make ENV=ICC/ICC_MKL_OMP (classic version)
make ENV=ICC/ICC_MKL_OMP HDF5=ON (new version)

Dear AllAs you might have realized after using KAPSEL, the output options were notvery flexible. If you chose to output field data, you had no choice but to output allof it (velocity, phi field, pressure, 5 components of the stress tensor), which
would quickly increase the file size to unmanageable proportions. Furthermore,
there were only two direct options to visualize the data, either gourmet orAVS/Express. The former was only useful for small systems, the latter was acommercial product. The latest version of KAPSEL, which you can downloadfrom the git repository, contains new output options that will hopefully help you in
the visualization and analysis of your simulation data.
In this updated version, we have added support for the hdf5 format (which looksto become the standard input/output library for scientific simulation codes) tohandle all data OUTPUT (fluid & particles). For the moment, all INPUT is still
handled using UDF (you can still enable output.udf for particle data if you wish).
There is even an hdf viewer/editor, similar to gourmet, which you can downloadfrom here.
However, this viewer is not capable of visualizing the data, for this, we use
the xdmf format, as a simple xml wrapper, to tell applications suchas Paraview and Visit how to load the data (both are free, both support xdmf
natively).

Howto:Compile:Compilation is the same as before. Make sure the hdf5 library (version 1.8) is
installed (modify the Makefile accordingly). You do not need to install the xdmf
library
Input:Old define/input files will continue to work. To use the new functionality choose'EXTENDED' as FilteType (before you could only choose ASCII/BINARY). The
EXTENDED options are as follows-Driver
Format = HDF5 (no other options available at this time)-Print_particleFirst= n (only data for particles n, n+1, n+2, ..., N_total - 1 will beprinted)-Print_fieldCrop= YES/NO (crop field data to hyperslab along x, y, or z
direction)
Yes:
Slab = YZ/XZ/XY (print slab parallel to yz/xz/xy planes,
perpendicular to x/y/z axis)
Start = n (start position : 0, 1, 2, ..., N_grid-1 )Width= n (number of planes to include in slab)
Vel: YES/NO (print fluid velocity)
Phi: YES/NO (print particle phi field)
Charge : YES/NO (print charge density fields for Electrolytesimulations)
Pressure: YES/NO (print pressure field)
Tau: YES/NO (print stress tensor field)
Visualize:
To generate the xdmf files simply run the h5kapsel2xdmf.py python script which
has been added to the Tools/ directory>$ ./h5kapsel2xdmf.py data.confwhere data.conf is the configuration file written by kapsel to the output directory.
This will generate two files: data_fluid.xdmf and data_particle.xdmf which you
can directly load into paraview/visit.
For data analysis, you can use the h5py python package to access the trajectorydata. Together with Mayavi, this should also give you an additional visualization
alternative (you can continue to use gourmet thanks to this python interface aswell).
Example:Attached is an example of the new input.udf/define.udf files for a system of 48
particles sedimenting in the -x direction (LX=128, LY=64, LZ=32).
The first 12 particles are skipped.
Only the fluid velocity data is saved, and only for a YZ slab of thickness 8 startingat (x) position 60. I have also included a brief howto guide to visualize this using
Paraview.
Implementation Notes:
If you have modified a previous version of KAPSEL, and would like toincorporate the new changes, it should be possible to do this with very little work.
The main modifications are in sp_3d_ns.cxx, where all references to AVS output
routines have been replaced with calls to corresponding output functions which
prepare all data and then call the specific writer (avs/hdf5/etc). The AVS code
has not been modified. The new output writers are implemented using a virtualbase class. It is therefore very easy to add new output writers. For a detailed
view of the changes please see commit 3b8a7f3 in the git repository(feature/output_data branch).
ps. Feel free to forward this information to anyone I have forgotten. Also, please
let us know if you find any bugs.
====================================
John MOLINA