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
On Sat, Apr 27, 2019 at 6:48 PM CHRISTINA-ANNA GATSIOU
<[email protected]> wrote:
>
> 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
>
> On 27 Apr 2019, at 7:11 PM, Christoph Junghans <[email protected]> wrote:
>
>
>
> On Fri, Apr 26, 2019, 07:52 <[email protected]> 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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>
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--
Christoph Junghans
Web: http://www.compphys.de
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