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| author | Ilhan Özgen Xian <iozgen@lbl.gov> | 2021-10-20 09:54:51 -0700 |
|---|---|---|
| committer | Ilhan Özgen Xian <iozgen@lbl.gov> | 2021-10-20 09:54:51 -0700 |
| commit | ff84ad5b38544156594e83a8347e65463d14c4a2 (patch) | |
| tree | f6dbc86b8a2c597d118be91f74a8ae8488d5d8cd | |
| parent | f219bb0290d6693136ebef1db841fe2d9f1bb587 (diff) | |
Wed Oct 20 09:54:51 2021
| -rw-r--r-- | README | 57 | ||||
| -rw-r--r-- | input/options.input | 4 |
2 files changed, 59 insertions, 2 deletions
@@ -31,6 +31,25 @@ hydrology solver amanzi/ats. + it requires hdf5 library with c++ support. + it uses openmp for shared memory parallelisation. +optional dependencies to use the bash scripts provided in tools/ to prepare +simulation input are the following common *nix tools: + ++ sed(1) ++ sort(1) ++ grep(1) ++ read(2) ++ awk + +if not available, read the bash scripts to replicate their functionality +with available tools. + +optional dependency to use the gnuplot scripts provided in tools/ to +quickly post-process results: + ++ gnuplot + +if not available, any other scripting language can be used to plot paths. + Installation ------------ @@ -53,6 +72,44 @@ $ ./ptracker -[a|c] <path/to/option/file> -c (c)ompiles the mesh, creating the output grid.h5 -a (a)dvects particles on the subgrid +Pre-processing +-------------- + +before running the program, you will need to produce the files: + ++ groups.txt: group names of the surface data ++ times.txt: time steps of the surface data ++ subgroups.txt: group names of the subsurface data ++ subtimes.txt: time steps of the subsurface data + +group names are a namespace for one snapshot of data for each time +step. the time steps specify the exact time the snapshot was taken. + +functionality to extract group names and time steps is provided in +tools/extract.sh. the usage is: + +$ bash extract.sh filename varname + +check the HDF5 file to see the names of the variables you can querry. +the script produces the files _tmpgroups.txt and _tmptimes.txt. +depending on whether a surface or subsurface file was analyzed, you +may rename these temporary files as groups.txt and times.txt or +subgroups.txt and subtimes.txt, respectively. + +Post-processing +--------------- + +you can use the gnuplot scipts in tools/: + +$ gnuplot plot-paths.gp + +plots 2D projections of the flow paths. + +$ gnuplot plot-paths-integrated.gp + +plots 3D projections of the flow paths. + + Acknowledgments --------------- diff --git a/input/options.input b/input/options.input index d6db646..2a1f315 100644 --- a/input/options.input +++ b/input/options.input @@ -4,11 +4,11 @@ n_agent : 1000 // Number of agents fuzz : 0.01 // Fuzzy equivalence constant, used for geometry seed : 108 // Random seed subgrid_dx : 5.0 // Subgrid cell size -start_time : 0.0 // Simulation start time (s) +start_time : 0.0 // Simulation start time (s) surfacemesh : ./example/ats_vis_surface_mesh.h5 // Surface mesh file surfacedata : ./example/ats_vis_surface_data.h5 // Surface data file -surfacetime : ./input/times.txt // Time levels for surface +surfacetime : ./input/times.txt // Time levels for surface surfacegroup : ./input/groups.txt // Group names for surface subsurfacemesh : ./example/ats_vis_mesh.h5 // Subsurface mesh file |