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 9.5 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 ... triclinic box = (0 0 0) to (9.975 7.186 23.982633) with tilt (0 -3.704136 0) 2 by 1 by 11 MPI processor grid reading atoms ... 192 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 128 bonds reading angles ... 96 angles reading impropers ... 32 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 4 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 4 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.009 seconds include parameters.dat bond_coeff 1 0.97 563.28 -1428.2 1902.1 # h* o* bond_coeff 2 1.5325 277.56 -433.25 2922.8 # o1S- s4o- angle_coeff 1 109.47 87.637 -98.528 174.89 # o1S- s4o- o1S- angle_coeff 2 103.7 49.84 -11.6 -8 # h* o* h* dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx improper_coeff 1 0 0 # * s_ * * angle_coeff 1 bb 130.45 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 bb -9.5 0.97 0.97 # h* o* h* angle_coeff 1 ba 0.0 0.0 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 ba 22.35 22.35 0.97 0.97 # h* o* h* 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 # * s_ * * pair_coeff 1 1 0 1.098 # hw - pair_coeff 2 2 0.2951 2.3959 # mg+ - pair_coeff 3 3 0.148 3.7824 # o* - pair_coeff 4 4 0.1436 3.6173 # o1S- - pair_coeff 5 5 0.24 4.08 # s4o- - 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 192 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) fix 2_2_1 all box/relax x 0.987 y 0.987 z 0.987 couple none vmax 0.01 dilate all 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 ... WARNING: System is not charge neutral, net charge = 0.0008 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.34435248 grid = 12 12 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0015842633 estimated relative force accuracy = 4.7709617e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2730 288 generated 0 of 10 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 3 2 5 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 Setting up cg style minimization ... Unit style : real Current step : 0 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.93 | 12.04 | 12.29 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 78.432622 725.6942 -43897.957 1719.0835 1.7654279 44176.715 66628.248 20888.908 -0.047342945 33132.86 0.26193689 -5870.5308 9.975 7.186 24.267 1.5707963 1.7240362 1.5707963 -1.7053026e-13 8.8817842e-14 -2.8421709e-14 100 3.6620468 21.095264 943.27252 1563.2717 1.9413887 -631.84029 -1579.7979 -618.17935 52.71546 2560.0595 -60.500312 -6513.5407 9.6764779 6.7699154 24.146442 1.5707963 1.7240362 1.5707963 -1.3899992e-13 -2.0072832e-13 -1.0669243e-13 200 3.7333319 19.897737 395.11499 1599.4243 1.8975065 -556.87821 -551.96893 -76.497825 -205.53666 259.46457 184.9007 -6524.4217 9.8081587 6.5887609 25.043308 1.5707963 1.7240362 1.5707963 9.6811448e-14 1.8474111e-13 1.9784174e-13 300 2.0081103 8.3218344 148.53205 1605.3967 1.8904473 -747.40112 -119.70801 421.51297 -55.559613 -1239.6898 140.55769 -6527.7905 9.7867308 6.5283774 25.424869 1.5707963 1.7240362 1.5707963 1.1599055e-13 -2.3181457e-13 3.0242475e-13 400 0.73903526 3.7786211 228.45538 1601.8028 1.8946889 -199.80613 -131.35033 -354.20967 15.727221 -1248.9188 33.327485 -6528.885 9.7530472 6.5130311 25.515543 1.5707963 1.7240362 1.5707963 6.0840222e-14 1.8751667e-13 -1.9217961e-13 500 0.59050575 3.4261481 287.48817 1598.043 1.8991467 -57.299583 -438.2982 -366.86672 18.605359 -1954.9799 10.743146 -6529.7874 9.72799 6.4926075 25.601501 1.5707963 1.7240362 1.5707963 2.4263924e-13 -1.2867485e-13 2.1849189e-13 600 0.24785657 1.4057556 -25.238414 1599.1476 1.8978348 43.546946 -3.6168079 35.785104 -5.7467514 -2304.3693 -6.6333351 -6529.9826 9.7233333 6.4847424 25.662555 1.5707963 1.7240362 1.5707963 2.9337643e-14 -8.9865615e-14 -2.1793678e-13 664 0.12711272 0.81259392 -6.6373869 1599.8439 1.8970089 