IMD

Distribution File Tools

The following utility programs deal with IMD distribution files:

dist2volume	convert distribution to volume file
dist2ppm	convert 2D distribution to PPM file
dist2ascii	convert binary distribution file to ASCII format
dist2hist	compute histogram of a distribution
dist_extract	extract one data slot from a distribution
atdist	analyse and convert atoms distributions
diffpat	analyse and convert diffraction patterns

dist2volume

Converts IMD distribution files to volume data files in various formats. Also movies can be created.

   Compilation: gmake dist2volume

   Usage: dist2volume [options] <infilebase> <suffix> 

   Options:  -l <llx> <lly> <llz>  lower left  corner
             -u <urx> <ury> <urz>  upper right corner
             -i <min> <max>        data cutuff interval
             -f <min> <max>        range of time steps
             -v <speed>            speed (seconds/frame)
             -s <int>              time step interval
             -t uv8|uv12|rvf|xvf   output format
             -n <n>                index of data slot
             -h                    this help

Currently supported output formats are uv8 and uv12 (8 and 12 bit per voxel, respectively) for the UltraVis renderer, and the rvf and xvf formats for the Virvo renderer.

dist2ppm

Converts a two-dimensional IMD distribution file to color PPM format.

   Compilation: gmake dist2ppm

   Usage: dist2ppm [options] <infile>

   Options:  -l <llx> <lly>   lower left  corner
             -u <urx> <ury>   upper right corner
             -i <min> <max>   data cutuff interval
             -n <n>           index of data slot
             -h               this help

dist2ascii

Writes a binary IMD distribution file in ASCII format to standard output, for easier inspection.

   Compilation: gmake dist2ascii

   Usage: dist2ascii <infile>

dist2hist

Writes a histogram of the selected data slot n in an IMD distribution file to standard output.

   Compilation: gmake dist2hist

   Usage: dist2hist <infile> <n>

dist_extract

Extracts the distribution of data slot n of an IMD distribution file into a separate distribution file. The file extension is chosen according to the file contents.

   Compilation: gmake dist_extract

   Usage: dist_extract <infile> <n>

sample2dist

Computes the distribution of the potential and the kinetic energy from an IMD checkpoint.

   Compilation: gmake sample2dist

   Usage: sample2dist <dimx> <dimy> <dimz> <chkpt-file> [--normalize]

dimx, dimy, and dimz are the dimensions of the distribution to be computed. If the flag --normalize is used, the distribution of the energy per atom is written, otherwise the distribution of the total energy. sample2dist creates two distribution files, <chkpt-file>.pot.dist and <chkpt-file>.kin.dist.

atdist

atdist is a utility program to analyse/convert atoms distribution files.

For 2D distributions,

    atdist file

writes a pgm file for each atom type if there are more than tree atoms types, and a ppm file otherwise. The atoms types are then encoded in red, green, and blue.

For 3D distributions,

    atdist file

projects the distribution onto the three axis, and writes these 1D histograms to the terminal. This helps to find out where the dense planes in the distribution are.

    atdist file dir min max

adds the slices from min to max perpendicular to dir, and writes a pgm file for each atom type if there are more than tree atoms types, and a ppm file otherwise. The atoms types are then encoded in red, green, and blue.

    atdist file xmin ymin zmin xmax ymax zmax

cuts a rectangular block from the volume and writes it in virvo xvf (RGBA) format. This mode works only with up to three atoms types, which are encoded in red, green, and blue.

diffpat

diffpat is a utility program to analyse/convert 3D diffraction patterns.

    diffpat file

projects the diffraction pattern onto the three axis, and writes these 1D histograms to the terminal. This helps to find out where the dense planes are.

    diffpat [-v] [-c fmax] [-l dyn] file dir min max

adds the slices min..max-1 perpendicular to dir, and writes a pgm file, or a virvo file if option -v is given. If fmax is given, the intensity is cut at fmax. By default, the intensities are mapped linearly to the gray values. If the option -l is given, the intensities are mapped logarithmically to the gray values, and intensities more than a factor dyn smaller than the maximum are set to zero.

    diffpat [-c fmax] [-l dyn] file xmin ymin zmin xmax ymax zmax

cuts a rectangular block from the volume and writes it in virvo xvf format. If fmax is given, the intensity is cut at fmax. By default, the intensities are mapped linearly to the gray values. If the option -l is given, the intensities are mapped logarithmically to the gray values, and intensities more than a factor dyn smaller than the maximum are set to zero.