Write scientific defaults upon close (Iteration::close or Series::close)

CMakeLists.txt

@@ -426,6 +426,11 @@ set(CORE_SOURCE
         src/backend/PatchRecord.cpp
         src/backend/PatchRecordComponent.cpp
         src/backend/Writable.cpp
+        src/backend/scientific_defaults/ScientificDefaults.cpp
+        src/backend/scientific_defaults/ScientificDefaults_auxiliary.cpp
+        src/backend/scientific_defaults/ProcessParsedAttribute.cpp
+        src/backend/scientific_defaults/AttributeReader.cpp
+        src/backend/scientific_defaults/ConfigAttribute.cpp
         src/auxiliary/OneDimensionalBlockSlicer.cpp
         src/helper/list_series.cpp
         src/snapshots/ContainerImpls.cpp

include/openPMD/Iteration.hpp

@@ -27,6 +27,8 @@
 #include "openPMD/auxiliary/Variant.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <cstdint>
 #include <deque>
@@ -145,13 +147,28 @@ namespace internal
         std::optional<DeferredParseAccess> m_deferredParseAccess{};
     };
 } // namespace internal
+
+class Meshes : public Container<Mesh>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
+
+class Particles : public Container<ParticleSpecies>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
+
 /** @brief  Logical compilation of data from one snapshot (e.g. a single
  * simulation cycle).
  *
  * @see
  * https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#required-attributes-for-the-basepath
  */
-class Iteration : public Attributable
+class Iteration
+    : public Attributable
+    , internal::ScientificDefaults
 {
     template <typename T, typename T_key, typename T_container>
     friend class Container;
@@ -164,6 +181,8 @@ class Iteration : public Attributable
     friend class StatefulSnapshotsContainer;
     template <typename>
     friend struct traits::GenerationPolicy;
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     Iteration(Iteration const &) = default;
@@ -279,8 +298,10 @@ class Iteration : public Attributable
     [[deprecated("This attribute is no longer set by the openPMD-api.")]] bool
     closedByWriter() const;
 
-    Container<Mesh> meshes{};
-    Container<ParticleSpecies> particles{}; // particleSpecies?
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
+    Meshes meshes{};
+    Particles particles{};
 
     virtual ~Iteration() = default;
 
@@ -442,14 +463,17 @@ class Iteration : public Attributable
      *
      * @param w The Writable representing the parent.
      */
-    virtual void linkHierarchy(Writable &w);
+    void linkHierarchy(Writable &w) override;
 
     /**
      * @brief Access an iteration in read mode that has potentially not been
      *      parsed yet.
      *
      */
     void runDeferredParseAccess();
+
+protected:
+    void scientificDefaults_impl(bool write, OpenpmdStandard) override;
 }; // Iteration
 
 namespace traits
@@ -513,4 +537,10 @@ class IndexedIteration : public Iteration
         : Iteration(std::forward<Iteration_t>(it)), iterationIndex(index)
     {}
 };
+
+class Iterations : public Container<Iteration, Iteration::IterationIndex_t>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
 } // namespace openPMD

include/openPMD/Mesh.hpp

@@ -23,7 +23,9 @@
 #include "openPMD/UnitDimension.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/BaseRecord.hpp"
+#include "openPMD/backend/Container.hpp"
 #include "openPMD/backend/MeshRecordComponent.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <ostream>
 #include <string>
@@ -41,6 +43,8 @@ class Mesh : public BaseRecord<MeshRecordComponent>
 {
     friend class Container<Mesh>;
     friend class Iteration;
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     Mesh(Mesh const &) = default;
@@ -322,12 +326,18 @@ class Mesh : public BaseRecord<MeshRecordComponent>
         typename = std::enable_if_t<std::is_floating_point<T>::value>>
     Mesh &setTimeOffset(T timeOffset);
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     Mesh();
 
     void
     flush_impl(std::string const &, internal::FlushParams const &) override;
     void read();
+    auto retrieveDimensionality() const -> uint64_t;
+
+protected:
+    void scientificDefaults_impl(bool write, OpenpmdStandard) override;
 }; // Mesh
 
 template <typename T>

include/openPMD/ParticlePatches.hpp

@@ -38,6 +38,8 @@ class ParticlePatches : public Container<PatchRecord>
     size_t numPatches() const;
     ~ParticlePatches() override = default;
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     ParticlePatches() = default;
     void read();

include/openPMD/ParticleSpecies.hpp

@@ -24,23 +24,31 @@
 #include "openPMD/Record.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <string>
 
 namespace openPMD
 {
 
-class ParticleSpecies : public Container<Record>
+class ParticleSpecies
+    : public Container<Record>
+    , internal::ScientificDefaults
 {
     friend class Container<ParticleSpecies>;
     friend class Container<Record>;
     friend class Iteration;
     template <typename T>
     friend T &internal::makeOwning(T &self, Series);
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     ParticlePatches particlePatches;
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     ParticleSpecies();
 
