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.
