DigiGraph

DigiGraph is a digitizer. DigiGraph makes it easy to digitize entire plots. It is designed to extract line plots. It can be used to extract fine detail from a digital (or scanned) photograph as well. Basic image processing tools like rotate and crop are also built in.

DigiGraph Sample Screen

Download DigiGraph

A bit of history

I was using an old surface roughness tester to measure surface roughness of cracks. The machine only gave printed output of the roughness profiles. I had to include the surface roughness plots in a journal paper. The choice was either to use the scanned images (low quality) or digitize the scanned images to create digital plots (high quality). I chose the latter since I did not like the quality of the scanned images. I wrote DigiGraph to digitize the printed output. DigiGraph is written in Matlab®.

LAMMPS related code

The following are some pre and post-processing codes for the molecular simulation code LAMMPS. LAMMPS is distributed by Sandia National Labs.
You can download all the functions below as a single file here : LAMMPS_proc.zip ; LAMMPS_proc.tar
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  • readlog.m
    This function reads data from a LAMMPS log file. It is robust and can read even if different number of variables are printed in the same log file. This can happen while using the custom command in LAMMPS or even in standard output when different fix commands are used (e.g. NPT and NVE).
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  • readdump_all.m
    This function reads all timesteps from a LAMMPS dump file. Useful when the dumpfile is small. Note that the entire dumpfile is stored in one structure. Hence it is unwise to use readdump_all.m for very large dump files.
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  • readdump_one.m
    This function reads one specified timestep from a LAMMPS dump file. Useful when the dumpfile is huge and need to enquire some specific timestep. It is also faster than readdump_all.m when reading dumpfiles with large number of timesteps.
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  • scandump.m
    As the name suggests, it scans all timesteps from a LAMMPS dump file and reports the available timesteps. It is useful when the dumpfile is huge. It is much faster than readdump_all.m and readdump_one.m especially when the filesize is large.
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  • readrdf.m
    This function reads radial distribution function (rdf) output from a LAMMPS rdf file. All available timesteps can be read individually and also just the average values can be read to save time while reading large files.
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  • readEAM.m
    The EAM potential file format used by DYNAMO is in a non-standard format. This function reads the EAM potential file and presents the data in a standard (column) format.
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  • lmp2cfg.m
    AtomEye is a visualization software for molecular systems. It requires data in a special format known as CFG. This function converts all timesteps from a LAMMPS dump file to the CFG configuration. It is very useful for automatically generating a sequence of numbered files from a dumpfile with multiple timestep data.
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