Multimesh_output

Multiple meshes can be written into a single hdf5 file. A set of xdmf files is written (1 xdmf for each mesh). HDF5 file also now contains a group that gives a mapping from timestep to the actual time (datatype: double unit: seconds)

1. Feature description was added to the changelog
2. Tests covering your feature were added?
3. Any new feature or behavior change was documented?

For updated version of this documention (with coming Merge requests See Wiki)

A copy of the changed part of the wiki documentation to reflect status of this merge request is here:

square_5x5_tris_32.h5

import h5py
def demo():
    with h5py.File('square_5x5_tris_32.h5') as myfile:
        # inspect what is inside the root of the file:
        # Each HDF will contain a group 'meshes' (with 1 or more meshes) and a group 'times' 
        # with time series
        myfile.keys()
        # Output: <KeysViewHDF5 ['meshes', 'times']>
        
        # Select the group 'meshes' and look what is inside and select a mesh
        meshes = myfile['meshes']
        meshes.keys()
        # < KeysViewHDF5['square_5x5_tris_32', 'square_5x5_tris_32_left_boundary', 'square_5x5_tris_32_right_boundary'] >

        # Select a mesh and check which attributes it contains
        mesh = meshes['square_5x5_tris_32']
        # Each mesh will contain 'geometry' and 'topology'. Optionally other attributes
        # < KeysViewHDF5['HydraulicFlow', 'MaterialIDs', 'geometry', 'pressure', 'topology', 'v']>    
        # Select an attribute
        # choose any key , here in example 'pressure', it is only a reference (no copy of data into memory)
        pressure = mesh['pressure']

        # get dimensions
        pressure.shape
        # example: (8, 25)
        # first dimension is time, here with length 8 - pressure is a variable attribute

        # e.g. for MateralIDs  we would get as number of time steps 1 - it is a constant attribute
        MaterialIDs = mesh['MaterialIDs']
        MaterialIDs.shape
        # (1, 25)
      
        # load data into memory (only selected data is loaded into memory)
        # example: load all timesteps and choose all data points 10:20
        p = pressure [:,10:20]

        # p can now be processed e.g. with numpy
        # import numpy
        # y = numpy.array(p)


        # In the example of pressure attribute we have 8 time steps for the variable attributes like pressure
        times = f['times']
        # list all time values
        times[:]
        # array([0. , 0.3, 0.6, 0.9, 1.2, 1.5, 1.8, 2. ])
        # To relate the values of pressure of timestep 2 (beginning with 0) to an actual time value we define:
        time_step = 2
        pressure_t2 = pressure[time_step,:]
        t2 = times[time_step]
        t2 
        # 0.6

File structures

Structure of HDF5 file

Output of all time steps is written into a single hdf5 - file. All data is written into group "meshes" and its mesh name.

Example #1:

h5dump -H square_5x5_tris_32.h5 square_5x5_tris_32.h5

HDF5 "square_5x5_tris_32.h5" {
GROUP "/" {
   GROUP "meshes" {
      GROUP "square_5x5_tris_32" {
         DATASET "HydraulicFlow" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 1, 25 ) / ( H5S_UNLIMITED, 25 ) }
         }
         DATASET "MaterialIDs" {
            DATATYPE  H5T_STD_I32LE
            DATASPACE  SIMPLE { ( 1, 25 ) / ( H5S_UNLIMITED, 25 ) }
         }
         DATASET "geometry" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 1, 25, 3 ) / ( H5S_UNLIMITED, 25, 3 ) }
         }
         DATASET "pressure" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 8, 25 ) / ( H5S_UNLIMITED, 25 ) }
         }
         DATASET "topology" {
            DATATYPE  H5T_STD_I32LE
            DATASPACE  SIMPLE { ( 1, 128 ) / ( H5S_UNLIMITED, 128 ) }
         }
         DATASET "v" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 8, 25, 2 ) / ( H5S_UNLIMITED, 25, 2 ) }
         }
      }
      GROUP "square_5x5_tris_32_left_boundary" {
         DATASET "bulk_element_ids" {
            DATATYPE  H5T_STD_U64LE
            DATASPACE  SIMPLE { ( 1, 4 ) / ( H5S_UNLIMITED, 4 ) }
         }
         DATASET "bulk_node_ids" {
            DATATYPE  H5T_STD_U64LE
            DATASPACE  SIMPLE { ( 1, 5 ) / ( H5S_UNLIMITED, 5 ) }
         }
         DATASET "geometry" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 1, 5, 3 ) / ( H5S_UNLIMITED, 5, 3 ) }
         }
         DATASET "pressure" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 8, 5 ) / ( H5S_UNLIMITED, 5 ) }
         }
         DATASET "topology" {
            DATATYPE  H5T_STD_I32LE
            DATASPACE  SIMPLE { ( 1, 16 ) / ( H5S_UNLIMITED, 16 ) }
         }
      }
      GROUP "square_5x5_tris_32_right_boundary" {
         DATASET "bulk_element_ids" {
            DATATYPE  H5T_STD_U64LE
            DATASPACE  SIMPLE { ( 1, 4 ) / ( H5S_UNLIMITED, 4 ) }
         }
         DATASET "bulk_node_ids" {
            DATATYPE  H5T_STD_U64LE
            DATASPACE  SIMPLE { ( 1, 5 ) / ( H5S_UNLIMITED, 5 ) }
         }
         DATASET "geometry" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 1, 5, 3 ) / ( H5S_UNLIMITED, 5, 3 ) }
         }
         DATASET "pressure" {
            DATATYPE  H5T_IEEE_F64LE
            DATASPACE  SIMPLE { ( 8, 5 ) / ( H5S_UNLIMITED, 5 ) }
         }
         DATASET "topology" {
            DATATYPE  H5T_STD_I32LE
            DATASPACE  SIMPLE { ( 1, 16 ) / ( H5S_UNLIMITED, 16 ) }
         }
      }
   }
   DATASET "times" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( 8 ) / ( 8 ) }
   }
}
}