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
> On 28 Apr 2019, at 9:31 PM, Christoph Junghans <[email protected]> wrote:
>
> 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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