2015-05-05 18:47 GMT-06:00 Vitalie Botan <[email protected]>: > 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 Basically, the Boltzmann inversion is U(x)=-k_B*T log(P(x)/norm(x)) with x being r (or the angle, bond length), which is undefined for P(x)=0, so in VOTCA we only invert for P(x)>min. Because of that the absolute barrier height is not a very good measure and relative difference in barriers are preferred.
Christoph > > 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]. >> > 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]. > 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]. 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.
