Proposed HDF5 input format and draft implementation

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.25) # Needed for CUDA, MPI, and CTest features
 
 project(
   EXP
-  VERSION "7.10.0"
+  VERSION "7.11.0"
   HOMEPAGE_URL https://github.com/EXP-code/EXP
   LANGUAGES C CXX Fortran)
 

doc/exp.cfg

@@ -48,7 +48,7 @@ PROJECT_NAME           = EXP
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 7.10.0
+PROJECT_NUMBER         = 7.11.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/exp.cfg.breathe

@@ -48,7 +48,7 @@ PROJECT_NAME           = EXP
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 7.10.0
+PROJECT_NUMBER         = 7.11.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

include/ScopeTimer.H

@@ -0,0 +1,64 @@
+#pragma once
+
+#include <chrono>
+#include <iostream>
+#include <string>
+
+class ScopeTimer {
+public:
+  using Clock = std::chrono::steady_clock;
+
+  // Define units for output
+  enum class Unit {
+    Seconds,
+    Milliseconds,
+    Microseconds,
+    Nanoseconds
+  };
+
+  // Default to Seconds if the user doesn't choose
+  explicit ScopeTimer(std::string task_name, Unit output_unit = Unit::Seconds) 
+    : name(std::move(task_name)), unit(output_unit), start_time(Clock::now()) {}
+
+  // Output on deletion of the object
+  ~ScopeTimer()
+  {
+    const auto end_time = Clock::now();
+    const auto delta = end_time - start_time;
+
+    // Convert natively using std::chrono based on user choice
+    switch (unit) {
+    case Unit::Seconds: {
+      std::chrono::duration<double> elapsed = delta;
+      std::cout << "[" << name << "] completed in " << elapsed.count() << " s\n";
+      break;
+    }
+    case Unit::Milliseconds: {
+      std::chrono::duration<double, std::milli> elapsed = delta;
+      std::cout << "[" << name << "] completed in " << elapsed.count() << " ms\n";
+      break;
+    }
+    case Unit::Microseconds: {
+      std::chrono::duration<double, std::micro> elapsed = delta;
+      std::cout << "[" << name << "] completed in " << elapsed.count() << " µs\n";
+      break;
+    }
+    case Unit::Nanoseconds: {
+      std::chrono::duration<double, std::nano> elapsed = delta;
+      std::cout << "[" << name << "] completed in " << elapsed.count() << " ns\n";
+      break;
+    }
+    default:
+      std::cerr << "Unknown time unit for ScopeTimer\n";
+      break;
+    }
+  }
+
+  ScopeTimer(const ScopeTimer&) = delete;
+  ScopeTimer& operator=(const ScopeTimer&) = delete;
+
+private:
+  std::string name;
+  Unit unit;
+  std::chrono::time_point<Clock> start_time;
+};

src/Component.H

@@ -184,6 +184,44 @@ struct loadb_datum
   specifying alternative parameters, using an old-style PSP file, or
   starting a new job with a previous output from another simulation)
   </ol>
+
+  <br> <b>Input data format</b> Component now supports reading from
+  HDF5 files on input.  The scheme for HDF5 input files is:
+  @verbatim
+  /
+  ├── Attributes
+  │ ├── num_particles (int)
+  │ ├── num_aux_ints (int)
+  │ └── num_aux_floats (int)
+  └── particles/ (Group)
+  ├── m (Dataset)
+  ├── x, y, z (Datasets)
+  ├── u, v, w (Datasets)
+  ├── index (optional Dataset)
+  ├── aux_int_0, aux_int_1, ... (Datasets)
+  └── aux_float_0, aux_float_1, ... (Datasets)
+  @endverbatim
+
+  @note
+  <ol>
+
+  <li> The <code>index</code> dataset is optional.  If it is not
+  present, the particles are assigned indices in the order they are read.
+
+  <li> The <code>aux_int_*</code> and <code>aux_float_*</code>
+  datasets are optional.  If they are not present, the corresponding
+  vectors are empty.  The number of auxiliary integer and float
+  datasets is determined by the <code>num_aux_ints</code> and
+  <code>num_aux_floats</code> attributes, respectively.
+
+  <li> The datatype for the <code>m</code>, <code>x</code>,
+  <code>y</code>, <code>z</code>, <code>u</code>, <code>v</code>,
+  <code>w</code> and <code>aux_float_*</code> datasets may be float or
+  double (i.e. float32 or float64).  Each dataset's precision is
+  detected independently, so datasets may have mixed precision within
+  the same file.
+
+  </ol>
 */
 class Component
 {
@@ -199,6 +237,8 @@ private:
   //! Parallel distribute and particle io
   void load_balance(void);
   void update_indices(void);
+  void read_bodies_and_distribute_init(void);
+  void read_bodies_and_distribute_hdf5(void);
   void read_bodies_and_distribute_ascii(void);
   void read_bodies_and_distribute_binary_out(istream *);
   void read_bodies_and_distribute_binary_spl(istream *);
@@ -367,6 +407,9 @@ protected:
   int  H5chunk = 4096;
   //@}
 
+  //! Detect float precision by inspecting dataset type
+  size_t detect_precision(const HighFive::DataSet& dataset);
+
 public:
 
   //! Describe the phase space coordinates