Ibi tutorial with lammps

169 views
Skip to first unread message

sandip khan

unread,
May 26, 2020, 2:59:57 PM5/26/20
to votca
Dear All,

        I was running the ibi tutorial with lammps for spce water model. I got following error in the inverse.log file for step001. However lammps simulation done in folder "step-001"

Topology does not have beads of type "Bead1"
This was specified in type1 of interaction "CG-CG"

Callstack:
/usr/local/share/votca/scripts/inverse/inverse.sh - linenumber 266
    do_external - linenumber 176 in /usr/local/share/votca/scripts/inverse/functions_common.sh
        /usr/local/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')
                        /usr/local/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')
#############################################################################################################################################################################
#########
#                                                                                                                                                                           
        #
# ERROR:                                                                                                                                                                    
        #
# critical: 'csg_stat --nt 20 --options /home/ws7/Downloads/share/votca/csg-tutorials/spce/ibi_lammps/settings.xml --top spce.data --trj traj.dump --begin 0 --first-frame 0'
 failed #
# For details see the logfile /home/ws7/Downloads/share/votca/csg-tutorials/spce/ibi_lammps/inverse.log                                                                     
        #
#                                                                                                                                                                           
        #
#############################################################################################################################################################################
#########
die: (called from 19206)  CSG_MASTER_PID is 16324

        Any thought on this.

Thanks,
Sandip



Christoph Junghans

unread,
May 26, 2020, 3:05:26 PM5/26/20
to vo...@googlegroups.com
On Tue, May 26, 2020 at 12:59 PM sandip khan <khans...@gmail.com> wrote:
>
> Dear All,
>
> I was running the ibi tutorial with lammps for spce water model. I got following error in the inverse.log file for step001. However lammps simulation done in folder "step-001"
>
What version of VOTCA are you using?
Can you post the beginning of the output of "csg_dump --top spce.data"?

Christoph
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/3682bf5c-2937-4042-8933-850ca677ad5e%40googlegroups.com.



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

sandip khan

unread,
May 27, 2020, 4:41:06 AM5/27/20
to votca
Thanks Christoph for your prompt reply. I have installed either master or stable version of Votca. I looked into the Cmakelists.txt and it is written as project version 1.6 and I installed it under /usr/local/

I am using ubuntu 16.04 LTS

Here is the output of "csg_dump --top spce.data"


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

I have 2180 beads in 2180 molecules
Boundary Condition: orthorhombic
 Box matix: 4.031 0 0
            0 4.031 0
            0 0 4.031
          
List of residues:
0 name: DUM id: 0
1 name: DUM id: 1
2 name: DUM id: 2
3 name: DUM id: 3
4 name: DUM id: 4
5 name: DUM id: 5
6 name: DUM id: 6

---
---
---

List of molecules:
molecule: 1 F1 beads: 1
0 Name F1 Type F1 Mass 18.0154 Resnr 1 Resname DUM Charge 0
molecule: 2 F1 beads: 1
1 Name F1 Type F1 Mass 18.0154 Resnr 2 Resname DUM Charge 0
molecule: 3 F1 beads: 1
2 Name F1 Type F1 Mass 18.0154 Resnr 3 Resname DUM Charge 0

Thanks,
Sandip

Christoph Junghans

unread,
May 27, 2020, 8:55:09 AM5/27/20
to vo...@googlegroups.com
Using the latest stable version (1.6), I get:
List of molecules:
molecule: 1 Be1 beads: 1
0 Name Bead1 Type Bead1 Mass 18.0154 Resnr 1 Resname DUM Charge 0
molecule: 2 Be1 beads: 1
1 Name Bead1 Type Bead1 Mass 18.0154 Resnr 2 Resname DUM Charge 0

which has type "Bead1" (instead of "F1").

Please make sure you are using the latest version.
Check your version by running: csg_call --version.

Christoph
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/d3a8c7ae-efce-4e10-9f63-8ee3c1ff0f70%40googlegroups.com.

sandip khan

unread,
May 27, 2020, 9:33:22 AM5/27/20
to votca
Thank you for your reply. Now I changed the bead type from Bead1 to F1 in the setting file and it is working.  Please find the version below that I am using.

ws7@ws7:/usr/local/share/votca/csg-tutorials/spce/ibi_lammps$ csg_call --version
csg_call, version 1.6 gitid: d8d9ab8
> To unsubscribe from this group and stop receiving emails from it, send an email to vo...@googlegroups.com.

Christoph Junghans

unread,
May 27, 2020, 10:06:53 AM5/27/20
to vo...@googlegroups.com
On Wed, May 27, 2020 at 7:33 AM sandip khan <khans...@gmail.com> wrote:
>
> Thank you for your reply. Now I changed the bead type from Bead1 to F1 in the setting file and it is working. Please find the version below that I am using.
That is a good workaround.

One last thing, can you post the output of "uname -a"?

Christoph
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/8ff3935e-2b30-491f-938d-ea16e7c45e5b%40googlegroups.com.

sandip khan

unread,
May 27, 2020, 12:13:09 PM5/27/20
to votca
Thanks Christoph. Here it is

uname -a
Linux ws7 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Reply all
Reply to author
Forward
0 new messages