Hi,
I am facing a peculiar problem while dumping data in LAMMPS.
I am running a TAD job. In one case, I am using NVT ensemble and for the other one I am using NVE+Langeven for thermostatting. And, this is the only difference between the two input scripts.
For the case of NVT, the dump file as produced by LAMMPS is an “ASCII:Text” file for which I am able to do post-processing using "awk’ or ‘shell’ scripts.
But for the other one (NVE+Langeven), the dump file is “DATA” file (as shown by “file dump.tad” command in Unix). While I am opening this file with a VIM editor, it shows some ‘binary’ characters. I am not able to post-process it using the ‘awk’ scripts or ‘shell scripts’.
I am not able to get the reason for that.
Can you please give some hint ?
Hi,
I am facing a peculiar problem while dumping data in LAMMPS.
I am running a TAD job. In one case, I am using NVT ensemble and for the
other one I am using NVE+Langeven for thermostatting. And, this is the only
difference between the two input scripts.
For the case of NVT, the dump file as produced by LAMMPS is an "ASCII:Text"
file for which I am able to do post-processing using "awk' or 'shell'
scripts.
But for the other one (NVE+Langeven), the dump file is "DATA" file (as shown
by "file dump.tad" command in Unix). While I am opening this file with a VIM
editor, it shows some 'binary' characters. I am not able to post-process it
using the 'awk' scripts or 'shell scripts'.
I am not able to get the reason for that.
neither am i. unless there is another difference
between the inputs that you didn't tell us about,
or some problem with the file system that
stores the trajectory files.
i would suggest you try a test run on a different
machine and if the problem persists (i.e. a potential
bug in LAMMPS) provide a (small) test example
for closer inspection.
axel.
Hi Axel,
Thanks for your response. I have examined more on the problem which I mentioned in my previous mail.
I just want to redefine the problem:
I have seen that this ‘binary’ characters in the dump files are occurring ONLY after I invoke the “tad …” command.
It does not depend upon the ‘ensemble’ description. I have attached a test example (taken from LAMMPS distribution. I have only added two dump command. One for the 'equillibration run and the other for the ‘tad’ part.) with this mail.
I have found that the dump file (dump.all in this case) for the equilibration is of “ASCII:Text” character, but the dump file which corresponds to the ‘tad’ part (dump.tad) contains the binary character in the very first line itself.
I have seen the same problem with other input files also consistently.
Best regards,
Hi Axel,
The present compilation of LAMMPS was done on Feb 06 , 2012. The distribution was downloaded on that day only.
Best regards,
I have been using fix langevin / fix nve a lot recently using the
2012-5-05 version of lammps and I have not run into this problem. If
you get a chance, try downloading the latest version and please report
back. Thanks.