LAMMPS (7 Jan 2022) using 1 OpenMP thread(s) per MPI task log 2.1_Initialize.out #------------------------------------------------------------------------------- # Stage 2.1: Initialize LAMMPS run for 3-d periodic #------------------------------------------------------------------------------- units real boundary p p p atom_style full pair_style lj/class2/coul/long 12 pair_modify mix sixthpower pair_modify tail yes bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0 box tilt large read_data structure.dat Reading data file ... orthogonal box = (0 0 0) to (5.64056 5.64056 5.64056) 2 by 1 by 3 MPI processor grid reading atoms ... 8 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.005 seconds include parameters.dat bond_coeff 1 0.0000 0.0000 0.0000 0.0000 # xxx xxx angle_coeff 1 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx improper_coeff 1 0.0 0.0 # xxx xxx xxx xxx angle_coeff 1 bb 0.0 0.0 0.0 # xxx xxx xxx angle_coeff 1 ba 0.0 0.0 0.0 0.0 # xxx xxx xxx dihedral_coeff 1 mbt 0.0000 0.0000 0.0000 0.0 # xxx xxx xxx xxx dihedral_coeff 1 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 aat 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 bb13 0.0 0.0 0.0 # xxx xxx xxx xxx improper_coeff 1 aa 0.0 0.0 0.0 120.0 120.0 120.0 # xxx xxx xxx xxx pair_coeff 1 1 0.05899 5.1728 # Cl - pair_coeff 2 2 0.3828 2.494 # Na+ - neighbor 2.0 bin neigh_modify delay 0 every 1 check yes kspace_style pppm 0.00001 variable R equal 0.00198722 variable sysvol equal vol variable sysmass equal mass(all)/6.0221367e+23 variable sysdensity equal v_sysmass/v_sysvol/1.0e-24 variable coulomb equal ecoul+elong variable etotal equal etotal variable pe equal pe variable ke equal ke variable evdwl equal evdwl variable epair equal epair variable ebond equal ebond variable eangle equal eangle variable edihed equal edihed variable eimp equal eimp variable lx equal lx variable ly equal ly variable lz equal lz variable Nthermo equal 0 variable cella equal lx variable cellb equal sqrt(ly*ly+xy*xy) variable cellc equal sqrt(lz*lz+xz*xz+yz*yz) variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc)) variable cellbeta equal acos(xz/v_cellc) variable cellgamma equal acos(xy/v_cellb) variable p equal press variable pxx equal pxx variable pyy equal pyy variable pzz equal pzz variable pyz equal pyz variable pxz equal pxz variable pxy equal pxy variable sxx equal -pxx variable syy equal -pyy variable szz equal -pzz variable syz equal -pyz variable sxz equal -pxz variable sxy equal -pxy variable fmax equal fmax variable fnorm equal fnorm variable time equal step*dt+0.000001 variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz) thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo_modify flush yes # # Set up the fixed and movable groups # group movable union all 8 atoms in group movable group fixed subtract all movable 0 atoms in group fixed compute sum_f1 movable reduce sum fx fy fz variable sum_fx equal c_sum_f1[1] variable sum_fy equal c_sum_f1[2] variable sum_fz equal c_sum_f1[3] log 2.2_Minimization.out #------------------------------------------------------------------------------- # Stage 2.2: Minimization #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.05 line fast reset_timestep 0 thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) dump sci all custom 1000 2.2.xyz id mol type q xs ys zs thermo 100 minimize 0.0 1.0 1000 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1170 36 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.795 | 8.462 | 8.796 Mbytes Step Fmax Fnorm Press Volume v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy PotEng v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz 0 1.2156942e-14 2.1999005e-14 28524.392 179.45959 2.1630931 -28524.392 -28524.392 -28524.392 4.7510073e-12 -6.7871532e-12 1.6289168e-11 -732.41929 5.64056 5.64056 5.64056 1.5707963 1.5707963 1.5707963 8.1046281e-15 -3.7414516e-14 -3.7834319e-15 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.018548839, slope is -0.000000000, started at -0.000000000 1 2.8699265e-14 4.7424453e-14 28524.392 179.45959 2.1630931 -28524.392 -28524.392 -28524.392 -6.7871532e-13 -1.2216876e-11 1.3574306e-11 -732.41929 5.64056 5.64056 5.64056 1.5707963 1.5707963 1.5707963 8.1046281e-15 -3.3917313e-14 -3.7834319e-15 Loop time of 0.00893738 on 6 procs for 1 steps with 8 atoms 96.4% CPU use with 6 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -732.419293351377 -732.419293351377 -732.419293351377 Force two-norm initial, final = 2.1999005e-14 4.7424453e-14 Force max component initial, final = 1.2156942e-14 2.8699265e-14 Final line search alpha, max atom move = 0.018548839 5.3233804e-16 Iterations, force evaluations = 1 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8127e-05 | 0.00050496 | 0.00088179 | 0.0 | 5.65 Bond | 2.1825e-05 | 2.4479e-05 | 2.7228e-05 | 0.0 | 0.27 Kspace | 0.0043011 | 0.004722 | 0.0052087 | 0.5 | 52.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022953 | 0.0027167 | 0.0029641 | 0.6 | 30.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009692 | | | 10.84 Nlocal: 1.33333 ave 2 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 4 Nghost: 1135.33 ave 1208 max 1098 min Histogram: 4 0 0 0 0 0 0 0 0 2 Neighs: 322.667 ave 552 max 0 min Histogram: 2 0 0 0 0 0 0 2 0 2 Total # of neighbors = 1936 Ave neighs/atom = 242 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci log 2.3_Velocities.out #------------------------------------------------------------------------------- # Stage 2.3: Set the initial velocities for $T #------------------------------------------------------------------------------- velocity all create 298.2 72489 dist gaussian mom yes rot no log 2.4_NVT.out #------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 100000 100000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 100 1 100 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1170 36 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 6.67 | 7.337 | 7.671 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 30109.308 179.45959 2.1630931 298.2 0 0 0 0 90.620582 -408.50411 -0.59158899 -414.53576 -732.41929 6.2221429 1000000 1000000 33968.101 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -405.26499 -0.59158899 -414.42512 -725.8998 4.6147201 Loop time of 187.215 on 6 procs for 1000000 steps with 8 atoms Performance: 461.501 ns/day, 0.052 hours/ns, 5341.452 timesteps/s 98.5% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3042 | 13.425 | 20.328 | 181.9 | 7.17 Bond | 0.43666 | 0.46579 | 0.51733 | 4.0 | 0.25 Kspace | 66.274 | 73.779 | 83.31 | 79.7 | 39.41 Neigh | 8.6769e-05 | 9.213e-05 | 9.4491e-05 | 0.0 | 0.00 Comm | 39.559 | 47.73 | 51.831 | 73.4 | 25.49 Output | 0.00090409 | 0.00093616 | 0.0009877 | 0.0 | 0.00 Modify | 43.609 | 47.365 | 55.076 | 73.2 | 25.30 Other | | 4.449 | | | 2.38 Nlocal: 1.33333 ave 3 max 0 min Histogram: 1 0 0 3 0 0 1 0 0 1 Nghost: 1223 ave 1305 max 1173 min Histogram: 2 0 2 0 0 0 0 1 0 1 Neighs: 326.833 ave 661 max 0 min Histogram: 1 0 1 1 1 0 0 0 1 1 Total # of neighbors = 1961 Ave neighs/atom = 245.125 Ave special neighs/atom = 0 Neighbor list builds = 1 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1170 36 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Setting up Verlet run ... Unit style : real Current step : 1000000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 6.671 | 7.505 | 7.672 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 1000000 1000000 33968.101 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -405.26499 -0.59158899 -414.42512 -725.8998 4.6147201 Loop time of 3.81717e-06 on 6 procs for 0 steps with 8 atoms 122.3% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.817e-06 | | |100.00 Nlocal: 1.33333 ave 3 max 0 min Histogram: 1 0 0 3 0 0 1 0 0 1 Nghost: 1223 ave 1305 max 1173 min Histogram: 2 0 2 0 0 0 0 1 0 1 Neighs: 326.833 ave 661 max 0 min Histogram: 1 0 1 1 1 0 0 0 1 1 Total # of neighbors = 1961 Ave neighs/atom = 245.125 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 log 2.5_NPT.out #------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- change_box all triclinic Changing box ... triclinic box = (0 0 0) to (5.64056 5.64056 5.64056) with tilt (0 0 0) kspace_style pppm 0.00001 reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (5.64056 5.64056 5.64056) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 x 1 1 100 y 1 1 100 z 1 1 100 drag 0 mtk yes nreset 20000 fix 2 movable ave/time 1 99999 100000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_averages.txt off 1 fix 3 movable ave/time 100 1 100 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt restart 1000000 2.5.restart dump sci all custom 100000 2.5.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.29166098 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00027054584 estimated relative force accuracy = 8.1474075e-07 using double precision KISS FFT 3d grid and FFT values/proc = 1815 128 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 6.704 | 7.541 | 7.71 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 33968.233 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -382.75569 -0.59158899 -436.93401 -725.8994 4.6147201 1000000 1000000 -1384.0653 204.12438 1.9017219 345.90265 0 0 0 0 64.379155 -354.17502 -0.52010601 -436.97713 -726.77299 7.2174906 Loop time of 279.146 on 6 procs for 1000000 steps with 8 atoms Performance: 309.516 ns/day, 0.078 hours/ns, 3582.357 timesteps/s 98.9% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.942 | 12.764 | 17.404 | 84.6 | 4.57 Bond | 0.46727 | 0.51492 | 0.56455 | 5.4 | 0.18 Kspace | 93.879 | 98.954 | 102.02 | 33.7 | 35.45 Neigh | 0.03463 | 0.034871 | 0.035116 | 0.1 | 0.01 Comm | 54.646 | 56.187 | 57.846 | 16.9 | 20.13 Output | 0.00099324 | 0.0010357 | 0.0010902 | 0.1 | 0.00 Modify | 95.719 | 100.51 | 107.46 | 48.8 | 36.01 Other | | 10.18 | | | 3.65 Nlocal: 1.33333 ave 3 max 1 min Histogram: 5 0 0 0 0 0 0 0 0 1 Nghost: 1197.33 ave 1269 max 1086 min Histogram: 1 0 0 1 0 0 2 0 0 2 Neighs: 301.667 ave 701 max 203 min Histogram: 5 0 0 0 0 0 0 0 0 1 Total # of neighbors = 1810 Ave neighs/atom = 226.25 Ave special neighs/atom = 0 Neighbor list builds = 583 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.5.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.27661212 grid = 6 6 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00088101585 estimated relative force accuracy = 2.6531531e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1430 72 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule Setting up Verlet run ... Unit style : real Current step : 1000000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 7.694 | 7.696 | 7.699 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 1000000 1000000 -1376.8693 204.12438 1.9017219 345.90265 0 0 0 0 64.379155 -376.64926 -0.52010601 -414.50031 -726.77041 7.2174906 Loop time of 3.86667e-06 on 6 procs for 0 steps with 8 atoms 125.0% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.867e-06 | | |100.00 Nlocal: 1.33333 ave 3 max 1 min Histogram: 5 0 0 0 0 0 0 0 0 1 Nghost: 1197.33 ave 1269 max 1086 min Histogram: 1 0 0 1 0 0 2 0 0 2 Neighs: 301.667 ave 701 max 203 min Histogram: 5 0 0 0 0 0 0 0 0 1 Total # of neighbors = 1810 Ave neighs/atom = 226.25 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 Total wall time: 0:07:46