Format the whole codebase

examples/10_streaming_read.cpp

@@ -8,8 +8,7 @@
 using std::cout;
 using namespace openPMD;
 
-int
-main()
+int main()
 {
 #if openPMD_HAVE_ADIOS2
  using position_t = double;

examples/10_streaming_write.cpp

@@ -8,8 +8,7 @@
 using std::cout;
 using namespace openPMD;
 
-int
-main()
+int main()
 {
 #if openPMD_HAVE_ADIOS2
  using position_t = double;

examples/12_span_write.cpp

@@ -48,8 +48,7 @@ void span_write( std::string const & filename )
  auto dynamicMemoryView = pos.storeChunk< position_t >(
  Offset{ 0 },
  extent,
- [ &fallbackBuffer, &fallbackBufferIsUsed ]( size_t size )
- {
+ [ &fallbackBuffer, &fallbackBufferIsUsed ]( size_t size ) {
  fallbackBufferIsUsed = true;
  fallbackBuffer.resize( size );
  return std::shared_ptr< position_t >(

examples/1_structure.cpp

@@ -20,39 +20,44 @@
  */
 #include <openPMD/openPMD.hpp>
 
-
 using namespace openPMD;
 
 int main()
 {
- /* The root of any openPMD output spans across all data for all iterations is a 'Series'.
+ /* The root of any openPMD output spans across all data for all iterations
+ * is a 'Series'.
  * Data is either in a single file or spread across multiple files. */
- Series series = Series("../samples/1_structure.h5", Access::CREATE);
+ Series series = Series( "../samples/1_structure.h5", Access::CREATE );
 
- /* Every element that structures your file (groups and datasets for example) can be annotated with attributes. */
- series.setComment("This string will show up at the root ('/') of the output with key 'comment'.");
+ /* Every element that structures your file (groups and datasets for example)
+ * can be annotated with attributes. */
+ series.setComment(
+ "This string will show up at the root ('/') of the output with key "
+ "'comment'." );
 
- /* Access to individual positions inside happens hierarchically, according to the openPMD standard.
- * Creation of new elements happens on access inside the tree-like structure.
- * Required attributes are initialized to reasonable defaults for every object. */
- ParticleSpecies electrons = series.iterations[1].particles["electrons"];
+ /* Access to individual positions inside happens hierarchically, according
+ * to the openPMD standard. Creation of new elements happens on access
+ * inside the tree-like structure. Required attributes are initialized to
+ * reasonable defaults for every object. */
+ ParticleSpecies electrons = series.iterations[ 1 ].particles[ "electrons" ];
 
- /* Data to be moved from memory to persistent storage is structured into Records,
- * each holding an unbounded number of RecordComponents.
- * If a Record only contains a single (scalar) component, it is treated slightly differently.
+ /* Data to be moved from memory to persistent storage is structured into
+ * Records, each holding an unbounded number of RecordComponents. If a
+ * Record only contains a single (scalar) component, it is treated slightly
+ * differently.
  * https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#scalar-vector-and-tensor-records*/
- Record  mass  = electrons["mass"];
- RecordComponent mass_scalar = mass[RecordComponent::SCALAR];
+ Record mass = electrons[ "mass" ];
+ RecordComponent mass_scalar = mass[ RecordComponent::SCALAR ];
 
- Dataset dataset = Dataset(Datatype::DOUBLE, Extent{1});
- mass_scalar.resetDataset(dataset);
+ Dataset dataset = Dataset( Datatype::DOUBLE, Extent{ 1 } );
+ mass_scalar.resetDataset( dataset );
 
  /* Required Records and RecordComponents are created automatically.
  * Initialization has to be done explicitly by the user. */
- electrons["position"]["x"].resetDataset(dataset);
- electrons["position"]["x"].makeConstant(20.0);
- electrons["positionOffset"]["x"].resetDataset(dataset);
- electrons["positionOffset"]["x"].makeConstant(22.0);
+ electrons[ "position" ][ "x" ].resetDataset( dataset );
+ electrons[ "position" ][ "x" ].makeConstant( 20.0 );
+ electrons[ "positionOffset" ][ "x" ].resetDataset( dataset );
+ electrons[ "positionOffset" ][ "x" ].makeConstant( 22.0 );
 
