Hi Christoph, Thanks again for your quick message.
It seems to run ok after the update. However, I think the forces are not correct in the LAMMPS table files. I might be mistaken. I'm attaching the input files needed to generate the run with (toVotca.tar.gz) csg-inverse --options settings.xml Below is a plot of what the Bond and Angle force from the generated table files (table_b1.pot and table_a1.pot) after step001. I'm taking a simple derivative as -deltaU/delta_r or -deltaU/delta_theta, and they don't seem to match up with what VOTCA is outputting for the forces in the file. I believe for the angle, that LAMMPS is expecting -dU/dtheta. Consequently, the temperature blows up nearly immediately, and then you see warnings in LAMMPS like "WARNING: 87 of 91 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../bond_table.cpp:380)". For some reason the angle potential is not triggering this warning, but I believe it should because it also does not appear to be consistent. (Note: checking the lammps source, it appears this check is not in the angle table code, so that's probably the reason.) The energies and forces from the pair coefficients appear to be correct. Any ideas about what I might be doing wrong, or a potential fix? I'm also not getting perfect agreement to the potential of mean force (e.g., -kTln(Pr))for the step001 angle and bond potentials either, but this might partially be due to the shifting you are doing. Thanks again for your help. Josh Bonds: Angles: On Monday, February 13, 2017 at 6:11:08 PM UTC-5, Christoph Junghans wrote: > 2017-02-13 14:06 GMT-07:00 Joshua Moore <[email protected] <javascript:>>: > > Thanks. I see now in step001. It does convert the table_a1.pot file as > you > > said. > > > > The issue seems to be that the LAMMPS potential file generated converts > the > > min/max from radians to degrees, but the <step>0.01</step> isn't > converted, > > so it tries to write out > 180 degrees in the LAMMPS file (18001 points) > or > > up to 18001*0.01*180/3.1415 = 10314.12 degrees. Is there a special way > to > > specify this step size after the unit conversion? > Sorry, I just realized there is a bug the potential conversion for > lammps. The conversion factor is applied twice. > 3.1415*(180/3.1415)**2=10313.5. > > I fixed that now: > < > https://github.com/votca/csg/commit/cb92bcd6b84a60b05698b5e409fc9d125959f03e> > > > That said, the support for lammps as a simulation backend is still > pretty rudimentary in VOTCA. > > Christoph > > > > > Thanks for all your help with this. > > > > > > Here is tail of the table_a1.pot LAMMPS file. > > > > 17989 1.03064e+04 7.9841910e-04 6.9526739e-04 > > 17990 1.03069e+04 3.9962120e-04 6.9677605e-04 > > 17991 1.03075e+04 0.0000000e+00 6.9814120e-04 > > 17992 1.03081e+04 -4.0036230e-04 6.9936284e-04 > > 17993 1.03087e+04 -8.0138340e-04 7.0044097e-04 > > 17994 1.03092e+04 -1.2029811e-03 7.0137559e-04 > > 17995 1.03098e+04 -1.6050732e-03 7.0216670e-04 > > 17996 1.03104e+04 -2.0075775e-03 7.0281430e-04 > > 17997 1.03109e+04 -2.4104117e-03 7.0331839e-04 > > 17998 1.03115e+04 -2.8134936e-03 7.0367897e-04 > > 17999 1.03121e+04 -3.2167410e-03 7.0389604e-04 > > 18000 1.03127e+04 -3.6200716e-03 7.0396961e-04 > > 18001 1.03132e+04 -4.0234033e-03 7.0389966e-04 > > > > > > On Monday, February 13, 2017 at 3:59:10 PM UTC-5, Christoph Junghans > wrote: > >> > >> 2017-02-13 13:43 GMT-07:00 Joshua Moore <[email protected]>: > >> > Hi Christoph, > >> > > >> > Thank you for the quick reply. Maybe I am not setting something > right > >> > in > >> > the settings.xml file, because the angle.pot file in step000 is still > >> > from 0 > >> > to 3.1415. Also my target distribution function is from 0 to 3.1415 > in > >> > radians, calculated with csg_stat. Do I need to convert that first > >> > before > >> > feeding it through csg_inverse to LAMMPS? > >> step_000 doesn't run any simulation and hence there is no > >> table_a1.pot, look in step_001. > >> > >> Christoph > >> > > >> > <bonded> > >> > <!-- name of the interaction --> > >> > <name>angle</name> > >> > <min>0.0</min> > >> > <max>3.1415</max> > >> > <step>0.01</step> > >> > <inverse> > >> > <kBT>0.59616108</kBT> > >> > <!-- target distribution --> > >> > <target>angle.dist.tgt</target> > >> > <lammps> > >> > <kBT>0.59616108</kBT> > >> > <table>table_a1.pot</table> > >> > </lammps> > >> > </inverse> > >> > </bonded> > >> > > >> > > >> > > >> > On Monday, February 13, 2017 at 3:31:56 PM UTC-5, Christoph Junghans > >> > wrote: > >> >> > >> >> 2017-02-13 12:56 GMT-07:00 Joshua Moore <[email protected]>: > >> >> > Hello, > >> >> > > >> >> > How do people handle the fact that the LAMMPS angle potential is > in > >> >> > degrees > >> >> > and not radians? > >> >> > > >> >> > If I convert the angle distribution to degrees, will csg_inverse > >> >> > calculate > >> >> > the correct comparison? > >> >> Before running the actual simulation in each iteration step, > >> >> csg_inverse will convert its internal format (.pot file) to a LAMMPS > >> >> table (name given in the xml file), it will do the conversion from > >> >> radians to degrees by default. > >> >> There is also a scaling factor for the non-bonded interactions in > case > >> >> you need to convert from nm to Angstrom. > >> >> > >> >> Christoph > >> >> > > >> >> > Thanks. > >> >> > > >> >> > 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 [email protected]. > >> >> > To post to this group, send email to [email protected]. > >> >> > 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 [email protected]. > >> > To post to this group, send email to [email protected]. > >> > 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 [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
toVotca.tar.gz
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