MPI-AMRVAC  2.0
The MPI - Adaptive Mesh Refinement - Versatile Advection Code
Slice output

Introduction

To alleviate the disk space requirements and overhead of full snapshot output, it is possible to write hypersurfaces at their own (short) intervals. Currently, these slices are aligned with the grid, with the benefit that only a sub-space of the forest has to be traversed to obtain a Morton ordered AMR- aware subgrid. The slice output is useful especially in expensive 3D simulations in cartesian geometry, but gives valid output for any dimension and geometry. The output is composed of the grid cells closest to the specified subdimensional plane and thus reflects non-interpolated simulation variables which can be handy for debugging purposes.

Setup in par file

D-1 dimensional slices are the third file format with output intervals that can be specified in the savelist section of the par file. To give an example, here we specify three slices, where the first is perpendicular to the first coordinate direction slicedir(1)=1 and intersects the first axis at a value of 0.6 slicecoord(1)=0.6. The second plane is parametrized perpendicular to the third coordinate direction slicedir(2)=3 and intersects the third axis at a value of 0.8 slicecoord(2)=0.8 and analoge for the third slice.

 &savelist;
        itsave(1,3)=0
        dtsave(3)=0.1d0
        nslices=3
        slicedir(1)=1
        slicecoord(1)=0.6
        slicedir(2)=3
        slicecoord(2)=0.8
        slicedir(3)=2
        slicecoord(3)=0.7
/

The total number of slices is specified by nslices. The data type of the slices is set by slice_type in filelist, which by default is 'vtuCC' in ascii form. if slice_type='dat', the implementation obtains a properly Morton ordered subdimensional forest with the same levels as the original simulation, such that the output .dat file can be used for restarts in lower dimension. User also has the option 'csv' to obtain comma-separated-value *.csv files of the cell-center variables. This can be useful especially for 2D simulations (1D line output) which can then be simply visualized using e.g. gnuplot. For 1D simulations, the code will always write a single *.csv file and append the point data together with the output time. The file then reads base_filename-d1-x.600.csv in the example above. For a quick look, the *.csv files can be imported in Paraview and be visualized as points using the filter Table to Points. The output filename is composed of the direction and offset values. For example, the first slice output name reads filenameout-d1-x.600-nXXXX.vtu and analoge for the other two slices. Note, that the order of the (reduced) dimensions in the resulting output files is preserved, e.g. the third slice in the example above will hold the x-direction as first coordinate and the z-direction as second coordinate. If you restart from a snapshot and continue the run with slicing, please choose the next file number x by slicenext=x in filelist to get continuous the file number of slices, otherwise it will start from 0 again overwriting old files.

Slicing of existing output

To slice existing *.dat files, the simulation can be restarted from a given output time and the code can be brought to a halt after zero iterations. This is done in the following way: its best to create a new *.par file (e.g. slices.par) and clear the savelist from any output to filetypes other than 3. We use itsave to demand a slice output for the zero-iteration.

 &savelist;
        itsave(1,3)=0
        nslices=3
        slicedir(1)=1
        slicecoord(1)=0.6
        slicedir(2)=3
        slicecoord(2)=0.8
        slicedir(3)=2
        slicecoord(3)=0.7
/

The stoplist should look like the following,

 &stoplist;
        reset_it=.true.
        it_max=0
/

where we reset the iteration counter (so that itsave(1,3)=0 will output slice data) and stop the code immediately after the IO by set it_max=0.

The code can then be started with

amrvac -i slices.par -slice 10 -if datamr/data0010.dat

which will take the output datamr/data0010.dat to create new slices with index 10 (-slice 10). The par-file is the newly created slices.par (-i slices.par) so that the default used to run the code can be left untouched. It is a simple exercise in shell scripting to run along all output-files in one go. For example with the BASH:

for i in {0..10}; do printf -v j "%04d" $i; ./amrvac -i slices.par -slice $i -if datamr/data$j.dat; done