On Wed, Jan 4, 2023 at 5:36 AM Saeed Norouzi <[email protected]> wrote: > > Dear Christoph, > > Thank you for your reply, I just realized that lammps could read dihedrals in > both radian and degree. > > Also, I am trying to change the extrapolation type for bonded interaction. I > am not sure how to select the extrapolation type for the setting file, and > also change the avg points. Do I have to change it in the > potential_extrapolate.sh script in the shared directory? Can I instead add > the extrapolation type and number of avg points to the setting file ? If so, > can you please help here? I don't think there is an option to change the avg points, but you could add an option here: https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/potential_to_lammps.sh#L132 similar to what we do for the function. However in https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/potential_extrapolate.sh#L36 we don't distinguish between avg points for left and right, so hence there is only one option. However it wouldn't be hard to implement that either.
Christoph > > > <!-- Dihedral Part --> > <bonded> > <!-- name of the interaction --> > <name>dihedral.1</name> > <min>-3.14159</min> > <max>3.14159</max> > <step>0.01</step> > <inverse> > <!-- target distribution --> > <target>dihedral.1.dist.tgt</target> > <lammps> > <table>table_d1.xvg</table> > <table_begin>-3.14159</table_begin> > <table_end>3.14159</table_end> > <table_left_extrapolation> exponential </table_left_extrapolation> > <table_right_extrapolation> exponential </table_right_extrapolation> > </lammps> > </inverse> > </bonded> > > > Best regards > Saeed > > On Tue, Jan 3, 2023 at 8:16 PM Christoph Junghans <[email protected]> wrote: >> >> On Tue, Jan 3, 2023 at 9:47 AM Saeed Norouzi <[email protected]> wrote: >> > >> > Dear Christoph, >> > Thank you so much for your help. I used the <table_begin> and >> > <table_end> in my setting file, and now it works. Could I also do the >> > extrapolation on my target distribution, so I do not have to do it for >> > every iteration and remove this interaction-specific from the setting file? >> That might work, but I am not sure! The problem with poorly sampled >> regions in IBI is that they can lead to systematic errors in the >> update. >> >> > Also, How could I have other than linear extrapolation for my data? >> Yes, there should be an option, >> inverse.lammps.table_left_exprapolation for each interaction (and same >> for right), options are constant, linear, quadratic, exponential and >> sasha. See "csg_call potential extrapolate --help" and "csg_call table >> extrapolate --help" for details. >> >> > Moreover, as you can see below, I have dihedral interaction in my settings >> > file and I am trying to do ibi for this part also. but the problem is the >> > VOTCA gives the potential file for dihedral in radian units not degree. I >> > am using lammps and I need to have the table function in degree units, as >> > VOTCA does for angle potential. Can you please help me out with this? >> >> Dihedrals are not fully implemented yet. But I think you could set >> inverse.lammps.scale to 180/pi=57.295 for that interaction. >> >> Christoph >> >> > >> > <!-- Dihedral Part --> >> > <bonded> >> > <!-- name of the interaction --> >> > <name>dihedral.1</name> >> > <min>-3.14159</min> >> > <max>3.14159</max> >> > <step>0.01</step> >> > <inverse> >> > <!-- target distribution --> >> > <target>dihedral.1.dist.tgt</target> >> > <lammps> >> > <table>table_d1.xvg</table> >> > <table_begin>-3.14159</table_begin> >> > <table_end>3.14159</table_end> >> > </lammps> >> > </inverse> >> > </bonded> >> > >> > >> > Best regards >> > Saeed >> > >> > >> > >> > >> > >> > >> > On Mon, Jan 2, 2023 at 4:16 PM Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> On Mon, Jan 2, 2023 at 7:51 AM Saeed Norouzi <[email protected]> wrote: >> >> > >> >> > Dear VOTCA Users, >> >> > >> >> > I am trying to use ibi for bonded interaction (bond,angle, and >> >> > dihedral). The problem is when I am using bond distribution we do not >> >> > have data for some ranges (like for bond distribution in this >> >> > tutorial), so during the iteration some bonds length is bigger or >> >> > smaller than the table outer or inner cutoff and I get error in LAMMPS. >> >> > does anyone has idea what can I do for this error? is there any option >> >> > in VOTCA to replace the zeros in the probability for bonds with some >> >> > small values so I can increase the table cutoff or I should do it >> >> > manually? >> >> There are interaction-specific properties inverse.lamps.table_begin >> >> and inverse.lamps.table_end that you can set for each interaction that >> >> can be smaller/ larger than VOTCA's min and max (the area where IBI is >> >> performed) . VOTCA will then do an extrapolation for that extra area. >> >> >> >> Christoph >> >> > >> >> > I am using LAMMPS for my ibi and here is an error I have currently. >> >> > >> >> > Per MPI rank memory allocation (min/avg/max) = 7.672 | 7.674 | 7.676 >> >> > Mbytes >> >> > Step Time TotEng PotEng Volume Density Temp Press >> >> > 0 0 963.12455 -1360.1188 151186.66 >> >> > 1.029793 600 -1094.7381 >> >> > 2000 20 928.00314 -1457.0206 151186.66 >> >> > 1.029793 615.95537 -1217.8225 >> >> > 4000 40 942.24742 -1472.8241 151186.66 >> >> > 1.029793 623.71551 917.70274 >> >> > 6000 60 925.95597 -1483.2126 151186.66 >> >> > 1.029793 622.19103 3122.7127 >> >> > 8000 80 921.17567 -1446.9757 151186.66 >> >> > 1.029793 611.59792 1398.679 >> >> > 10000 100 972.68412 -1498.2288 151186.66 >> >> > 1.029793 638.13709 3228.6631 >> >> > 12000 120 968.92421 -1504.366 151186.66 >> >> > 1.029793 638.75105 2570.6902 >> >> > 14000 140 973.39445 -1546.9816 151186.66 >> >> > 1.029793 650.91141 -2645.2069 >> >> > 16000 160 826.48486 -1573.7195 151186.66 >> >> > 1.029793 619.87591 164.50872 >> >> > ERROR on proc 20: Bond length > table outer cutoff: type 3 length >> >> > 4.4888905 (src/MOLECULE/bond_table.cpp:605) >> >> > Last command: run 50000 >> >> > >> >> > >> >> > Best regards >> >> > Saeed >> >> > >> >> > -- >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> > --- >> >> > 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 view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/votca/de34c1df-ca77-466b-a29d-3af382daed5en%40googlegroups.com. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> >> >> >> -- >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> --- >> >> 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 view this discussion on the web visit >> >> https://groups.google.com/d/msgid/votca/CAHG27e5LqWxmX2BZL%2BfOYOCQ-MEQVHZon-c2jpu%3DkByywUZGAA%40mail.gmail.com. >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > 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 view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/CAJZjMJbERZcwt5CDFXznUw83UYwFiLGTLFjWeXm%2BpTm2mjQwzw%40mail.gmail.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5-SFkgL8OBEkz6MM4uMD2_9EytwqjCHn07sLYRERefmQ%40mail.gmail.com. > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAJZjMJaXXNcVhb2CAzTPjFS%3DG4st_nWO%3DUQ_FnAudTj%2BrBaJ%3Dw%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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