On Thu, Aug 15, 2013 at 10:48 PM, Christoph Junghans <[email protected]>wrote:
> 2013/8/15 Chandan Choudhury <[email protected]>: > > Dear votca users, > > > > The atomisitc trajectory produces a distribution of AB bond in the range > > from 0.44 to 0.45 nm. While the potential (input) is also generated. This > > distribution and potential are generated using csg_stat and latter from > both > > the plots, the bad sampled regions are removed. Kepping the range same. > > > > Now, when I procede for iteration at step_001. The peak positon for AB > bond > > is off and the range is from 0.34 to 0.40. My final aim is to converge > both > > the distributions. Thus using IBI. > > > > Now problem what I encounter, is that if the min and max in the > cg.bonded > > is kept according to the atomistic distribution, then I miss out the > > distribution in the iteration step (steep_001). > > When I decrease the min to 0.30 and increase the max to 0.54, I do find > the > > AB distribution in step_001. But after that the following error is > > encountered: > > > > > > working directory: > > > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/iterate_bond/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.OYNVr > > AB.bond.dist.tgt_extrapolated.4g5KN' (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.4g5KN > > 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.plline > > 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') > > > ########################################################################################################################################################################### > > # > > # > > # ERROR: > > # > > # do_external: subscript > > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.pl > > AB.bond.dpot.pure_ibi AB.bond.dpot.new (from tags dpot shift_bonded) > failed > > # > > # For details see the logfile > > > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/iterate_bond/inverse.log > > # > > # > > # > > > ########################################################################################################################################################################### > > > > > > The AB.bond.dpot.pure_ibi contains 0 for all the values between 0.3 to > 0.54. > > Can anyone guide me regarding this? > Strange! > > Can you send me AB.bond.dist.tgt AB.bond.dist.new AB.bond.pot.cur from > that step? > > Dear Christoph, Thanks for looking at it. Please find in the files in the attachment. Chandan > Christoph > > > > -- > > 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. > -- 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.
AB.tar.gz
Description: GNU Zip compressed data
