2017-01-12 21:44 GMT-07:00 Bijay Shrestha <[email protected]>: > 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]. > 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.
