Yes it worked. Thank you. On Friday, January 13, 2017 at 8:55:44 AM UTC-6, Christoph Junghans wrote: > > 2017-01-12 21:44 GMT-07:00 Bijay Shrestha <[email protected] > <javascript:>>: > > 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 <[email protected]>: > >> > 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]. > >> > 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 >
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