2017-02-16 13:05 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> Hi Christoph,
>
> Thanks again. I think I've implemented all your suggestions except for
>
> "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="$(csg_get_interaction_property inverse.lammps.pressure_file)" "
>
> I will have to think about that one. I think just a single pressure makes
> sense, no?
Multi-component pressure correction is bit tricky. You would need the
contribution from each individual interaction.
The standard version of Gromacs cannot calculated that and hence we
just use the total pressure.
You could also do a version where it fails back to total pressure,
something like:
p_file="$(csg_get_interaction_property --allow-empty
inverse.lammps.pressure_file)"
[[ -z ${p_file] ]] && p_file="$(csg_get_interaction_property
inverse.lammps.pressure_file)"
One more thing, please add documentation for new xml options to
share/xml/csg_defaults.xml.
>
> The other issue was a typo. Thanks for suggesting that. I had
> <post_update></post_update> in twice, the second time, with nothing in it,
> so think it overrides the previous block. Seems to be updating now.
Good that you found it, I have seen that problem before!
Christoph
>
> I will do a pull request later today after a bit more testing, but I think
> it's ok now.
>
> Thanks.
>
> Josh
>
>
>
> On Thursday, February 16, 2017 at 1:46:29 PM UTC-5, Christoph Junghans
> wrote:
>>
>> 2017-02-16 10:20 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>> > 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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