2013/8/12 Chandan Choudhury <[email protected]>: > > Dear votca users, > > I am trying to iterate the bonded interaction (as of now just the bonds). > While doing so, I have encountered the following error (in 1st step): > > settings file: > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re-ibi/settings_nb_bon.xml > working directory: > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re-ibi/step_001' > Running critical command 'mktemp AB.bond.dist.tgt_extrapolated.XXXXX' > Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 > --region leftright AB.bond.dist.tgt_smooth.Ncssw > AB.bond.dist.tgt_extrapolated.2Jhj5' (from tags table extrapolate) dir > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse > Running subscript 'dist_adjust.pl AB.bond.dist.tgt_extrapolated.2Jhj5 > AB.bond.dist.tgt' (from tags dist adjust) dir > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse > Running subscript 'update_ibi_pot.pl AB.bond.dist.tgt AB.bond.dist.new > AB.bond.pot.cur AB.bond.dpot.pure_ibi' (from tags update ibi_pot) dir > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p' > Running subscript 'dpot_shift_bo.pl AB.bond.dpot.pure_ibi AB.bond.dpot.new' > (from tags dpot shift_bonded) dir > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse > No valid value found in AB.bond.dpot.pure_ibi at > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.pl line > 51. > > Callstack: > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/inverse.sh - linenumber > 265 > do_external - linenumber 171 in > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/functions_common.sh > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/update_ibi.sh - > linenumber 32 > for_all - linenumber 17 (see 'csg_call --cat function for_all') > do_external - linenumber 19 (see 'csg_call --cat > function do_external') > > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/update_ibi_single.sh - > linenumber 42 > do_external - linenumber 22 (see 'csg_call --cat > function do_external') > die - linenumber 2 (see 'csg_call --cat > function die') > ########################################################################################################################################################################### > > When I manually check AB.bond.dist.new the values are 0. > > AB.bond.dist.new > > 0.42 0 i > 0.422 0 i > 0.424 0 i > 0.426 0 i > 0.428 0 i > 0.43 0 i > 0.432 0 i > 0.434 0 i > 0.436 0 i > 0.438 0 i > 0.44 0 i > 0.442 0 i > 0.444 0 i > 0.446 0 i > 0.448 0 i > 0.45 0 i > 0.452 0 i > 0.454 0 i > 0.456 0 i > 0.458 0 i > 0.46 0 i > 0.462 0 i > 0.464 0 i > 0.466 0 i > 0.468 0 i > 0.47 0 i > 0.472 0 i > 0.474 0 i > 0.476 0 i > 0.478 0 i > 0.48 0 i > 0.482 0 i > 0.484 0 i > 0.486 0 i > 0.488 0 i > 0.49 0 i > 0.492 0 i > 0.494 0 i > 0.496 0 i > 0.498 0 i > 0.5 0 i > 0.502 0 i > 0.504 0 i > 0.506 0 i > 0.508 0 i > 0.51 0 i > 0.512 0 i > 0.514 0 i > 0.516 0 i > 0.518 0 i > 0.52 0 i > > Surprisingly, it can be noticed that all the values are integers. > While when I manually execute the csg_stat command (after the completiotion > of simulation), the values are float: > 0.42 0.0474763 i > 0.422 0.0174913 i > 0.424 0.0144928 i > 0.426 0.0169915 i > 0.428 0.00849575 i > 0.43 0.0129935 i > 0.432 0.0104948 i > 0.434 0.0104948 i > 0.436 0.00649675 i > 0.438 0.00849575 i > 0.44 0.0104948 i > 0.442 0.0089955 i > 0.444 0.011994 i > 0.446 0.00749625 i > 0.448 0.00849575 i > 0.45 0.0114943 i > 0.452 0.0049975 i > 0.454 0.00449775 i > 0.456 0.00949525 i > 0.458 0.0104948 i > 0.46 0.007996 i > 0.462 0.0114943 i > 0.464 0.00549725 i > 0.466 0.00849575 i > 0.468 0.00949525 i > 0.47 0.00849575 i > 0.472 0.00649675 i > 0.474 0.011994 i > 0.476 0.0109945 i > 0.478 0.0124938 i > 0.48 0.007996 i > 0.482 0.0124938 i > 0.484 0.0124938 i > 0.486 0.0089955 i > 0.488 0.0129935 i > 0.49 0.015992 i > 0.492 0.0089955 i > 0.494 0.007996 i > 0.496 0.00849575 i > 0.498 0.0029985 i > 0.5 0.00549725 i > 0.502 0.00549725 i > 0.504 0.00549725 i > 0.506 0.0029985 i > 0.508 0.0029985 i > 0.51 0.0029985 i > 0.512 0.00349825 i > 0.514 0.001999 i > 0.516 0.00049975 i > 0.518 0.00049975 i > 0.52 0.00149925 i > > I donot understand why this happens. Is this a bug? Any insight to this > would be very helpful. Hmm, that is very strange. Obviosly your xml input files are correct. Can you run the exact same csg_stat command as in csg_inverse? And look at the result? Find it with $ grep csg_stat inverse.log
Christoph > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
