sandbox/acastillo/output_fields/readme

    Output Fields

    This module provides routines for field output and specialized quantity computations for post-processing simulation results.

    Quantity Computation Routines

    reference_height()

    Location: available_potential.h

    Description: Routines useful to evaluate the reference height required for the available potential energy in stratified flows.

    Example: Examples are available in test_available_potential.c and heating.c.

    profile_foreach_region()

    Location: profiles_foreach_region.h

    Description: Extracts profiles from specified regions of the computational domain. Adapted from Antoon’s profile utilities.

    Example: Examples are available in test_profiles_foreach_region.c.

    File Format Output Routines

    output_vtu() and output_vtu_box()

    Location: vtu/output_vtu.h and vtu/output_vtu_box.h

    Description: Compatible with the VTK XML unstructured grid format which can be read using ParaView. These functions write scalar and vector fields in binary format for efficiency. The unstructured grid format is required for quadtree and octree meshes. In MPI mode, each process writes its own file, linked together using .pvtu master files.

    Key Features:

    • Binary data output for performance
    • MPI support with .pvtu master files
    • Box region selection with output_vtu_box()

    Examples: Examples are available in the tests_outputs/ directory:

    output_xdmf()

    Location: xdmf/output_xdmf.h

    Description: Compatible with the XDMF Model and Format which can be read using ParaView or Visit. Data is split into Light data (XML metadata) and Heavy data (HDF5 binary). This used parallel I/O and is compatible with multiple visualization tools including ParaView, Visit, Matlab, and Tecplot.

    Installation Requirements:

    # Serial HDF5
sudo apt install libhdf5-dev hdf5-tools
export HDF5_INCDIR=/usr/include/hdf5/serial
export HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/serial

# Parallel HDF5  
sudo apt install libhdf5-mpi-dev hdf5-tools
export HDF5_INCDIR=/usr/include/hdf5/openmpi
export HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi

    which have to be linked, for instance by adding

    CFLAGS+= -disable-dimensions
HDFLIBS=-I$(HDF5_INCDIR) -L$(HDF5_LIBDIR) -lhdf5 -lhdf5_hl
LIBS+=-I$(BASILISK) $(HDFLIBS)

    to your Makefile.

    HDF5 Setup for Basilisk:

    Currently, HDF5 can’t pass through qcc without adding

    echo "@include <hdf5.h>" > $BASILISK/ast/std/hdf5.h
echo "@include <hdf5_hl.h>" > $BASILISK/ast/std/hdf5_hl.h
echo "typedef hid_t, hsize_t, herr_t, H5L_info_t;" >> $BASILISK/ast/defaults.h

    and disabling dimensional analysis. This is more an HDF5 problem than a Basilisk problem, but it’s still worth using.

    Examples: Examples are available in tests_outputs/test_output_xmf*.c.

    output_vtkhdf() and output_vtkhdf_box()

    Location: vtkhdf/output_vtkhdf.h and vtkhdf/output_vtkhdf_box.h

    Description: Compatible with the modern VTK-HDF format which can be read using ParaView or Visit. This format provides robust parallel capabilities. VTK-HDF files use a structured HDF5 layout with VTKHDF groups containing datasets for points, connectivity, and field data.

    Examples: Examples are available in tests_outputs/test_output_vtkhdf*.c.

    Note: Routines in the deprecated/ folder may be outdated and are provided for compatibility purposes only.