Hi Christoph, It came to my attention only recently that the --min option of the command above does change the potential barrier hight. It is not clear from the description which minimum value is meant. Could you please comment what exactly does it mean:
csg_call dist invert --min 0.001 Thanks. Best, --Vitalie On Friday, December 5, 2014 at 6:25:04 PM UTC+1, Christoph Junghans wrote: > > I am not quite sure what you want to achieve with that call. > > I guess what you want is > $ csg_call dist invert > > see > $ csg_call dist invert --help > and > $ csg_call -l > for all possible calls. > > Christoph > > > > --Vitalie > > > > On Thursday, December 4, 2014 5:27:57 PM UTC+1, Christoph Junghans > wrote: > >> > >> 2014-12-04 8:21 GMT-07:00 Vitalie Botan <[email protected]>: > >> > Hi Christoph, > >> > > >> > It looks there is a problem with the angle potential routine, it > fails > >> > with > >> > the following error: > >> > > >> > ERROR: > >> > do_external: subscript > >> > /opt/votca/share/votca/scripts/inverse/table_extrapolate.pl > --function > >> > linear --avgpoints 3 --region leftright ABB.pot.smooth.lQm2b > >> > ABB.pot.extrapol.CUPup > >> > (from tags table extrapolate) failed > >> > For details see the logfile > >> > > >> > I searched the log file and found a command, which could cause this > >> > error: > >> > > >> > Running subscript 'potential_to_lammps.sh ABB.extra.pot > ABB.bonded.pot' > >> > (from tags convert_potential lammps) dir > >> > /opt/votca/share/votca/scripts/inverse > >> > Convert ABB.extra.pot to ABB.bonded.pot > >> > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) > >> > .*/\1/p' > >> > Running critical command 'mktemp ABB.pot.scale.XXXXX' > >> > Running subscript 'table_linearop.pl --on-x ABB.extra.pot > >> > ABB.pot.scale.d4RZ0 57.2957795 0' (from tags table linearop) dir > >> > /opt/votca/share/votca/scripts/inverse > >> > table_linearop.pl: ABB.extra.pot to ABB.pot.scale.d4RZ0 with x' = > >> > 57.2957795*x + 0 > >> > Running critical command 'mktemp ABB.pot.smooth.XXXXX' > >> > Running critical command 'csg_resample --in ABB.pot.scale.d4RZ0 --out > >> > ABB.pot.smooth.lQm2b --grid 0:114.592:180' > >> > Running critical command 'mktemp ABB.pot.extrapol.XXXXX' > >> > Running subscript 'potential_extrapolate.sh --type angle > >> > ABB.pot.smooth.lQm2b ABB.pot.extrapol.CUPup' (from tags potential > >> > extrapolate) dir /opt/votca/share/votca/scripts/inverse > >> > Extrapolate ABB.pot.smooth.lQm2b to ABB.pot.extrapol.CUPup > >> > Running subscript 'table_extrapolate.pl --function linear > --avgpoints 3 > >> > --region leftright ABB.pot.smooth.lQm2b ABB.pot.extrapol.CUPup' (from > >> > tags > >> > table extrapolate) dir /opt/votca/share/votca/scripts/inverse > >> > Use of uninitialized value in subtraction (-) at > >> > /opt/votca/share/votca/scripts/inverse/table_extrapolate.pl line > 227. > >> > Use of uninitialized value in subtraction (-) at > >> > /opt/votca/share/votca/scripts/inverse/table_extrapolate.pl line > 227. > >> > Illegal division by zero at > >> > /opt/votca/share/votca/scripts/inverse/table_extrapolate.pl line > 227. > >> > > >> > The question is if it was really intended to be resampled with the > >> > stepsize > >> > 114.592 (see the bold line above) or it is a typo? > >> Ok, I think I know what went wrong. The step size given in xml file > >> has to be in VOTCA units (radian). > >> And 2.0 in radian is a bit big. You want to go something like 0.034 > >> radian = 2 degree. > >> > >> Christoph > >> > >> > > >> > -- > >> > 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/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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