16.089174 12.25634 -8.4333536 -3.5376769 -2300.8883 -2.4908373 -6529.994 9.7258443 6.4826089 25.675547 1.5707963 1.7240362 1.5707963 1.3899992e-13 -1.6137092e-13 -4.8309967e-13 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Loop time of 0.987677 on 22 procs for 664 steps with 192 atoms 99.0% CPU use with 22 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -5870.5307638573 -6529.99265796996 -6529.99575453708 Force two-norm initial, final = 2195.0224 0.9856837 Force max component initial, final = 1670.4662 0.40862944 Final line search alpha, max atom move = 2.764857e-05 1.129802e-05 Iterations, force evaluations = 664 1401 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084809 | 0.15093 | 0.19834 | 8.5 | 15.28 Bond | 0.0015628 | 0.0022905 | 0.0032712 | 1.1 | 0.23 Kspace | 0.37695 | 0.42931 | 0.49393 | 5.4 | 43.47 Neigh | 0.0039826 | 0.0040789 | 0.0042917 | 0.1 | 0.41 Comm | 0.15836 | 0.17345 | 0.18113 | 1.4 | 17.56 Output | 0.00085544 | 0.00086129 | 0.00091292 | 0.0 | 0.09 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2267 | | | 22.96 Nlocal: 8.72727 ave 11 max 5 min Histogram: 3 2 0 1 0 4 0 0 6 6 Nghost: 2528.64 ave 2546 max 2525 min Histogram: 12 5 3 0 0 0 0 0 0 2 Neighs: 3320.73 ave 4306 max 1895 min Histogram: 3 2 0 1 4 0 0 3 3 6 Total # of neighbors = 73056 Ave neighs/atom = 380.5 Ave special neighs/atom = 2.3333333 Neighbor list builds = 16 Dangerous builds = 5 undump sci unfix 2_2_1 log 2.3_Minimization.out #------------------------------------------------------------------------------- # Stage 2.3: 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 dump sci all custom 1000 2.3.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) = 0.35251408 grid = 15 10 27 stencil order = 5 estimated absolute RMS force accuracy = 0.00097750438 estimated relative force accuracy = 2.9437254e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3040 300 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule Setting up cg style minimization ... Unit style : real Current step : 0 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Per MPI rank memory allocation (min/avg/max) = 11.95 | 12.08 | 12.3 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 0.12814237 0.81347953 -5.5277751 1599.8439 1.8970089 13.63689 10.002883 -7.0564477 -3.4136547 -2300.5967 -2.4984927 -6529.9928 9.7258443 6.4826089 25.675547 1.5707963 1.7240362 1.5707963 -7.3635542e-14 -1.5520918e-13 -5.4971305e-13 1 0.13297113 0.75635587 46.138371 1599.8439 1.8970089 -28.353801 -94.264855 -15.796457 -0.2244886 -2310.0603 -3.8985376 -6529.9934 9.7258443 6.4826089 25.675547 1.5707963 1.7240362 1.5707963 2.0539126e-14 -3.8215264e-13 -6.0867977e-14 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Loop time of 0.00313866 on 22 procs for 1 steps with 192 atoms 97.0% CPU use with 22 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -6529.99278353071 -6529.99278353071 -6529.99337218823 Force two-norm initial, final = 0.81347953 0.75635587 Force max component initial, final = 0.12814237 0.13297113 Final line search alpha, max atom move = 0.0015407773 0.00020487891 Iterations, force evaluations = 1 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00027799 | 0.00051244 | 0.00067498 | 0.0 | 16.33 Bond | 7.321e-06 | 9.46e-06 | 1.3072e-05 | 0.0 | 0.30 Kspace | 0.0014368 | 0.0016181 | 0.0018487 | 0.3 | 51.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057082 | 0.00061838 | 0.00064845 | 0.0 | 19.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003803 | | | 12.12 Nlocal: 8.72727 ave 11 max 5 min Histogram: 2 0 0 8 0 0 0 0 6 6 Nghost: 2543.91 ave 2553 max 2523 min Histogram: 4 2 0 0 0 0 0 0 6 10 Neighs: 3320.55 ave 4280 max 1898 min Histogram: 2 0 3 5 0 0 0 2 4 6 Total # of neighbors = 73052 Ave neighs/atom = 380.47917 Ave special neighs/atom = 2.3333333 Neighbor list builds = 0 Dangerous builds = 0 undump sci Total wall time: 0:00:01