I took a closer look at update_ibi_pot.pl and it seems this lack of overlap
is definitely the issue, since the script only calculates dU in regions
where both distributions are non-zero:
--------------------update_ibi_pot.pl, lines 70-72-------------------
if (($rdf_aim[$i] > 1e-10) && ($rdf_cur[$i] > 1e-10)) {
$dpot[$i]=log($rdf_cur[$i]/$rdf_aim[$i])*$pref;
$flag[$i]="i";
----------------------------------------------------------------------------
Are there any suggestions on ways to work around this? One though I had was
to edit this script to check first for overlap, and if non exists, then set
$rdf_aim[$i]= 1e-9. This would allow dU to be calculated in the region
where rdf_cur is non-zero and would solve the problem of having the dU
output file containing only zeros. I am not familiar/experienced enough
with IBI to know if this would be a reasonable work around though. Any
suggestions or advice would be greatly appreciated!
Thank you again,
- Amy
On Wednesday, March 14, 2018 at 6:02:12 PM UTC-5, Amy Rice wrote:
>
> Hi all,
>
> I am trying to use IBI to refine one of the bonded potentials in my CG
> system. The initial guess and step_001 gromacs simulation run without
> issue, but it fails to update the potential at this step. The detailed
> error output from inverse.log is pasted below. It seems to me that the
> issue isn't with the potential_shift.pl step, which (I think) just fails
> because SNa-SC2.dpot.pure_ibi has no non-zero values in it; I think the
> problem arises during the "update_ibi_pot" step when dU is calculated. I
> noticed that the current rdf is quite far from the target distribution and
> wonder if this could be causing some problems? I've attached the two
> distributions, the current potential and pure_ibi files, and the full log
> file. Please let me know if there is any other information I can provide
> that will be of help troubleshooting this problem.
>
> ------------------------------------from
> inverse.log---------------------------------------------------------------
>
> Running critical command 'mktemp SNa-SC2.dist.tgt_extrapolated.XXXXX'
> Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
> --region leftright SNa-SC2.dist.tgt_smooth.PP6mM
> SNa-SC2.dist.tgt_extrapolated.w36Sf' (from tags table extrapolate) dir
> /home/arice3/Programs/votca/share/votca/scripts/inverse
> table_extrapolate.pl: extrapolating the left using linear with gradient 0
> table_extrapolate.pl: extrapolating the right using linear with gradient 0
> Running subscript 'dist_adjust.pl SNa-SC2.dist.tgt_extrapolated.w36Sf
> SNa-SC2.dist.tgt' (from tags dist adjust) dir
> /home/arice3/Programs/votca/share/votca/scripts/inverse
> Running subscript 'update_ibi_pot.pl SNa-SC2.dist.tgt SNa-SC2.dist.new
> SNa-SC2.pot.cur SNa-SC2.dpot.pure_ibi 2.49435' (from tags update ibi_pot)
> dir /home/arice3/Programs/votca/share/votca/scripts/inverse
> Running subscript 'potential_shift.pl --type bond SNa-SC2.dpot.pure_ibi
> SNa-SC2.dpot.new' (from tags potential shift) dir
> /home/arice3/Programs/votca/share/votca/scripts/inverse
> No valid value found in SNa-SC2.dpot.pure_ibi at
> /home/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl
> line 87.
>
> Callstack:
> /home/arice3/Programs/votca/share/votca/scripts/inverse/inverse.sh -
> linenumber 264
> do_external - linenumber 176 in
> /home/arice3/Programs/votca/share/votca/scripts/inverse/functions_common.sh
>
> /home/arice3/Programs/votca/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')
>
> /home/arice3/Programs/votca/share/votca/scripts/inverse/update_ibi_single.sh
> - linenumber 42
> do_external - linenumber 22 (see 'csg_call
> --cat function do_external')
> die - linenumber 2 (see 'csg_call --cat
> function die')
>
> #################################################################################################################################
> #
>
> #
> #
> ERROR:
>
> #
> # do_external:
> subscript
>
> #
> # /home/arice3/Programs/votca/share/votca/scripts/inverse/
> potential_shift.pl --type bond SNa-SC2.dpot.pure_ibi SNa-SC2.dpot.new #
> # (from tags potential shift)
> failed
>
> #
> # For details see the logfile
> /local/VOTCA/IBI_test/inverse.log
>
> #
> #
>
> #
>
> #################################################################################################################################
> die: (called from 16487) CSG_MASTER_PID is 12694
> die: pids to kill: 12694 15891 16472 16487
>
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
>
> Thank you for the help,
> - Amy
>
>
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