IBI on a binary mixture

christian...@gmail.com

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Apr 26, 2019, 9:52:22 AM4/26/19

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Hi,

I have attached the neccessary files. IBI seems to be failing before the inversion of the initial distributions! Some help would be very much appreciated.

Best regards,

Christianna

CG_urea_water.zip

Christoph Junghans

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Apr 27, 2019, 12:12:01 PM4/27/19

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On Fri, Apr 26, 2019, 07:52 <christian...@gmail.com> wrote:

Hi,

I have attached the neccessary files. IBI seems to be failing before the inversion of the initial distributions! Some help would be very much appreciated.

What is the error message?

Christoph

Best regards,
Christianna

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CHRISTINA-ANNA GATSIOU

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Apr 27, 2019, 8:48:05 PM4/27/19

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The error message looks like this

for_all: run 'do_external prepare_single ibi' for interaction named 'P2-P1'

Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /scratch/cgatsiou/votca/share/votca/scripts/inverse

Callstack:

/scratch/cgatsiou/votca/share/votca/scripts/inverse/inverse.sh - linenumber 156

do_external - linenumber 176 in /scratch/cgatsiou/votca/share/votca/scripts/inverse/functions_common.sh

/scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic.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')

/scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic_single.sh - linenumber 34

csg_get_interaction_property - linenumber 44 (see 'csg_call --cat function csg_get_interaction_property')

has_duplicate - linenumber 1 (see 'csg_call --cat function has_duplicate')

die - linenumber 2 (see 'csg_call --cat function die')

########################################################################

# #

# ERROR: #

# has_duplicate: Missing argument #

# For details see the logfile /home/cgatsiou/CG_urea_water/inverse.log #

# #

########################################################################

die: (called from 14553) CSG_MASTER_PID is 13536

die: pids to kill: 13536 14455 14538 14553

Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'

Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p’

The has_duplicate signifies the existence of a duplicate interaction, or option somewhere in the input but I cannot find an error in the inputs.

Best regards,

Christianna

Christoph Junghans

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Apr 28, 2019, 2:31:56 PM4/28/19

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I found it, it was actually a bug in the code, when using multiple
mapping files, which I fixed here:
https://github.com/votca/csg/pull/371

As a workaround apply the patch or revert the order of the mapping
files in your settings.xml for now:
--- settings.xml.orig 2019-04-27 19:42:45.434237893 -0600
+++ settings.xml 2019-04-27 19:43:08.314463798 -0600
@@ -122,7 +122,7 @@
<pot_max>1000000</pot_max>
<table_end>2.4</table_end>
</gromacs>
- <map>p4_topol.xml p2p1_topol.xml</map>
+ <map>p2p1_topol.xml p4_topol.xml</map>
<filelist>grompp.mdp topol.top conf.gro index.ndx table.xvg</filelist>
<iterations_max>30</iterations_max>
<convergence_check>

Christoph

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

CHRISTINA-ANNA GATSIOU

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May 8, 2019, 3:43:34 AM5/8/19

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Hi,

Thanks for the help! The error message I get now looks like this:

Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update ibi_pot) dir /usr/s
hare/votca/scripts/inverse
readin_table: could not open file P4_P4.dist.new

Callstack:
D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/inverse.sh - linenumber 301
do_external - linenumber 240 in D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/functions_common.sh
/usr/share/votca/scripts/inverse/update_ibi.sh - linenumber 32

for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat function do_external')

/usr/share/votca/scripts/inverse/update_ibi_single.sh - linenumber 39
do_external - linenumber 22 (see 'csg_call --cat function do_external')

die - linenumber 2 (see 'csg_call --cat function die')

######################################################################################################################

# #
# ERROR: #

# do_external: subscript                                                                                             #
# /usr/share/votca/scripts/inverse/update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi #
# (from tags update ibi_pot) failed                                                                                  #
# For details see the logfile /d/MAPS/DEMO2/CG_urea_water_2/inverse.log                                              #
#                                                                                                                    #
######################################################################################################################
die: (called from 5888) CSG_MASTER_PID is 12388
die: pids to kill: 0

Do you have ideas on what might be the problem.

Best regards,

Christianna

Christoph Junghans

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May 8, 2019, 9:00:18 AM5/8/19

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The error message says it all: could not open file P4_P4.dist.new

This file is missing.

Christoph

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CHRISTINA-ANNA GATSIOU

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May 8, 2019, 10:22:19 AM5/8/19

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Yes I understand this but I what I do not understand why or where it fails to generate this.

inverse.log

Christoph Junghans

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May 8, 2019, 10:38:03 AM5/8/19

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On Wed, May 8, 2019 at 8:22 AM CHRISTINA-ANNA GATSIOU
<christian...@gmail.com> wrote:
>
> Yes I understand this but I what I do not understand why or where it fails to generate this.

It should be generated by csg_stat. Just look for the last csg_stat
execution in the log file before the error occurs.

Christoph

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CHRISTINA-ANNA GATSIOU

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May 8, 2019, 12:40:30 PM5/8/19

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Hi,

I would like to ask one additional question. So the csg_stat during IBI is calculated by the following scripts:

1)calc_rdf_generic.sh

2)calc_target_rdf_generic.sh

I guess the second one is not used during inversion. Are there any additional scripts used.

Christianna

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Christoph Junghans

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May 8, 2019, 1:33:33 PM5/8/19

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On Wed, May 8, 2019 at 10:40 AM CHRISTINA-ANNA GATSIOU
<christian...@gmail.com> wrote:
>
> Hi,
> I would like to ask one additional question. So the csg_stat during IBI is calculated by the following scripts:
> 1)calc_rdf_generic.sh
> 2)calc_target_rdf_generic.sh
>
> I guess the second one is not used during inversion. Are there any additional scripts used.

It is 1.) [2.) is used for the optimizer method, when the rdf is a
target property).

The log file should tell you, which exact command got run, e.g.
csg_stat --options ..., so you can run this manually to see why
P4_P4.dist.new didn't get generated. The log file should also tell
you, which files csg_stat did write.

Christoph

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CHRISTINA-ANNA GATSIOU

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May 9, 2019, 8:24:55 AM5/9/19

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Hi, I would like to ask a slightly different question. In case I want to run a parallel lammps job. What would be the entry in settings.xml?

I tried

<program>lammps</program>

<command> mpirun lammps</command>

But it does not seem to work. I get the error message that the command is not found.

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Christoph Junghans

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May 9, 2019, 9:54:29 AM5/9/19

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On Thu, May 9, 2019 at 6:24 AM CHRISTINA-ANNA GATSIOU
<christian...@gmail.com> wrote:
>
> Hi, I would like to ask a slightly different question. In case I want to run a parallel lammps job. What would be the entry in settings.xml?
> I tried
> <program>lammps</program>
> <lammps>
> <command> mpirun lammps</command>

Run "mpirun -nt 4 lammps" here and drop the <opts> part below, <opts>
is mainly for when you need to hand options to lammps beside the
script.

Christoph

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