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
On Wed, Nov 18, 2020 at 8:29 PM Christoph Junghans <[email protected]>
wrote:
> On Wed, Nov 18, 2020 at 7:29 AM sandipan c <[email protected]>
> wrote:
> >
> > 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?
>
> 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
> >
> > Thanks,
> > Sandipan
> >
> > On Tue, Nov 17, 2020 at 7:49 PM Christoph Junghans <[email protected]>
> wrote:
> >>
> >> On Tue, Nov 17, 2020 at 5:51 AM sandipan c <[email protected]>
> 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
> >> >
> >> > As mentioned earlier, this is a tutorial example taken from:
> >> > https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps
> >> > I am attaching the inverse.log and settings.xml files.
> >> >
> >> > Thanks,
> >> > Sandipan
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Sun, Nov 15, 2020 at 8:11 PM Christoph Junghans <
> [email protected]> wrote:
> >> >>
> >> >> 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
> >> >>
> >> >>
> >> >> On Sun, Nov 15, 2020 at 12:22 AM sandipan c <
> [email protected]> wrote:
> >> >> >
> >> >> > 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
> >> >> >
> >> >> > --
> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> > ---
> >> >> > You received this message because you are subscribed to the Google
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> send an email to [email protected].
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> .
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
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> .
> >> >
> >> > --
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> .
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
> >> --
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> .
> >
> > --
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
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> .
>
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<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>CG-CG</name>
<!-- types involved in this interaction -->
<type1>Bead1</type1>
<type2>Bead1</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.0</min>
<max>0.9</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf) -->
<target>CG-CG.dist.tgt</target>
<lammps>
<!-- name of the table for lammps run -->
<table>CG_CG.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- votca units 300*0.00831451 kJ/mol -->
<kBT>2.49435</kBT>
<!-- use lammps as simulation program -->
<program>lammps</program>
<!-- lammps specific options -->
<lammps>
<command>/media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/lammps-11Aug17/src/lmp_serial</command>
<!-- lammps script to run !-->
<script>spce.in</script>
<!-- topology to be used by csg_stat !-->
<topol>spce.data</topol>
<!-- traj file created by lammps !-->
<traj>traj.dump</traj>
</lammps>
<initial_configuration>maindir</initial_configuration>
<!-- these files are copied for each new run -->
<filelist>spce.data spce.in</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
</inverse>
</cg>
