2017-02-13 14:06 GMT-07:00 Joshua Moore <[email protected]>: > 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]. > 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.
