Thank you for the help. 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 <[email protected] > <javascript:>>: > > 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 <[email protected]>: > >> > 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. > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at https://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de >
-- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
