Dear Christoph,
Thank you for your suggestions. Now, I am able to perform my LAMMPS run in
step_001.
But, again I am getting the following error:
ERROR:
# critical: 'csg_stat --nt 20 --options
/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings.xml --top
PEO-CG-TOPOLOGY.data --trj traj.dump --begin 0 --first-frame 0 --ext
dist.new' failed
# For details see the logfile
/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/inverse.log
Again, when I am going into step_001 and running the following command as
pointed out in the error message above:
csg_stat --nt 20 --options
/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings.xml --top
PEO-CG-TOPOLOGY.data --trj traj.dump --begin 0 --first-frame 0 --ext
dist.new
I get the following error:
Unable to associate mass 45.061650 with element assuming pseudo atom,
assigning name Bead1 .
Unable to associate mass 44.053680 with element assuming pseudo atom,
assigning name Bead2 .
Unable to associate mass 59.088790 with element assuming pseudo atom,
assigning name Bead3 .
Segmentation fault (core dumped)
Can you please help me with this?
Thank you.
Sanjeet
On Friday, October 28, 2022 at 1:06:39 PM UTC-4 Sanjeet Singh wrote:
> Dear Christoph,
>
> Thank you for your prompt response.
>
> I also have the following warnings in my inverse.log file.
>
> WARNING: Communication cutoff 9.6 is shorter than a bond length based
> estimate of 10.39475. This may lead to errors. (src/comm.cpp:730)
> WARNING: Inconsistent image flags (src/domain.cpp:814)
> WARNING: Bond/angle/dihedral extent > half of periodic box length
> (src/domain.cpp:935)
>
> Is my error related to this?
>
> Thank you.
>
> Sanjeet
>
> On Friday, October 28, 2022 at 12:38:08 PM UTC-4 Christoph Junghans wrote:
>
>> On Fri, Oct 28, 2022 at 10:27 AM Sanjeet Singh <[email protected]>
>> wrote:
>> >
>> > Hello Christoph,
>> >
>> > I hope you are doing well!
>> >
>> > I have a query regarding the Iterative Boltzmann Inversion Method.
>> Actually, I am trying to perform IBI for a polymer for non-bonded
>> interactions only. I have already got my bonded potential using Simple
>> Boltzmann Inversion. So here when I am running the following command:
>> >
>> > csg_inverse --options settings.xml
>> >
>> > I am getting the following error:
>> >
>> > ERROR:
>> > # do_external: subscript
>> > # /usr/share/votca/scripts/inverse/run_genericsim.sh
>> > # (from tags run lammps) failed
>> > # For details see the logfile
>> /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/inverse.log #
>> >
>> > Can you please help me with this?
>> If you scroll up a little in inverse.log, you can see that your lammps
>> run has crashed. It is a bit hard to say why, but you can always go
>> into step_001 and run lammps manually.
>> E.g. lmp -in MY.in
>> If your simulation crashes that usually means one of the potentials
>> isn't set up quite correctly.
>>
>> Christoph
>>
>> >
>> > I am also attaching the inverse.log and settings.xml file for your
>> reference.
>> >
>> >
>> >
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
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>> .
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>
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