From 7aa68b7680dc203f91fb5b89a55a60d576dd0e2b Mon Sep 17 00:00:00 2001
From: Jonas Lippuner <jlippuner@lanl.gov>
Date: Thu, 29 Apr 2021 13:46:28 -0500
Subject: [PATCH] address review comments

need to update gold because metadata names changed:
NumVariables => NumComponents
VariableNames => ComponentNames
---
 src/interface/params.hpp       | 28 ++++++++++++++++------------
 src/outputs/parthenon_hdf5.cpp | 20 ++++++++++----------
 src/parthenon_manager.cpp      |  2 +-
 3 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/src/interface/params.hpp b/src/interface/params.hpp
index cdda8c2cb476..1f141ba5d3d7 100644
--- a/src/interface/params.hpp
+++ b/src/interface/params.hpp
@@ -114,9 +114,11 @@ class Params {
 
 #ifdef HDF5OUTPUT
 
+ private:
   // will write all params with type T to the given HDF5 group as an attribute
   template <typename T>
-  void WriteToHDF5(const std::string &prefix, const HDF5::H5G &group) const {
+  void WriteToHDF5AllParamsOfTypeT(const std::string &prefix,
+                                   const HDF5::H5G &group) const {
     for (const auto &p : myParams_) {
       const auto &key = p.first;
       const auto type = myTypes_.at(key);
@@ -128,20 +130,22 @@ class Params {
   }
 
   template <typename T>
-  void WriteTVecToHDF5(const std::string &prefix, const HDF5::H5G &group) const {
-    WriteToHDF5<T>(prefix, group);
-    WriteToHDF5<std::vector<T>>(prefix, group);
+  void WriteToHDF5AllParamsOfTypeTOrVecT(const std::string &prefix,
+                                         const HDF5::H5G &group) const {
+    WriteToHDF5AllParamsOfTypeT<T>(prefix, group);
+    WriteToHDF5AllParamsOfTypeT<std::vector<T>>(prefix, group);
   }
 
+ public:
   void WriteAllToHDF5(const std::string &prefix, const HDF5::H5G &group) const {
-    WriteTVecToHDF5<bool>(prefix, group);
-    WriteTVecToHDF5<int32_t>(prefix, group);
-    WriteTVecToHDF5<int64_t>(prefix, group);
-    WriteTVecToHDF5<uint32_t>(prefix, group);
-    WriteTVecToHDF5<uint64_t>(prefix, group);
-    WriteTVecToHDF5<float>(prefix, group);
-    WriteTVecToHDF5<double>(prefix, group);
-    WriteTVecToHDF5<std::string>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<bool>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<int32_t>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<int64_t>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<uint32_t>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<uint64_t>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<float>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<double>(prefix, group);
+    WriteToHDF5AllParamsOfTypeTOrVecT<std::string>(prefix, group);
   }
 
 #endif // ifdef HDF5OUTPUT
diff --git a/src/outputs/parthenon_hdf5.cpp b/src/outputs/parthenon_hdf5.cpp
index 4a7becd2d797..d4a025e27ea2 100644
--- a/src/outputs/parthenon_hdf5.cpp
+++ b/src/outputs/parthenon_hdf5.cpp
@@ -955,27 +955,27 @@ void PHDF5Output::WriteOutputFileImpl(Mesh *pm, ParameterInput *pin, SimTime *tm
     }
   }
 
-  // NumVariables - number of variables within each dataset
-  std::vector<size_t> numVariables;
-  // VariablesNames - Names of variables within each dataset
-  std::vector<std::string> variableNames;
+  // number of components within each dataset
+  std::vector<size_t> num_components;
+  // names of components within each dataset
+  std::vector<std::string> component_names;
 
   for (const auto &vi : all_unique_vars) {
     const auto &component_labels = vi.component_labels;
 
     if (component_labels.size() > 0) {
-      numVariables.push_back(component_labels.size());
+      num_components.push_back(component_labels.size());
       for (const auto &label : component_labels) {
-        variableNames.push_back(label);
+        component_names.push_back(label);
       }
     } else {
-      numVariables.push_back(1);
-      variableNames.push_back(vi.label);
+      num_components.push_back(1);
+      component_names.push_back(vi.label);
     }
   }
 
-  HDF5WriteAttribute("NumVariables", numVariables, info_group);
-  HDF5WriteAttribute("VariableNames", variableNames, info_group);
+  HDF5WriteAttribute("NumComponents", num_components, info_group);
+  HDF5WriteAttribute("ComponentNames", component_names, info_group);
 
   // write SparseInfo and SparseFields (we can't write a zero-size dataset, so only write
   // this if we have sparse fields)
diff --git a/src/parthenon_manager.cpp b/src/parthenon_manager.cpp
index 61e9fa5bd6df..aec2f660f170 100644
--- a/src/parthenon_manager.cpp
+++ b/src/parthenon_manager.cpp
@@ -223,7 +223,7 @@ void ParthenonManager::RestartPackages(Mesh &rm, RestartReader &resfile) {
 
   // Get list of variables, assumed same for all blocks
 
-  // TODO(JL) this doesn't work anymore, will update this in sparse update
+  // TODO(JL) this won't work when reading true sparse variables, will be updated in PR #383
 
   auto ciX = MeshBlockDataIterator<Real>(
       mb.meshblock_data.Get(),