2017-02-16 10:20 GMT-07:00 Joshua Moore <[email protected]>:
> Hi Christoph,
>
> I think I have it basically working now, but I might be having a few issues.
> Here is what I did
>
> 1) I created a calc_pressure_lammps.sh file as you suggested. It is
> attached, but it is basically just calculating the average of a column of
> pressures I've outputted from LAMMPS using awk and assigning this to the
> p_new variable. I have hard coded the name of the lammps file (called
> lammps.pressure), as I wasn't sure how this could be read into the script.
Nice, it looks very good!
I would add an option to xml file in lammps block, e.g.
<cg>
...
<inverse>
<lammps>
...
<traj>traj.dump</traj>
...
<pressure_file>lammps.pressure</pressure_file>
</lammps>
</inverse>
</cg>
and then you can read its value inside the script using:
p_file="$(csg_get_property cg.inverse.lammps.pressure_file)"
If you want to allow a pressure file per-interaction add
<pressure_file> to <lammps> block inside the <non-bonded> block
and use
p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
In addition, I would check if the pressure file exists before invoking awk:
[[ -f ${p_file} ]] || die "${0##*/}: pressure file '${p_file}" doesn't exist"
and check that awk actually ran correctly:
p_now=$(...) || die "${0##*/}: pressure averaging failed"
(Note "${0##*/}" is just the name of the script)
>
> 2)
> Added "pressure lammps calc_pressure_lammps.sh" in csg_table below "pressure
> gromacs calc_pressure_gromacs.sh"
>
> 3) Commented out in postupd_pressure.sh this line
>
> #[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for
> ${sim_prog} is not implemented yet!"
I would change it to that:
[[ $sim_prog != @(gromacs|lammps) ]] && die "${0##*/}: pressure
correction for ${sim_prog} is not implemented yet!"
so that it only works for lammps and gromacs
Can you do a pull request with these changes?
Details:
<https://github.com/votca/csg/wiki/BugFix#for-users-contribute-a-bug-fix>
>
> 4) It seems to be running and the pressure appears to be improving. I have
> 3 bead types for the hexane example, and 3 interactions, A-A, B-B, and A-B.
> VOTCA is only writing a A-A.pressure and a A-B.pressure file. It doesn't
> seem to be writing a B-B.pressure file, so I'm not sure if it is updating
> the B-B interaction??
That is a bit more tricky. I am guessing there is a typo in the xml
file, but I will look more in detail later.
I would look for the output and check:
- if the IBI update itself done for A-B
- if pressure is listed as a Post-update for the A-B interaction
- check inverse.log if calc_pressure_lammps.sh is called for A-B at all.
Christoph
>
> I am attaching the settings.xml file where I am calling for the pressure
> correction. Can you take a look to see if it is defined correctly there?
>
> In the *tar.gz I am attaching my current version of the ibi for LAMMPS with
> real units and pressure correction.
>
> Thanks again for all your help.
>
> Josh
>
>
> On Wednesday, February 15, 2017 at 11:05:47 AM UTC-5, Joshua Moore wrote:
>>
>> Hello,
>>
>> It appears the pressure correction for LAMMPS is not implemented.
>>
>> I saw this post by Frank
>>
>> https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ
>>
>> It seems like in order to make it work, you would just have to feed in the
>> pressure from LAMMPS.
>>
>> What would be required for this?
>>
>> Could I have LAMMPS output an average pressure, and then this could be fed
>> into pressure_cor_simple.pl as my $p_now=$ARGV[0]; ??
>>
>> How does Gromacs do it? Does Gromacs calculate an average pressure and
>> that is fed in as $ARGV[0] into the perl script?
>>
>> Thanks.
>>
>> Josh
>
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Christoph Junghans
Web: http://www.compphys.de
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