Allow in memory manipulation of nalu yaml files

.gitignore

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

app/exawind/exawind.cpp

@@ -3,6 +3,7 @@
 #include "OversetSimulation.h"
 #include "MPIUtilities.h"
 #include "mpi.h"
+#include "yaml-editor.hpp"
 #ifdef EXAWIND_HAS_STD_FILESYSTEM
 #include <filesystem>
 #endif
@@ -88,8 +89,10 @@ int main(int argc, char** argv)
 #endif
     std::ofstream out;
 
-    const auto nalu_inps = node["nalu_wind_inp"].as<std::vector<std::string>>();
-    const int num_nwsolvers = nalu_inps.size();
+    YAML::Node nalu_node = node["nalu_wind_inp"];
+    // make sure it is a list for now
+    assert(nalu_node.IsSequence());
+    const int num_nwsolvers = nalu_node.size();
     if (num_nwind_ranks < num_nwsolvers) {
         throw std::runtime_error(
             "Number of Nalu-Wind ranks is less than the number of Nalu-Wind "
@@ -181,10 +184,50 @@ int main(int argc, char** argv)
                                   ? node["nonlinear_iterations"].as<int>()
                                   : 1;
 
+    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)
+        if (nalu_comms.at(i) != MPI_COMM_NULL) {
+            YAML::Node yaml_replace_instance;
+            std::string nalu_inpfile, logfile;
+            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 (this_instance["logfile"]) {
+                    logfile = this_instance["logfile"].as<std::string>();
+                } else {
+                    logfile = exawind::NaluWind::change_file_name_suffix(
+                        nalu_inpfile, ".log", i);
+                }
+            } else {
+                nalu_inpfile = this_instance.as<std::string>();
+                logfile = exawind::NaluWind::change_file_name_suffix(
+                    nalu_inpfile, ".log");
+            }
+
+            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);
+            }
+            if (yaml_replace_instance) {
+                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_inps.at(i), nalu_vars);
+                i + 1, nalu_comms.at(i), nalu_yaml, logfile, nalu_vars);
+        }
     }
 
     if (amr_comm != MPI_COMM_NULL) {

src/NaluWind.cpp

@@ -32,14 +32,11 @@ void NaluWind::finalize()
 NaluWind::NaluWind(
     int id,
     stk::ParallelMachine comm,
-    const std::string& inpfile,
+    const YAML::Node& inp_yaml,
+    const std::string& logfile,
     const std::vector<std::string>& fnames,
     TIOGA::tioga& tg)
-    : m_id(id)
-    , m_comm(comm)
-    , m_doc(YAML::LoadFile(inpfile))
-    , m_fnames(fnames)
-    , m_sim(m_doc)
+    : m_id(id), m_comm(comm), m_doc(inp_yaml), m_fnames(fnames), m_sim(m_doc)
 {
     auto& env = sierra::nalu::NaluEnv::self();
     env.parallelCommunicator_ = comm;
@@ -48,11 +45,6 @@ NaluWind::NaluWind(
 
     ::tioga_nalu::TiogaRef::self(&tg);
 
-    int extloc = inpfile.rfind(".");
-    std::string logfile = inpfile;
-    if (extloc != std::string::npos) {
-        logfile = inpfile.substr(0, extloc) + ".log";
-    }
     env.set_log_file_stream(logfile);
 }
 

src/NaluWind.h

@@ -27,10 +27,24 @@ class NaluWind : public ExawindSolver
 public:
     static void initialize();
     static void finalize();
+    static std::string change_file_name_suffix(
+        std::string inpfile, std::string suffix, int index = -1)
+    {
+        int extloc = inpfile.rfind(".");
+        std::string logfile = inpfile;
+        if (index >= 0) {
+            suffix = "_" + std::to_string(index) + suffix;
+        }
+        if (extloc != std::string::npos) {
+            logfile = inpfile.substr(0, extloc) + suffix;
+        }
+        return logfile;
+    }
     explicit NaluWind(
         int id,
         stk::ParallelMachine comm,
-        const std::string& inp_file,
+        const YAML::Node& inp_yaml,
+        const std::string& logfile,
         const std::vector<std::string>& fnames,
         TIOGA::tioga& tg);
     ~NaluWind();

src/yaml-editor.hpp

@@ -0,0 +1,84 @@
+#include "yaml-cpp/yaml.h"
+#include <stdexcept>
+#include <iostream>
+
+namespace YEDIT {
+
+class YamlNodeMatchException : public std::exception
+{
+public:
+    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_;
+};
+
+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()));
+            }
+        }
+        break;
+    case YAML::NodeType::Sequence:
+        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;
+    }
+}
+} // 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);
+    }
+}
+
+// case 1: it's a map
+//- pass the contents of the map recursively
+// case 2: it's a list
+//- pass the contents of the list recursively
+// 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