  /* The files in 'series' are still open until the object is destroyed, on
  * which it cleanly flushes and closes all open file handles.

examples/2_read_serial.cpp

@@ -20,77 +20,81 @@
  */
 #include <openPMD/openPMD.hpp>
 
+#include <cstddef>
 #include <iostream>
 #include <memory>
-#include <cstddef>
-
 
 using std::cout;
 using namespace openPMD;
 
 int main()
 {
- Series series = Series(
- "../samples/git-sample/data%T.h5",
- Access::READ_ONLY
- );
- cout << "Read a Series with openPMD standard version "
- << series.openPMD() << '\n';
+ Series series =
+ Series( "../samples/git-sample/data%T.h5", Access::READ_ONLY );
+ cout << "Read a Series with openPMD standard version " << series.openPMD()
+ << '\n';
 
- cout << "The Series contains " << series.iterations.size() << " iterations:";
- for( auto const& i : series.iterations )
+ cout << "The Series contains " << series.iterations.size()
+ << " iterations:";
+ for( auto const & i : series.iterations )
  cout << "\n\t" << i.first;
  cout << '\n';
 
- Iteration i = series.iterations[100];
+ Iteration i = series.iterations[ 100 ];
  cout << "Iteration 100 contains " << i.meshes.size() << " meshes:";
- for( auto const& m : i.meshes )
+ for( auto const & m : i.meshes )
  cout << "\n\t" << m.first;
  cout << '\n';
- cout << "Iteration 100 contains " << i.particles.size() << " particle species:";
- for( auto const& ps : i.particles ) {
+ cout << "Iteration 100 contains " << i.particles.size()
+ << " particle species:";
+ for( auto const & ps : i.particles )
+ {
  cout << "\n\t" << ps.first;
- for( auto const& r : ps.second ) {
+ for( auto const & r : ps.second )
+ {
  cout << "\n\t" << r.first;
  cout << '\n';
  }
  }
 
- openPMD::ParticleSpecies electrons = i.particles["electrons"];
- std::shared_ptr<double> charge = electrons["charge"][openPMD::RecordComponent::SCALAR].loadChunk<double>();
+ openPMD::ParticleSpecies electrons = i.particles[ "electrons" ];
+ std::shared_ptr< double > charge =
+ electrons[ "charge" ][ openPMD::RecordComponent::SCALAR ]
+ .loadChunk< double >();
  series.flush();
- cout << "And the first electron particle has a charge = " << charge.get()[0];
+ cout << "And the first electron particle has a charge = "
+ << charge.get()[ 0 ];
  cout << '\n';
 
- MeshRecordComponent E_x = i.meshes["E"]["x"];
+ MeshRecordComponent E_x = i.meshes[ "E" ][ "x" ];
  Extent extent = E_x.getExtent();
  cout << "Field E/x has shape (";
- for( auto const& dim : extent )
+ for( auto const & dim : extent )
  cout << dim << ',';
  cout << ") and has datatype " << E_x.getDatatype() << '\n';
 
- Offset chunk_offset = {1, 1, 1};
- Extent chunk_extent = {2, 2, 1};
- auto chunk_data = E_x.loadChunk<double>(chunk_offset, chunk_extent);
+ Offset chunk_offset = { 1, 1, 1 };
+ Extent chunk_extent = { 2, 2, 1 };
+ auto chunk_data = E_x.loadChunk< double >( chunk_offset, chunk_extent );
  cout << "Queued the loading of a single chunk from disk, "
  "ready to execute\n";
  series.flush();
  cout << "Chunk has been read from disk\n"
  << "Read chunk contains:\n";
- for( size_t row = 0; row < chunk_extent[0]; ++row )
+ for( size_t row = 0; row < chunk_extent[ 0 ]; ++row )
  {
- for( size_t col = 0; col < chunk_extent[1]; ++col )
- cout << "\t"
- << '(' << row + chunk_offset[0] << '|' << col + chunk_offset[1] << '|' << 1 << ")\t"
- << chunk_data.get()[row*chunk_extent[1]+col];
+ for( size_t col = 0; col < chunk_extent[ 1 ]; ++col )
+ cout << "\t" << '(' << row + chunk_offset[ 0 ] << '|'
+ << col + chunk_offset[ 1 ] << '|' << 1 << ")\t"
+ << chunk_data.get()[ row * chunk_extent[ 1 ] + col ];
  cout << '\n';
  }
 
