partrac is a particle tracker that can advect passive (possibly diffusive) particles in time-dependent velocity fields. On top of this, stretching of lines and sheets with automatic refinement/coarsening is possible. We plan to fully implement the diffusive strip/method on top of this. It is written in C++.
structured/lbm: Uses trilinear interpolation of cubically ordered velocity data. The typical input for partrac is the output of the Lattice Boltzmann code FELBM, but any other data can be used as input by a suitable conversion.fenics: Uses unstructured meshes, in the form of Fenics/Dolfin HDF5 files.triangle/tet: Better and faster implementation offenics.analytic: Analytic input
parse_xdmf.py translates from FELBM output XDMF file to partrac input. This is run by:
python3 parse_xdmf.py data_example/L64x256_a1/felbm_output/output.xdmf
This creates a file timestamps.dat in the same folder as output.xdmf that is used as input for partrac.
Straightforward:
cmake .
make
sudo make install
Passive tracers example:
./trace data_example/L64x256_a1/felbm_output/timestamps.dat Dm=0 T=591000 dt=1.0 Nrw=10000 dump_intv=100.0 stat_intv=100.0 checkpoint_intv=1000 verbose=true x0=0 y0=0 z0=0 int_order=1 init_mode=line_x init_weight=uy write_mode=hdf5 interpolation_test=0 dump_chunk_size=10 refine=false refine_intv=10 hist_chunk_size=0 ds_max=0.05 Nrw_max=10000
This creates the folder data_example/L64x256_a1/felbm_output/RandomWalkers/Dm0..../ and puts the simulation data into it.
Plotting the position:
python3 plot_pos.py data_example/L64x256_a1/felbm_output/RandomWalkers/Dm0..../
| Parameter | Default value | Description |
|---|---|---|
| folder | "" | Folder to store files in |
| restart_folder | "" | Folder to restart from |
| Dm | 1.0 | Diffusion constant |
| t0 | 0.0 | Initial simulation time |
| T | 10000000.0 | Total simulation time |
| Nrw | 100 | Initial number of particles |
| dump_intv | 100.0 | Time interval between dumping particle data |
| stat_intv | 100.0 | Time interval between dumpting ensemble statistics |
| checkpoint_intv | 1000.0 | Time interval between each checkpoint |
| dump_chunk_size | 50 | Number of time stamps in a single hdf5 file |
| verbose | false | Verbose output |
| U0 | 1.0 | Rescale velocity (not active) |
| x0 | 0.0 | x parameter for initial distribution |
| y0 | 0.0 | y parameter for initial distribution |
| z0 | 0.0 | z parameter for initial distribution |
| dt | 1.0 | Time step size |
| int_order | 1 | Explicit integration order (1 or 2) |
| init_mode | "line_x" | Initialization mode (see below) |
| init_weight | "none" | Initialization weighting ("none", "ux", "uy", "uz", "u") |
| write_mode | "hdf5" | Dump mode ("hdf5" or "txt") |
| interpolation_test | 0 | Number of particles to test the interpolation with |
| refine | false | Refine edges |
| refine_intv | 100.0 | Time interval between when to refine |
| hist_chunk_size | 10 | Number of stats_intv between when to output histograms |
| ds_max | 1.0 | Maximum accepted edge length |
| Nrw_max | -1 | Maximum number of particles |
Parameters that are also stored in the event of a restart:
t, Lx, Ly, Lz, nx, ny, nz, n_accepted, n_declined
| Mode | Description | Depends on |
|---|---|---|
| "line_x" | Nrw particles along x | init_weight, y0, z0 |
| "line_y" | Nrw particles along y | init_weight, x0, z0 |
| "line_z" | Nrw particles along z | init_weight, x0, y0 |
| "plane_xy" | Nrw particles in the xy plane | init_weight, z0 |
| "plane_xz" | Nrw particles in the xz plane | init_weight, y0 |
| "plane_yz" | Nrw particles in the yz plane | init_weight, x0 |
| "volume" | Nrw particles in the whole domain | init_weight |
| "pair_xyz" | Two particles separated by ds_max rotated randomly in 3D | x0, y0, z0 |
| "pair_xy" | Two particles separated by ds_max rotated randomly in the xy plane | x0, y0, z0 |
| "pair_xz" | Two particles separated by ds_max rotated randomly in the xz plane | x0, y0, z0 |
| "pair_yz" | Two particles separated by ds_max rotated randomly in the yz plane | x0, y0, z0 |
| "pairs_xyz_x" | Nrw/2 pairs of particles along x separated by ds_max rotated randomly in 3D | y0, z0 |
| "pairs_xyz_y" | Nrw/2 pairs of particles along y separated by ds_max rotated randomly in 3D | x0, z0 |
| "pairs_xyz_z" | Nrw/2 pairs of particles along z separated by ds_max rotated randomly in 3D | x0, y0 |
| "pairs_xy_x" | Nrw/2 pairs of particles along x separated by ds_max rotated randomly in the xy plane | y0, z0 |
| "pairs_xy_y" | Nrw/2 pairs of particles along y separated by ds_max rotated randomly in the xy plane | x0, z0 |
| "pairs_xy_z" | Nrw/2 pairs of particles along z separated by ds_max rotated randomly in the xy plane | x0, y0 |
| "pairs_xz_x" | Nrw/2 pairs of particles along x separated by ds_max rotated randomly in the xz plane | y0, z0 |
| "pairs_xz_y" | Nrw/2 pairs of particles along y separated by ds_max rotated randomly in the xz plane | x0, z0 |
| "pairs_xz_z" | Nrw/2 pairs of particles along z separated by ds_max rotated randomly in the xz plane | x0, y0 |
| "pairs_yz_x" | Nrw/2 pairs of particles along x separated by ds_max rotated randomly in the yz plane | y0, z0 |
| "pairs_yz_y" | Nrw/2 pairs of particles along y separated by ds_max rotated randomly in the yz plane | x0, z0 |
| "pairs_yz_z" | Nrw/2 pairs of particles along z separated by ds_max rotated randomly in the yz plane | x0, y0 |
pairs_[xyz]_[xyz] |
Nrw/2 pairs of particles in [xyz](1) space rotated randomly in [xyz](2) space |
[x0, y0, z0] |
| "uniform_x" | Nrw particles separated uniformly along x | y0, z0 |
| "uniform_y" | Nrw particles separated uniformly along y | x0, z0 |
| "uniform_z" | Nrw particles separated uniformly along z | x0, y0 |