphPath_(currentNode + ":" + accumulatedPath)
-  {
-  }
-  const char* what() const noexcept override{
-    return graphPath_.c_str();
-  }
+    YamlNodeMatchException(
+        std::string currentNode, std::string accumulatedPath = "")
+        : std::exception()
+    {
+        std::string extra =
+            accumulatedPath.empty() ? "" : ":" + accumulatedPath;
+        graphPath_ = currentNode + extra;
+    }
+    const char* what() const noexcept override { return graphPath_.c_str(); }
+
 private:
-  std::string graphPath_;
+    std::string graphPath_;
 };
 
-namespace{
-void impl_find_and_replace(YAML::Node src, YAML::Node key){
-  switch (key.Type()){
+namespace {
+void impl_find_and_replace(YAML::Node src, YAML::Node key)
+{
+    switch (key.Type()) {
     case YAML::NodeType::Map:
-      for(auto n : key){
-        std::string k = static_cast<std::string>(n.first.Scalar());
-        try{
-          impl_find_and_replace(src[k], key[k]);
-        }
-        catch(YamlNodeMatchException& e)
-        {
-          throw YamlNodeMatchException(k, std::string(e.what()));
+        for (auto n : key) {
+            std::string k = static_cast<std::string>(n.first.Scalar());
+            try {
+                impl_find_and_replace(src[k], key[k]);
+            } catch (YamlNodeMatchException& e) {
+                throw YamlNodeMatchException(k, std::string(e.what()));
+            }
         }
-      }
-      break;
+        break;
     case YAML::NodeType::Sequence:
-      for(int i=0; i<key.size(); ++i){
-        impl_find_and_replace(src[i], key[i]);
-      }
-      break;
-    case YAML::NodeType::Scalar:
-      {
-      if(src.Type() != key.Type()){
-          // we have a invalid path in the key
-          throw YamlNodeMatchException("");
-      }
-      src = key;
-      break;
-      }
+        for (int i = 0; i < key.size(); ++i) {
+            try {
+                impl_find_and_replace(src[i], key[i]);
+            } catch (YamlNodeMatchException& e) {
+                throw YamlNodeMatchException(
+                    "[" + std::to_string(i) + "]", std::string(e.what()));
+            }
+        }
+        break;
+    case YAML::NodeType::Scalar: {
+        if (src.Type() != key.Type()) {
+            // we have a invalid path in the key
+            throw YamlNodeMatchException(key.as<std::string>());
+        }
+        src = key;
+        break;
+    }
     default:
-      break;
-  }
-}
+        break;
+    }
 }
+} // namespace
 
-void find_and_replace(YAML::Node src, YAML::Node key){
-  try{
-    impl_find_and_replace(src, key);
-  }
-  catch(YamlNodeMatchException& e){
-    auto failingPath = static_cast<std::string>(e.what());
-    std::string message = "\nFailure trying to replace YAML\nFailing Graph:\n\t";
-    message+=failingPath+"\n";
-    message+="Please double check and make sure this matches the source YAML";
-    throw std::runtime_error(message);
-  }
+void find_and_replace(YAML::Node src, YAML::Node key)
+{
+    try {
+        impl_find_and_replace(src, key);
+    } catch (YamlNodeMatchException& e) {
+        auto failingPath = static_cast<std::string>(e.what());
+        std::string message =
+            "\nFailure trying to replace YAML\nFailing Graph:\n\t";
+        message += failingPath + "\n";
+        message +=
+            "Please double check and make sure this matches the source YAML";
+        throw std::runtime_error(message);
+    }
 }
 
-//case 1: it's a map
+// case 1: it's a map
 //- pass the contents of the map recursively
-//case 2: it's a list
+// case 2: it's a list
 //- pass the contents of the list recursively
-//case 3: it's a scalar
+// case 3: it's a scalar
 //- replace value
 
-}
+} // namespace YEDIT

test/CMakeLists.txt

@@ -61,3 +61,4 @@ add_test_r(nalu-nalu-cylinder)
 add_test_r(amr-nalu-cylinder)
 add_test_r(nalu-nalu-cylinder-motion)
 add_test_r(amr-nalu-cylinder-motion)
+add_test_r(hybrid-multi-cylinder)

test/test_files/hybrid-multi-cylinder/cylinder-amr.inp

@@ -0,0 +1,62 @@
+#
+#            SIMULATION STOP            #
+#.......................................#
+time.stop_time               =   22000.0     # Max (#
+tim.max_step = -1
+time.fixed_dt = 0.15
+time.cfl = 1.0
+time.plot_interval = 10
+time.checkpoint_interval = -10
+io.plot_file = out/plt
+io.check_file = out/chk
+#               PHYSICS                 #
+#.......................................#
+incflo.gravity          =   0.  0. 0.0  # Gravitational force (3D)
+
+incflo.use_godunov = 1
+incflo.do_initial_proj = 0
+incflo.initial_iterations = 0
+transport.viscosity = 0.005
+turbulence.model = Laminar
+
+
+incflo.physics = FreeStream
+incflo.velocity = 1.0 0.0 0.0
+incflo.density = 1.0
+
+amr.n_cell              = 160 56 4 # Grid cells at coarsest AMRlevel
+amr.max_level           = 0           # Max AMR level in hierarchy 
+amr.blocking_factor_z = 4
+amr.blocking_factor_x = 8
+amr.blocking_factor_y = 8
+amr.max_grid_size_z = 4
+amr.max_grid_size_x = 16
+amr.max_grid_size_y = 16
+
+geometry.prob_lo        =   -15 -5.0 -0.375 # Lo corner coordinates
+geometry.prob_hi        =   7.5 5.0 0.375 # Hi corner coordinates
+geometry.is_periodic    =   0   0   1   # Periodicity x y z (0/1)
+
+
+# Boundary conditions
+xlo.type = "mass_inflow"
+xlo.velocity = 1.0 0.0 0.0
+xlo.density = 1.0
+xhi.type = "pressure_outflow"
+xhi.pressure = 0.0
+ylo.type = "slip_wall"
+yhi.type = "slip_wall"
+#zlo.type = "slip_wall"
+#zhi.type = "slip_wall"
+
+incflo.verbose          =   0          # incflo_level
+amrex.fpe_trap_invalid  =   0           # Trap NaNs
+amrex.throw_exception = 1
+amrex.signal_handling = 0
+
+mac_proj.verbose = 0
+nodal_proj.verbose = 0
+nodal_proj.mg_rtol = 1.0e-6
+nodal_proj.mg_atol = 1.0e-10
+nodal_proj.num_pre_smooth = 10
+nodal_proj.num_post_smooth = 10