Error: spce - ibi_lammps example

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sandipan c

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Nov 15, 2020, 2:22:39 AM11/15/20
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Hi Everyone,

I am trying to run the ibi_lammps example provided in VOTCA tutorials, collected from this page: https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps

I am getting the error: Unrecognized line in .data file.

This error is coming after completion of 2 iterations. So, the LAMMPS simulations run a couple of times before throwing this error. I am attaching the inverse.log and spce.data files.

Could you please suggest what could be the reason for getting this error?

Error details:
WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles:
angle
atom
bond
full
molecule

These styles use the following formats in the atom block:
atom-ID molecule-ID atom-type charge x y z
atom-ID molecule-ID atom-type charge x y z nx ny nz
atom-ID molecule-ID atom-type x y z
atom-ID molecule-ID atom-type x y z nx ny nz
atom-ID atom-type x y z
atom-ID atom-type x y z nx ny nz

an error occurred:
Unrecognized line in lammps .data file:
1 1 28.15 5.43 2.37

Callstack:
/media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/inverse.sh - linenumber 266
    do_external - linenumber 177 in /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/functions_common.sh
        /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/update_ibi.sh - linenumber 31
            for_all - linenumber 22 (see 'csg_call --cat function for_all')
                    do_external - linenumber 19 (see 'csg_call --cat function do_external')
                        /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/calc_rdf_generic.sh - linenumber 84
                            critical - linenumber 4 (see 'csg_call --cat function critical')
                                die - linenumber 2 (see 'csg_call --cat function die')
#######################################################################

Thanks,
Sandipan                     
inverse.log
spce.data

Christoph Junghans

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Nov 15, 2020, 9:41:20 AM11/15/20
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Ok, it seems your data file has windows line endings and the reader
doesn't like that.

You can fix the input file using do2unix:
$ dos2unix spec.data
or sed:
sed -i 's/\r//g' spce.data
(on mac you might need to do)
sed 's/\r//g' spce.data > spce.data.new && mv spce.data.new spce.data

I made an issue: https://github.com/votca/csg/issues/613

Christoph
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sandipan c

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Nov 17, 2020, 7:51:51 AM11/17/20
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Thank you, Christoph.

I used the command
$dos2unix spce.data
and the error regarding "unrecognized line in data file" is gone.

Now, I am getting the following message in the inverse.log file:
Unable to associate mass 18.01540 with element assuming pseudo atom, assigning name Bead1

Could you please suggest why I am getting this?

As mentioned earlier, this is a tutorial example taken from:
I am attaching the inverse.log and settings.xml files.

Thanks,
Sandipan






inverse.log
settings.xml

Christoph Junghans

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Nov 17, 2020, 9:19:06 AM11/17/20
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On Tue, Nov 17, 2020 at 5:51 AM sandipan c <sandi.c...@gmail.com> wrote:
>
> Thank you, Christoph.
>
> I used the command
> $dos2unix spce.data
> and the error regarding "unrecognized line in data file" is gone.
FYI, we fixed that issue in the latest master and stable versions.
>
> Now, I am getting the following message in the inverse.log file:
> Unable to associate mass 18.01540 with element assuming pseudo atom, assigning name Bead1
This is usually just a warning.

>
> Could you please suggest why I am getting this?
Can you run the last command by hand
$ cd /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/step_001
$ csg_stat --nt 4 --options
/media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/settings.xml
--top spce.data --trj traj.dump --begin 0 --first-frame 0

and see what the error is?

Christoph
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAB-cU%3D47qhFJyrL6nUjbF0WJfM5p7d01UCMqTmZX33jKA8ViLA%40mail.gmail.com.

sandipan c

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Nov 18, 2020, 9:29:10 AM11/18/20
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Hi Chrristoph,

Thank you for  fixing the earlier issue.

Now, no error as such is being thrown, but the process is getting stuck forever. I am getting the following message:
csg_stat --nt 4 --options /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/settings.xml --top spce.data --trj traj.dump --begin 0 --first-frame 0

begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 1


WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles:
angle
atom
bond
full
molecule

These styles use the following formats in the atom block:
atom-ID molecule-ID atom-type charge x y z
atom-ID molecule-ID atom-type charge x y z nx ny nz
atom-ID molecule-ID atom-type x y z
atom-ID molecule-ID atom-type x y z nx ny nz
atom-ID atom-type x y z
atom-ID atom-type x y z nx ny nz

Unable to associate mass 18.01540 with element assuming pseudo atom, assigning name Bead1 .
------------------------------------------------------------------------------------------------------------------------------------------------
When I was running the spce example from  /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce, the job was getting stuck with the following message:

csg_inverse --options settings.xml
Appending to existing logfile inverse.log
We are doing Method: ibi
Prepare (dir step_000)
Using initial guess from dist CG-CG.dist.tgt for CG-CG
step 0 done
Doing iteration 1 (dir step_001)
Simulation with lammps
Make update for ibi
Calculating rdfs with csg_stat using 4 tasks 
-----------------------------------------------------------------------------
The process was getting stuck after that. Nothing was being written in the inverse.log file for a very long time (days). Could you please suggest how I can resolve this issue?

Thanks,
Sandipan

Christoph Junghans

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Nov 18, 2020, 9:59:30 AM11/18/20
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I have no good idea, can you pack the input files (settings.xml
spce.data traj.dump) in a zip,
create an new issue for csg(https://github.com/votca/csg/issues/new)
and attach them?

Thanks,

Christoph
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAB-cU%3D6yyzbOO4xwBoGRZnA9xNEWTV6__kZR5abu%2BpbOnT8v4A%40mail.gmail.com.

sandipan c

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Nov 19, 2020, 11:15:00 AM11/19/20
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Thank you, Christoph.

When I run the examplke with the settings.xml, as it is
 provided, I was getting the error:
#########################################################################
#                                                                                                                                                     #
# ERROR:                                                                                                                                              #
# Command/function lmp not found (when calling from csg_call you might need to add --simprog option or set cg.inverse.program in the xml file)        #
# For details see the logfile /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/inverse.log #
#                                                                                                                                                     #
#########################################################################################

So, I had added the path of my lammps executable by adding the following line in settings.xml:
<command>/media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/lammps-11Aug17/src/lmp_serial</command>

I am attaching the settings.xml

Is this correct or should I do something different?

Thanks,
Sandipan

settings.xml

Christoph Junghans

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Nov 19, 2020, 11:36:45 AM11/19/20
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On Thu, Nov 19, 2020 at 9:15 AM sandipan c <sandi.c...@gmail.com> wrote:
>
> Thank you, Christoph.
>
> When I run the examplke with the settings.xml, as it is
> provided, I was getting the error:
> #########################################################################
> # #
> # ERROR: #
> # Command/function lmp not found (when calling from csg_call you might need to add --simprog option or set cg.inverse.program in the xml file) #
> # For details see the logfile /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/inverse.log #
> # #
> #########################################################################################
>
> So, I had added the path of my lammps executable by adding the following line in settings.xml:
> <command>/media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/lammps-11Aug17/src/lmp_serial</command>
>
> I am attaching the settings.xml
>
> Is this correct or should I do something different?
That is the correct way! cg.inverse.lammps.command is the right option for that.

Christoph
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAB-cU%3D4jrF3u2hoBmWRuRV_BNSbT4%3D9_8CUkvThz86-VR7xsrg%40mail.gmail.com.
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