- auto all_data = E_x.loadChunk<double>();
+ auto all_data = E_x.loadChunk< double >();
  series.flush();
  cout << "Full E/x starts with:\n\t{";
- for( size_t col = 0; col < extent[1] && col < 5; ++col )
- cout << all_data.get()[col] << ", ";
+ for( size_t col = 0; col < extent[ 1 ] && col < 5; ++col )
+ cout << all_data.get()[ col ] << ", ";
  cout << "...}\n";
 
  /* The files in 'series' are still open until the object is destroyed, on

examples/2a_read_thetaMode_serial.cpp

@@ -20,31 +20,30 @@
  */
 #include <openPMD/openPMD.hpp>
 
+#include <cstddef>
 #include <iostream>
 #include <memory>
-#include <cstddef>
-
 
 using std::cout;
 using namespace openPMD;
 
 int main()
 {
  Series series = Series(
- "../samples/git-sample/thetaMode/data%T.h5",
- Access::READ_ONLY
- );
+ "../samples/git-sample/thetaMode/data%T.h5", Access::READ_ONLY );
 
- Iteration i = series.iterations[500];
- MeshRecordComponent E_z_modes = i.meshes["E"]["z"];
- Extent extent = E_z_modes.getExtent();  // (modal components, r, z)
+ Iteration i = series.iterations[ 500 ];
+ MeshRecordComponent E_z_modes = i.meshes[ "E" ][ "z" ];
+ Extent extent = E_z_modes.getExtent(); // (modal components, r, z)
 
  // read E_z in all modes
- auto E_z_raw = E_z_modes.loadChunk<double>();
+ auto E_z_raw = E_z_modes.loadChunk< double >();
  // read E_z in mode_0 (one scalar field)
- auto E_z_m0 = E_z_modes.loadChunk<double>(Offset{0, 0, 0}, Extent{1, extent[1], extent[2]});
+ auto E_z_m0 = E_z_modes.loadChunk< double >(
+ Offset{ 0, 0, 0 }, Extent{ 1, extent[ 1 ], extent[ 2 ] } );
  // read E_z in mode_1 (two fields; skip mode_0 with one scalar field)
- auto E_z_m1 = E_z_modes.loadChunk<double>(Offset{1, 0, 0}, Extent{2, extent[1], extent[2]});
+ auto E_z_m1 = E_z_modes.loadChunk< double >(
+ Offset{ 1, 0, 0 }, Extent{ 2, extent[ 1 ], extent[ 2 ] } );
  series.flush();
 
  // all this is still mode-decomposed data, not too useful for users
@@ -54,8 +53,8 @@ int main()
  // user change frequency: time ~= component >> theta >> selected modes
  // thetaMode::ToCylindrical toCylindrical("all");
  // thetaMode::ToCylindricalSlice toCylindricalSlice(1.5708, "all")
- // reconstruction to 2D slice in cylindrical coordinates (r, z) for a fixed theta
- // E_z_90deg = toCylindricalSlice(E_z_modes).loadChunk<double>();
+ // reconstruction to 2D slice in cylindrical coordinates (r, z) for a fixed
+ // theta E_z_90deg = toCylindricalSlice(E_z_modes).loadChunk<double>();
  // E_r_90deg = toCylindricalSlice(i.meshes["E"]["r"]).loadChunk<double>();
  // E_t_90deg = toCylindricalSlice(i.meshes["E"]["t"]).loadChunk<double>();
  // reconstruction to 3D cylindrical coordinates (r, t, z)
@@ -64,9 +63,10 @@ int main()
 
