Re: [votca] Error when do ibi for --first-frame 0' failed

[Christoph Junghans]

On Wed, May 10, 2023 at 9:02 AM Annie Wu <wu.ann...@gmail.com> wrote:
>
> Hi votca,
>
> I work on a two-type CG system, trying to correct the non-bond potential, but file at the first frame, I follow the example in spce:ibi_lammps, I believe I have the same in.file and lammps part in setting.xml, but have no idea why this error comes, any help will be appreciated, I attach the files below. Thanks for your time.

What exactly is the error message?

>
> Best,
> Annie
>
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Christoph Junghans
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[Annie Wu]

this is the error part in the log.file, I compare this log with the example, I really think they are very similar, I put all the input files in the first attach, hope could get some guide about this error.

On Wed, May 10, 2023 at 11:21 PM Annie Wu <wu.ann...@gmail.com> wrote:

Thanks for the reply, please check the log.file, it said : environment：line 1: 2169250 para wrong               "$@", but I did not see this any place and also compare with the spce example, I could run the example directly, but this keep error.

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[Christoph Junghans]

On Wed, May 10, 2023 at 9:42 AM Annie Wu <wu.ann...@gmail.com> wrote:

this is the error part in the log.file, I compare this log with the example, I really think they are very similar, I put all the input files in the first attach, hope could get some guide about this error.

I would try to run the last command manual to see what is going on:

go to step_001 and run

$ csg_stat --nt 6 --options ../settings.xml --top spce.data --trj traj.dump --begin 0 --first-frame 0

Christoph

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[Annie Wu]

begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3

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 0 beads in 0 molecules

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


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


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


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


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

Reading frame, timestep 10000
Segmentation fault

__________________________________________________________________________________

this is the result after only run the last command, but seems nothing information gives out, it really comfuse. 

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[Christoph Junghans]

Well, it segfaults, which isn't good.

But it also says:

0 beads in 0 molecules

so VOTCA has 0 molecules, which is wrong as well.

The problem is that lammps' data file has no molecular information, but votca needs that.

The easiest way to fix that is to use a xml topology file instead.

Example: https://github.com/votca/votca/blob/master/csg-tutorials/propane/imc-ibiintra/topology.xml

Documentation here: https://www.votca.org/csg/input_files.html#advanced-topology-handling

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[Christoph Junghans]

On Wed, May 10, 2023 at 10:50 AM Annie Wu <wu.ann...@gmail.com> wrote:

But the data I used include the molecular id, in the traj.dump also includes the molecular information, so I really want to figure this out, if it's possible could anyone try my package? 

You can run

$ csg_dump --top spce.data 

to see what VOTCA reads from the data file.

But looking at the data file you provided in the "atom" section it reads

1       1       -7.585826176    5.537340182     -12.30895777

Which is this style:

atom-ID atom-type x y z

and hence there is no molecule info.

You will have to create a data file one of the other styles, e.g.

atom-ID molecule-ID atom-type x y z

to add in molecule info.

Christoph

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[Annie Wu]

Running critical command 'csg_stat --nt 6 --options /usr/local/share/votca/csg-tutorials/spce/ibi_lammps/try-ibi-lammps/settings.xml --top topol.xml --trj traj.dump --begin 0 --first-frame 0'

begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3

I have 4000 beads in 800 molecules
Reading frame, timestep 10000
an error occurred:
The max of interaction "CG1-CG1" bigger is than half the box.

Callstack:
/usr/local/share/votca/scripts/inverse/inverse.sh - linenumber 266
    do_external - linenumber 177 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 6 --options /usr/local/share/votca/csg-tutorials/spce/ibi_lammps/try-ibi-lammps/settings.xml --top topol.xml --trj traj.dump --begin 0 --first-frame 0' failed #
# For details see the logfile /usr/local/share/votca/csg-tutorials/spce/ibi_lammps/try-ibi-lammps/inverse.log                                                                             #
#                                                                                                                                                                                         #
###########################################################################################################################################################################################
die: (called from 2209634)  CSG_MASTER_PID is 2203960
die: pids to kill: 2203960 2209464 2209620 2209634 

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

I have added a topol.xml with a new error, I have <min><max>and <table_begin>, is there get some effect by the bond and angle? but I did not add any coefficient for bond and angle in the input file, for this error, could you give some suggestions? Thanks again for your time.

On Thu, May 11, 2023 at 12:49 AM Annie Wu <wu.ann...@gmail.com> wrote:

But the data I used include the molecular id, in the traj.dump also includes the molecular information, so I really want to figure this out, if it's possible could anyone try my package? 

On Thu, May 11, 2023 at 12:15 AM Christoph Junghans <jung...@votca.org> wrote:

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[Christoph Junghans]

On Wed, May 10, 2023 at 12:01 PM Annie Wu <wu.ann...@gmail.com> wrote:

I change the data file with molecular id and added a topol.xml file, updating the new attachment, really appreciate your reply, could you have a look at my files? Thanks  really alot.

On Thu, May 11, 2023 at 1:40 AM Annie Wu <wu.ann...@gmail.com> wrote:

Running critical command 'csg_stat --nt 6 --options /usr/local/share/votca/csg-tutorials/spce/ibi_lammps/try-ibi-lammps/settings.xml --top topol.xml --trj traj.dump --begin 0 --first-frame 0'
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3
I have 4000 beads in 800 molecules
Reading frame, timestep 10000
an error occurred:
The max of interaction "CG1-CG1" bigger is than half the box.

This error means that the max of the CG1-CG1 interaction is larger than 1/2 box, which due to minimum image convention is not good, so suggest use a bigger box or a smaller cutoff.

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[Annie Wu]

I change the cutoff, but I think it's not very reasonable, I change it to 0.35,it could run but with a new error, I have change table_begin for 1-2 potential, but not very useful, is there any command I could change?

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[Christoph Junghans]

On Wed, May 10, 2023 at 1:00 PM Annie Wu <wu.ann...@gmail.com> wrote:

I change the cutoff, but I think it's not very reasonable, I change it to 0.35,it could run but with a new error, I have change table_begin for 1-2 potential, but not very useful, is there any command I could change?

If changing the cutoff isn't reasonable, just make the simulation box bigger by a factor 2 in each direction.

Christoph

 

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[Annie Wu]

If I change the volume to two time, how could I make sure the density is correct? since I use nve to control the density and use pressure correction to adjust the pressure. 

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[Christoph Junghans]

On Wed, May 10, 2023 at 1:40 PM Annie Wu <wu.ann...@gmail.com> wrote:

If I change the volume to two time, how could I make sure the density is correct? since I use nve to control the density and use pressure correction to adjust the pressure. 

Sorry, I meant, take your original box and stack 8 of them together (2 in each dimension), so you have the same density.

Christoph

 

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[Annie Wu]

get it, thanks for your explain, I will try it.

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[Christoph Junghans]

Annie,

is it working now?

Christoph

[Annie Wu]

Thanks for asking, it still meets problem, I enlarge the box, but still with error, and I change the cutoff, but the value is unreasonably, so I keep enlarging the box, but I think this is not a good solution. 

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[Christoph Junghans]

On Wed, May 24, 2023 at 7:35 AM Annie Wu <wu.ann...@gmail.com> wrote:

Thanks for asking, it still meets problem, I enlarge the box, but still with error, and I change the cutoff, but the value is unreasonably, so I keep enlarging the box, but I think this is not a good solution. 

I would try to decrease table_begin in the <lammps> block of the setting a little more.

Christoph

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