@@ -53,6 +61,9 @@ class ParticleSpecies : public Container<Record>
     {
         return m_containerData;
     }
+
+protected:
+    void scientificDefaults_impl(bool write, OpenpmdStandard) override;
 };
 
 namespace traits

include/openPMD/Record.hpp

@@ -23,6 +23,7 @@
 #include "openPMD/RecordComponent.hpp"
 #include "openPMD/UnitDimension.hpp"
 #include "openPMD/backend/BaseRecord.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <string>
 #include <type_traits>
@@ -34,6 +35,7 @@ class Record : public BaseRecord<RecordComponent>
     friend class Container<Record>;
     friend class Iteration;
     friend class ParticleSpecies;
+    friend class internal::ScientificDefaults;
 
 public:
     Record(Record const &) = default;
@@ -48,13 +50,18 @@ class Record : public BaseRecord<RecordComponent>
     template <typename T>
     Record &setTimeOffset(T);
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     Record();
 
     void
     flush_impl(std::string const &, internal::FlushParams const &) override;
 
     [[nodiscard]] internal::HomogenizeExtents read();
+
+protected:
+    void scientificDefaults_impl(bool write, OpenpmdStandard) override;
 }; // Record
 
 template <typename T>

include/openPMD/RecordComponent.hpp

@@ -27,6 +27,8 @@
 #include "openPMD/auxiliary/UniquePtr.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/BaseRecordComponent.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 // comment to prevent this include from being moved by clang-format
 #include "openPMD/DatatypeMacros.hpp"
@@ -110,7 +112,9 @@ namespace internal
 template <typename>
 class BaseRecord;
 
-class RecordComponent : public BaseRecordComponent
+class RecordComponent
+    : public BaseRecordComponent
+    , protected internal::ScientificDefaults
 {
     template <typename T, typename T_key, typename T_container>
     friend class Container;
@@ -128,6 +132,8 @@ class RecordComponent : public BaseRecordComponent
     friend class MeshRecordComponent;
     template <typename T>
     friend T &internal::makeOwning(T &self, Series);
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     enum class Allocation
@@ -482,11 +488,13 @@ class RecordComponent : public BaseRecordComponent
     auto visit(Args &&...args) -> decltype(Visitor::template call<char>(
         std::declval<RecordComponent &>(), std::forward<Args>(args)...));
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
     static constexpr char const *const SCALAR = "\vScalar";
 
 protected:
     void flush(std::string const &, internal::FlushParams const &);
-    void read(bool require_unit_si);
+    void read();
 
 private:
     /**
@@ -534,12 +542,15 @@ OPENPMD_protected
         BaseRecordComponent::setData(m_recordComponentData);
     }
 
-    void readBase(bool require_unit_si);
+    void readBase();
 
     template <typename T>
     void verifyChunk(Offset const &, Extent const &) const;
 
     void verifyChunk(Datatype, Offset const &, Extent const &) const;
+
+protected:
+    void scientificDefaults_impl(bool write, OpenpmdStandard) override;
 }; // RecordComponent
 
 namespace internal

include/openPMD/Series.hpp

@@ -31,6 +31,7 @@
 #include "openPMD/auxiliary/Variant.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
 #include "openPMD/backend/ParsePreference.hpp"
 #include "openPMD/config.hpp"
 #include "openPMD/snapshots/Snapshots.hpp"
@@ -64,7 +65,6 @@ namespace openPMD
 class ReadIterations;
 class StatefulIterator;
 class Series;
-class Series;
 
 namespace internal
 {
@@ -100,8 +100,8 @@ namespace internal
         SeriesData &operator=(SeriesData &&) = delete;
 
         using IterationIndex_t = Iteration::IterationIndex_t;
-        using IterationsContainer_t = Container<Iteration, IterationIndex_t>;
-        IterationsContainer_t iterations{};
+        using IterationsContainer_t = Iterations;
+        Iterations iterations{};
 
         /**
          * Series::readIterations() returns an iterator type that modifies the
@@ -385,7 +385,7 @@ class Series : public Attributable
      * Type for a container of Iterations indexed by IterationIndex_t.
      */
     using IterationsContainer_t = internal::SeriesData::IterationsContainer_t;
-    IterationsContainer_t iterations;
+    Iterations iterations;
 
     /**
      * @brief Is this a usable Series object?
@@ -778,6 +778,8 @@ class Series : public Attributable
      */
     void close();
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
     /**
      * This overrides Attributable::iterationFlush() which will fail on Series.
      */