Hi Sikandar Ok, understood, thank you by your clear answer. Best Regards Marc
On Mon, Apr 14, 2014 at 3:18 PM, Sikandar Mashayak <[email protected]>wrote: > Hi Marc > > The advantage of Cubic B-splines functional form is that it is very > flexible and it can capture any shape provided that sufficiently large > number of knot values are used. > > The knot values determine the grid-size for B-splines, i.e., dr = > Rcut/(nknots-3). Smaller the grid size more flexible > is the B-spline. But decreasing grid size, i.e. more knot values, > increases computational time of RE. So you > have to estimate the minimum number of knot values that will capture the > CG potential shape. > > In the case of water, CG potential is known to have two-minima > core-softened shape. Hence to capture such a > shape we used 48 knot values to model B-Splines. Since, we use cut-off of > 0.9 nm, the grid size for B-spline is 0.02 nm (cut-off/(nknots-3)). > > I hope this helps. > > Regards > Sikandar > > > On Mon, Apr 14, 2014 at 12:50 PM, Marc Segovia <[email protected]>wrote: > >> Hi all >> >> I am running RE tutorial in develpment version, but a question arise. >> When is estimated the potential using cubic splines, how do you >> specifed the number of knots ? in the tutorial they are 48. >> >> <!-- function form for the potential (lj126 or ljg or cbspl)--> >> <function>cbspl</function> >> <cbspl> >> <!-- no. of knots for cbspl function --> >> <nknots>48</nknots> >> >> Thanking in advance your help >> >> Best Regards >> >> Marc >> >> Dr. Marc Segovia >> CCBG-DETEMA >> Facultad de Quimica >> Universidad de la Republica >> 11800 Montevideo >> Uruguay >> >> >> >> On Fri, Nov 1, 2013 at 11:57 PM, Sikandar Mashayak >> <[email protected]>wrote: >> >>> Hi Marc >>> >>> The option "nknots_cutoff" was earlier used in the settings.xml file to >>> specify number of cubic B-spline knots near the cut off which should be >>> forced to value 0.0 to ensure that CG potential smoothly goes to zero near >>> the cut-off. >>> >>> Later, I decided to fix this nknots_cutoff = 4 because I think fixing 4 >>> knot values near the cut-off is sufficient in most of the cases and user >>> should not worry about this number. Hence, instead of taking this number as >>> an input from user, it is fixed in the source code. >>> >>> You should not get the error "property not found: nknots_cutoff" if you >>> are using latest source code of votca-csg (i.e., revision > >>> 681d33b7942b<http://code.google.com/p/votca/source/detail?r=681d33b7942bba2d3d213f4e321b17e0c6a00676&repo=csg>). >>> >>> >>> So could you please check if you are correctly downloading the latest >>> version and installing it. Because, I dont get the same error, when I test >>> the water spce relative entropy tutorial with the latest development >>> version of csg source code. >>> >>> You can check if you are using the latest version of votca-csg by >>> running "csg_inverse -h" it will print out the version of votca-csg that >>> you are using. >>> >>> Let us know if you face issues with updating and installing the latest >>> development version of votca-csg. >>> >>> Thanks >>> Sikandar >>> >>> >>> >>> On Fri, Nov 1, 2013 at 6:03 PM, Marc Segovia <[email protected]>wrote: >>> >>>> Good Night Everyone >>>> >>>> I am trying to run re tutorial with spce, but an error appear about >>>> nknots_cutoff property, I update my dev version without sucess, any >>>> suggestion ? >>>> >>>> Wishing a very good weekend and thanking in advance . >>>> >>>> Marc >>>> >>>> Dr. Marc Segovia >>>> CCBG >>>> Facultad de Quimica >>>> Universidad de la Republica >>>> 11800 Montevideo >>>> Uruguay >>>> >>>> ~/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/step_000 >>>> Generating potential tables from the initial parameters >>>> Running critical command 'csg_reupdate --gentable true --param-in-ext >>>> param.new --options >>>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml' >>>> an error occurred: >>>> property not found: nknots_cutoff >>>> >>>> Callstack: >>>> /home/marc/votca1.3/share/votca/scripts/inverse/inverse.sh - linenumber >>>> 166 >>>> do_external - linenumber 171 in >>>> /home/marc/votca1.3/share/votca/scripts/inverse/functions_common.sh >>>> /home/marc/votca1.3/share/votca/scripts/inverse/prepare_re.sh - >>>> linenumber 36 >>>> critical - linenumber 4 (see 'csg_call --cat function >>>> critical') >>>> die - linenumber 2 (see 'csg_call --cat function die') >>>> >>>> ################################################################################################################################################################ >>>> # >>>> # >>>> # >>>> ERROR: >>>> # >>>> # critical: 'csg_reupdate --gentable true --param-in-ext param.new >>>> --options >>>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml' >>>> failed # >>>> # For details see the logfile >>>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/inverse.log >>>> # >>>> # >>>> # >>>> >>>> ################################################################################################################################################################ >>>> die: (called from 318) CSG_MASTER_PID is 31799 >>>> die: pids to kill: 31799 318 >>>> >>>> -- >>>> 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. >>> >> >> -- >> 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. >> > > -- > 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. > -- 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.
