---------------------------------------- Enrique Martinez Saez MST-8, MS G755 Los Alamos National Laboratory Los Alamos, NM, 87544 Ph: 505 606 2149 Fax: 505 667 8021 enriquem@lanl.gov http://enriquemasa.snack.ws > On Nov 3, 2016, at 3:25 PM, Axel Kohlmeyer wrote: > > what happens, when comment out the following line? > > neigh_modify exclude molecule all > > axel. > > On Wed, Nov 2, 2016 at 10:54 PM, MICHAEL GOYTIA wrote: >> Hello, >> >> I am using the December 15, 2015, intel complied version of lammps and have come into a pickle with comparing potential energies with HOOMD. >> >> My inputs and data file are shown below after this section. >> >> I am switching from HOOMD to LAMMPS because of some core pinning issues and want to get the correct energies for a 2D simulation of a simple model. The potential energies from the HOOMD run and lammps run are not consistent(-4.7 reduced energy units vs -0.5). I calculated the potential energy by hand to see which energy it was nearest too and it was hoomd. I feel confident in my calculation of the potential energy( ~ -4.6) so I am wondering what I am doing wrong in my process in LAMMPS. I checked both end results which give me the roughly the same final configuration and distance between atoms (important in verifying my potential energy calculation). I have interconverted between lammps and hoomd before in 3D and had no problems but that was with units real in LAMMPS in which I constructed similar units in HOOMD. Wondering if there might be a bug or if I am not accounting for something right. >> >> Thanks, >> >> Michael Goytia >> >> >> >> in.mol >> units lj >> atom_style full >> boundary p p p >> dimension 2 >> variable tempi equal 0.75 >> variable tempf equal 0.0123 >> >> read_data random.data >> >> pair_style lj/cut 2.5 >> pair_coeff 1 1 0.182097851198 1.04308220858 2.60770552144 >> pair_coeff 1 2 0.702854451025 0.866639911779 2.16659977945 >> pair_coeff 1 3 0.973685740843 0.777251743894 1.94312935973 >> pair_coeff 2 2 0.169736804547 0.690197614981 1.72549403745 >> pair_coeff 2 3 0.570151175955 0.600809447096 1.50202361774 >> pair_coeff 3 3 0.24318312159 0.600809447096 1.27855319803 >> >> #pair_modify shift yes >> neigh_modify exclude molecule all >> timestep 0.005 >> >> fix 2d all enforce2d >> >> thermo 1000 >> thermo_style custom step temp pe ke etotal press vol >> >> dump myDump all dcd 1000 random.dcd >> write_dump all custom random.lammpstrj id mol type x y z >> restart 100000 2d.restart >> fix 1 all rigid molecule langevin ${tempi} ${tempf} 500 10 >> run 4000000 >> >> >> .data file >> #Goytia's random molecule generator >> >> 6 atoms >> 3 atom types >> >> -6.0 6.0 xlo xhi >> -6.0 6.0 ylo yhi >> -5.0 5.0 zlo zhi >> >> Masses >> >> 1 5.00065548514 >> 2 1.44874411347 >> 3 0.589396705833 >> >> Atoms >> >> 1 1 1 0 -5.01247611056 0 0 >> 2 1 2 0 -3.5 0 0 >> 3 1 3 0 -3.83528420926 0.66167837418 0 >> 4 2 1 0 1.98752388944 0 0 >> 5 2 2 0 3.5 0 0 >> 6 2 3 0 3.16471579074 0.66167837418 0 >> ------------------------------------------------------------------------------ >> Developer Access Program for Intel Xeon Phi Processors >> Access to Intel Xeon Phi processor-based developer platforms. >> With one year of Intel Parallel Studio XE. >> Training and support from Colfax. >> Order your platform today. http://sdm.link/xeonphi >> _______________________________________________ >> lammps-users mailing list >> lammps-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/lammps-users > > > > -- > Dr. Axel Kohlmeyer akohlmey@gmail.com http://goo.gl/1wk0 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > lammps-users mailing list > lammps-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/lammps-users