2017-03-07 9:12 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > Nevermind. That was in my original distribution, so VOTCA was inverting it. > > How can you measure the dihedral distribution during the IBI without having > a discontinuity at the end? Otherwise the dpot would try to include this > discontinuity. Sorry, my experience with dihedral interactions are pretty limited.
In the case of gromacs we force the table to be periodic: https://github.com/votca/csg/blob/master/share/scripts/inverse/table_to_xvg.pl#L99 You might want to copy that part for LAMMPS as well. Christoph > > Do you measure just a bit less than 3.1415? > > > On Tuesday, March 7, 2017 at 10:35:54 AM UTC-5, Joshua Moore wrote: >> >> The current calculation is causing a discontinuity in the dihedral at the >> ends, and I think this is occasionally leading to issues in the simulation, >> at least I think this is the reason. Please see attached. >> >> Do we need to add back in the end calculation as you were mentioning? >> Maybe that was needed. >> >> Thanks. >> >> Josh >> >> >> >> >> >> On Saturday, March 4, 2017 at 11:45:23 PM UTC-5, Christoph Junghans wrote: >>> >>> 2017-03-04 11:26 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>: >>> > 1) Angles >>> > >>> > I realized I was not using the development version. Sorry about this. >>> > This >>> > issue seems to have been corrected in the development version. I'm >>> > still >>> > not exactly what the change was to fix this, but it is correct in the >>> > development version. >>> > >>> > 2) Dihedrals >>> > >>> > I found two issues >>> > >>> > a) In potential_to_lammps.sh, there was a scaling to degrees for the >>> > "scale" >>> > step. This seems to be the cause of it dropping points in the >>> > smoothing >>> > step. If you remove this being applied to the $bondtype="dihedral", >>> > this >>> > issue goes away. >>> The issue is that the table beginning and ending should be converted >>> to degrees as well in the case of dihedral potentials. For the "angle" >>> type this issue doesn't appear as the table always goes from 0 to 180 >>> (both in degrees already.) >>> >>> > >>> > However, there was a second issue related to the units LAMMPS expects >>> > for >>> > the dihedral. I originally thought the default was radians, but it >>> > appears >>> > it is degrees. We need to add this to table_to_tab.pl so that LAMMPS >>> > knows >>> > the table is in radians. Then remove the previous check for dihedrals >>> > when >>> > it is scaling. >>> > >>> > } elsif ($type eq "dihedral" ) { >>> > printf(OUTFILE "VOTCA"\n"); >>> > printf(OUTFILE "N %i RADIANS\n\n",$#r+1); >>> > . >>> > . >>> > . >>> > >>> > LAMMPS seems to be finicky for the derivative for the dihedrals, and I >>> > think >>> > the amount of noise in the distribution is causing an issue for short >>> > runs >>> > and LAMMPS is complaining that the dihedral table has inconsistent >>> > forces. >>> > I'm assuming VOTCA is generating these from a spline? The issue seems >>> > to be >>> > alleviated with longer runs. However, LAMMPS has an option to leave >>> > off the >>> > forces for the dihedral table and let LAMMPS calculate them. I'll look >>> > into >>> > this some more to see if this helps. >>> > >>> > I'll work on a pull request if you agree. >>> Thanks Josh! Your pull request at >>> <https://github.com/votca/csg/pull/202> seems to fix the two issues >>> above. >>> >>> Christoph >>> >>> > >>> > Thanks. >>> > >>> > Josh >>> > >>> > >>> > >>> > >>> > >>> > On Friday, March 3, 2017 at 9:34:52 PM UTC-5, Joshua Moore wrote: >>> >> >>> >> Hello, >>> >> >>> >> I am seeing some issues with angle and dihedral translation issues. >>> >> >>> >> 1) Angles >>> >> >>> >> In the attached ANGLE_ISSUE.PNG, I illustrate the issue. >>> >> >>> >> On step000, the initial angle potential is inverted correctly from the >>> >> angle distribution. The unit conversion appears to be correct. On >>> >> step001, >>> >> it also is translated corrected during the scale, smoothing, >>> >> extrapolation, >>> >> interpolation, and shifting steps. However, it appears when the >>> >> LAMMPS >>> >> table file is written for the angle, something goes wrong. Here I >>> >> compare >>> >> to the initial inversion by hand which is shifted in step000, which >>> >> accounts >>> >> for the difference. The smoothing, extrapolation, interpolation steps >>> >> fall >>> >> on top of one another, and the shifting step is shifted of course. >>> >> >>> >> Again here the issue appears to be the lammps table writing step, >>> >> although >>> >> I haven't been able to find the issue in the code. Any ideas? >>> >> >>> >> 2) Dihedrals >>> >> >>> >> See attached DIHEDRAL_ISSUE.PNG >>> >> >>> >> Here, there may very well be a LAMMPS table writing issue as with the >>> >> angles, but on step001 the first issue that occurs is on the smoothing >>> >> steps, where it drops most of the data points and fits only 11 points. >>> >> This >>> >> is the cause for the difference. This is then populated through to >>> >> the next >>> >> steps including writing the LAMMPS table file. Although the smooth, >>> >> extrapolation, interpolation, and shifting steps are in radians, the >>> >> scaling >>> >> step writes the file in degrees, although it appears this is not >>> >> subsequently used. This scaling step is correct in the translation of >>> >> the >>> >> potential and the number of points. The next step I think after this >>> >> is the >>> >> smoothing step which again drops most of the points and appears to be >>> >> the >>> >> major issue here. >>> >> >>> >> I think the dihedral issue might be a general issue in VOTCA and not >>> >> necessarily a problem with interfacing with LAMMPS? >>> >> >>> >> >>> >> Thanks in advance. >>> >> >>> >> Josh >>> >> >>> >> >>> > -- >>> > 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 votca+un...@googlegroups.com. >>> > To post to this group, send email to vo...@googlegroups.com. >>> > Visit this group at https://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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
