Regarding Iterative Boltzmann Inversion Error

[Sanjeet Singh]

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?

I am also attaching the inverse.log and settings.xml file for your reference.

                                                                                             

 

[Christoph Junghans]

On Fri, Oct 28, 2022 at 10:27 AM Sanjeet Singh <sanje...@gmail.com> 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.
>
>
>
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Sanjeet Singh]

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

[Sanjeet Singh]

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

[Christoph Junghans]

On Fri, Oct 28, 2022 at 11:06 AM Sanjeet Singh <sanje...@gmail.com> 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?

I am not a lammps expert, so this might be more a question for the
lammps mailing, but I read the error message as: increase the
communication cutoff.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/687c52de-0a37-4c11-a805-ab17d33cc2e6n%40googlegroups.com.

[Sanjeet Singh]

Dear Christoph,

Thank you for your suggestions. Now, I am able to solve the error.

Thank you.

Sanjeeet