2017-01-12 21:44 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>:
> Thank you for the help.
Does it work now?

>
> On Thursday, January 12, 2017 at 9:34:39 PM UTC-6, Christoph Junghans wrote:
>>
>> 2017-01-12 10:10 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>:
>> > I am currently using VOTCA v1.3.1 and I took a look at the values of r
>> > and I
>> > couldn't find repeated values of r. I have attached the files of the
>> > resample and the initial file.
>> Your function_resample.pot is full of out of range values (3rd column
>> is "o"), this must have happened in some early step when working with
>> the potential. (see section 3.6 of the manual
>> http://votca.github.io/doxygen/manual.pdf)
>>
>> You can workaround that by telling csg_call ignore the flags using the
>> "sloppy-table" option:
>> $ csg_call --sloppy-tables table extrapolate function_resample.pot
>> table_extrapolate.pot
>>
>> However, I would do the table conversion like this:
>> $ csg_call --options bond.xml --ia-name bond --ia-type bond
>> convert_potential gromacs R3-C1-func.pot.ib R3-C1-func.pot.xvg
>> with bond.xml (starting from
>>
>> https://github.com/votca/csg-tutorials/blob/master/hexane/atomistic/bond.xml
>> only modifying min and max t  0.3 and 0.46):
>> $ cat bond.xml
>> <cg>
>>   <bonded>
>>     <!-- name of the interaction -->
>>     <name>bond</name>
>>     <min>0.3</min>
>>     <max>0.46</max>
>>     <step>0.01</step>
>>   </bonded>
>>   <inverse>
>>     <gromacs>
>>       <pot_max>1e8</pot_max>
>>       <table_end>2.0</table_end>
>>       <table_bins>0.002</table_bins>
>>     </gromacs>
>>   </inverse>
>> </cg>
>>
>> Cheers,
>>
>> Christoph
>> >
>> > On Thursday, January 12, 2017 at 9:29:33 AM UTC-6, Christoph Junghans
>> > wrote:
>> >>
>> >> 2017-01-11 20:14 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>:
>> >> > Output:
>> >> >
>> >> > Running subscript 'table_extrapolate.pl function_resample.pot
>> >> > function_extra.pot' (from tags table extrapolate) dir
>> >> > /usr/local/votca/share/votca/scripts/inverse
>> >> > Use of uninitialized value in subtraction (-) at
>> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > line
>> >> > 227.
>> >> > Use of uninitialized value in subtraction (-) at
>> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > line
>> >> > 227.
>> >> > Use of uninitialized value in subtraction (-) at
>> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > line
>> >> > 227.
>> >> > Use of uninitialized value in subtraction (-) at
>> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > line
>> >> > 227.
>> >> > Illegal division by zero at
>> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > line
>> >> > 227.
>> >> >
>> >> > Callstack:
>> >> > /usr/local/votca/bin/csg_call - linenumber 199
>> >> >     do_external - linenumber 177 in
>> >> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
>> >> >         die - linenumber 109 in
>> >> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
>> >> >
>> >> >
>> >> > ##############################################################################################################
>> >> > #
>> >> > #
>> >> > # ERROR:
>> >> > #
>> >> > # do_external: subscript
>> >> > #
>> >> > # /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl
>> >> > function_resample.pot function_extra.pot #
>> >> > # (from tags table extrapolate) failed
>> >> > #
>> >> > # Details can be found above
>> >> > #
>> >> > #
>> >> > #
>> >> >
>> >> >
>> >> > ##############################################################################################################
>> >> >
>> >> >
>> >> > On Wednesday, January 11, 2017 at 8:55:41 PM UTC-6, Bijay Shrestha
>> >> > wrote:
>> >> >>
>> >> >> Hi there,
>> >> >>     I was stuck in the post processing of the potential (to be
>> >> >> specific
>> >> >> on
>> >> >> the extrapolation of the potential). Firstly, I clipped the
>> >> >> irregular
>> >> >> distributions especially the borders. Then I did the csg_resample
>> >> >> and
>> >> >> obtained the resampled table .pot file. Then when I went for the
>> >> >> extrapolation using csg_call and got error messages. The command
>> >> >> that I
>> >> >> gave
>> >> >> was:
>> >> >> >> csg_call table extrapolate table_resample.pot \
>> >> >> >> table_extrapolate.pot
>> >> >>
>> >> >> The error message said that was it was dividing by zero and hence
>> >> >> couldn't
>> >> >> proceed. Are there any criteria for the process (because I was able
>> >> >> to
>> >> >> perform the extrapolation of some potential)?
>> >> What version of VOTCA is this?
>> >>
>> >> Looking at line 227 of table_extrapolate.pl:
>> >>
>> >>
>> >> https://github.com/votca/csg/blob/master/share/scripts/inverse/table_extrapolate.pl#L227
>> >> it seems the only way to get a division by zero error is if you have
>> >> repeated r values in the first column of the table.
>> >> Can you check that?
>> >>
>> >> In VOTCA 1.4 you could use
>> >> $ csg_call --options options.xml --ia-type non-bonded --ia-name X-X
>> >> convert_potential gromacs <inputfile> <outputfile>
>> >> instead do to all steps at once. (Search the mailing list for details.)
>> >>
>> >> Christoph
>> >>
>> >> >>
>> >> >> Thank you in advance.
>> >> >
>> >> > --
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>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
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-- 
Christoph Junghans
Web: http://www.compphys.de

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