It is admittedly tedious and repetitive to scan through output files for every completed job, and this reality is what usually gives way to corner-cutting and the inevitable instance where a routine simulation goes horribly wrong but remains undetected. Fortunately, UNIX-like systems come with tools to streamline the processing of simulation output.

grep is a standard UNIX utility that searches files for instances of a phrase and prints them to the screen. It is arguably the most useful tool for quickly digesting simulation output, as it can extract and summarize the data you want while skipping over everything else. For example, if your simulation output is in a file called out.300, you can quickly look at how the system temperature evolved over the course of that simulation by grepping for the phrase "temperature" by issuing grep temperature out.300 in same directory as your output:

$ grep 'temperature' out.300
old reference temperature = 0.20000D+04
new reference temperature = 0.30000D+03
temperature 0.32738174E+03 std dev 0.18819916E+03
temperature 0.30000000E+03
velocities scaled to temperature of 300.000 after 2000 iterations
old temperature was 0.30502881E+03
temperature 0.30001813E+03 std dev 0.44833240E+01
temperature 0.30000000E+03
...
temperature 0.34382206E+03 std dev 0.51213221E+01
temperature 0.34598132E+03
temperature 0.34646638E+03 std dev 0.49272970E+01
temperature 0.35067531E+03
index <temperature> <poten. energy> <pressure> <total energy>

This quickly reveals a wealth of information relevant directly to the temperature of the simulation. However, each print contains both the average and instantaneous temperature. To extract only the average temperature, you can refine the phrase for which you grep:

$ grep 'temperature.*std' out.300
temperature 0.32738174E+03 std dev 0.18819916E+03
temperature 0.30001813E+03 std dev 0.44833240E+01
temperature 0.29998880E+03 std dev 0.38058309E+01
...
temperature 0.34382206E+03 std dev 0.51213221E+01
temperature 0.34646638E+03 std dev 0.49272970E+01

This refined search phrase temperature.*std returns any line that contains both temperature and std separated by any text (.*). To extract only the instantaneous temperature, you can pipe the results of one grep to another:

$ grep 'temperature   ' out.300 | grep –v 'std'
temperature 0.30000000E+03
temperature 0.30000000E+03
temperature 0.30000000E+03
...
temperature 0.34143007E+03
temperature 0.34598132E+03
temperature 0.35067531E+03

The first grep searches for instances of the phrase temperature followed by at least three spaces, and the results of this search are then grepped for lines that do not include (-v) the phrase std. Sometimes refining the extraction of certain data requires a degree of cleverness. For example, try grepping for instantaneous temperatures as above, but don't include the extra spaces after temperature.

It is very common to save the results of such greps to a file so the data can be plotted. Redirecting grep's output is a simple matter of using the output redirect (&gt;) operator:

$ grep 'temperature.*std' out.300 > avgtemp.300
$ grep 'temperature ' out.300 | grep –v 'std' > insttemp.300

Using grep and redirecting output are standard features of any UNIX-like system. Googling for "grep" and "redirect stdout" will reveal a wealth of information and tutorials. You can also play with egrep and awk, which are capable of much more sophisticated data extraction.

You can also quickly visualize this data using gnuplot. This is covered in the next section.

Next page: Plotting Data with gnuplot