  // reconstruction to 3D and 2D cartesian: E_x, E_y, E_z
  // thetaMode::ToCylindrical toCartesian({'x': 1.e-6, 'y': 1.e-6}, "all");
- // ... toCartesianSliceYZ({'x': 1.e-6, 'y': 1.e-6}, 'x', 0., "all"); // and absolute slice position
- // E_z_xyz = toCartesian(E_z_modes).loadChunk<double>(); # (x, y, z)
- // E_z_yz = toCartesianSliceYZ(E_z_modes).loadChunk<double>(); # (y, z)
+ // ... toCartesianSliceYZ({'x': 1.e-6, 'y': 1.e-6}, 'x', 0.,
+ // "all"); // and absolute slice position E_z_xyz =
+ // toCartesian(E_z_modes).loadChunk<double>(); # (x, y, z) E_z_yz =
+ // toCartesianSliceYZ(E_z_modes).loadChunk<double>(); # (y, z)
  // series.flush();
 
  /* The files in 'series' are still open until the object is destroyed, on

examples/3_write_serial.cpp

@@ -20,54 +20,50 @@
  */
 #include <openPMD/openPMD.hpp>
 
+#include <cstdlib>
 #include <iostream>
 #include <memory>
 #include <numeric>
-#include <cstdlib>
-
 
 using std::cout;
 using namespace openPMD;
 
-int main(int argc, char *argv[])
+int main( int argc, char * argv[] )
 {
  // user input: size of matrix to write, default 3x3
- size_t size = (argc == 2 ? atoi(argv[1]) : 3);
+ size_t size = ( argc == 2 ? atoi( argv[ 1 ] ) : 3 );
 
  // matrix dataset to write with values 0...size*size-1
- std::vector<double> global_data(size*size);
- std::iota(global_data.begin(), global_data.end(), 0.);
+ std::vector< double > global_data( size * size );
+ std::iota( global_data.begin(), global_data.end(), 0. );
 
  cout << "Set up a 2D square array (" << size << 'x' << size
  << ") that will be written\n";
 
  // open file for writing
- Series series = Series(
- "../samples/3_write_serial.h5",
- Access::CREATE
- );
+ Series series = Series( "../samples/3_write_serial.h5", Access::CREATE );
  cout << "Created an empty " << series.iterationEncoding() << " Series\n";
 
  MeshRecordComponent rho =
- series
- .iterations[1]
- .meshes["rho"][MeshRecordComponent::SCALAR];
- cout << "Created a scalar mesh Record with all required openPMD attributes\n";
+ series.iterations[ 1 ].meshes[ "rho" ][ MeshRecordComponent::SCALAR ];
+ cout << "Created a scalar mesh Record with all required openPMD "
+ "attributes\n";
 
- Datatype datatype = determineDatatype(shareRaw(global_data));
- Extent extent = {size, size};
- Dataset dataset = Dataset(datatype, extent);
- cout << "Created a Dataset of size " << dataset.extent[0] << 'x' << dataset.extent[1]
- << " and Datatype " << dataset.dtype << '\n';
+ Datatype datatype = determineDatatype( shareRaw( global_data ) );
+ Extent extent = { size, size };
+ Dataset dataset = Dataset( datatype, extent );
+ cout << "Created a Dataset of size " << dataset.extent[ 0 ] << 'x'
+ << dataset.extent[ 1 ] << " and Datatype " << dataset.dtype << '\n';
 
- rho.resetDataset(dataset);
- cout << "Set the dataset properties for the scalar field rho in iteration 1\n";
+ rho.resetDataset( dataset );
+ cout << "Set the dataset properties for the scalar field rho in iteration "
+ "1\n";
 
  series.flush();
  cout << "File structure and required attributes have been written\n";
 
- Offset offset = {0, 0};
- rho.storeChunk(shareRaw(global_data), offset, extent);
+ Offset offset = { 0, 0 };
+ rho.storeChunk( shareRaw( global_data ), offset, extent );
  cout << "Stored the whole Dataset contents as a single chunk, "
  "ready to write content\n";