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 (38.8222 38.2464 46.9556) 4 by 2 by 4 MPI processor grid reading atoms ... 3120 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 1824 bonds reading angles ... 1680 angles reading impropers ... 768 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 = 0.022 seconds include parameters.dat bond_coeff 1 1.5325 277.56 -433.25 2922.8 # o1S- s4o- bond_coeff 2 0.97 563.28 -1428.2 1902.1 # h* o* 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 0.05899 5.1728 # Cl - pair_coeff 2 2 0 1.098 # hw - pair_coeff 3 3 0.4691 3.292 # K+ - pair_coeff 4 4 0.2951 2.3959 # mg+ - pair_coeff 5 5 0.148 3.7824 # o* - pair_coeff 6 6 0.1436 3.6173 # o1S- - pair_coeff 7 7 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 3120 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 ... WARNING: System is not charge neutral, net charge = 0.0192 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25812978 grid = 30 30 36 stencil order = 5 estimated absolute RMS force accuracy = 0.003608555 estimated relative force accuracy = 1.0867056e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4928 1800 generated 0 of 21 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 = 6 6 7 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 Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 11.22 | 12.26 | 12.94 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 1139.3168 3178.5228 -608.65763 69720.116 1.1179105 4166.203 -3443.317 1103.0869 -606.44425 419.69789 836.36035 -177414.03 38.8222 38.2464 46.9556 1.5707963 1.5707963 1.5707963 9.876544e-13 1.1368684e-12 -1.3287149e-12 1 9015.2122 25464.474 -1556.0383 69720.116 1.1179105 6652.2 -3387.9141 1403.8291 -543.46367 1230.1249 954.42467 -179454.37 38.8222 38.2464 46.9556 1.5707963 1.5707963 1.5707963 1.3454127e-11 -2.6361135e-12 -1.2398971e-12 Loop time of 0.161826 on 32 procs for 1 steps with 3120 atoms 98.3% CPU use with 32 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -177414.032213651 -177414.032213651 -179454.365147643 Force two-norm initial, final = 3178.5228 25464.474 Force max component initial, final = 1139.3168 9015.2122 Final line search alpha, max atom move = 4.8234773e-05 0.43484672 Iterations, force evaluations = 1 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0424e-05 | 0.055424 | 0.10442 | 19.2 | 34.25 Bond | 2.9022e-05 | 0.00040518 | 0.00074598 | 0.0 | 0.25 Kspace | 0.044949 | 0.094287 | 0.1502 | 14.8 | 58.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057861 | 0.0082012 | 0.0095739 | 1.4 | 5.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003509 | | | 2.17 Nlocal: 97.5 ave 189 max 0 min Histogram: 8 0 0 8 0 0 0 8 0 8 Nghost: 3048 ave 3562 max 2602 min Histogram: 16 0 0 0 0 0 0 8 0 8 Neighs: 36914.1 ave 69175 max 0 min Histogram: 8 8 0 0 0 0 0 0 0 16 Total # of neighbors = 1181250 Ave neighs/atom = 378.60577 Ave special neighs/atom = 2.2461538 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_NPT.out #------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 3 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 528 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (38.8222 38.2464 46.9556) 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 (38.8222 38.2464 46.9556) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000 fix 2 movable ave/time 1 299999 300000 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 2.4_averages.txt off 1 fix 3 movable ave/time 300 1 300 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 2.4_instantaneous.txt restart 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0192 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26069637 grid = 32 32 36 stencil order = 5 estimated absolute RMS force accuracy = 0.002976358 estimated relative force accuracy = 8.9632137e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5520 2048 generated 0 of 21 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 = 6 6 7 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 Verlet run ... Unit style : real Current step : 0 Time step : 1 SHAKE stats (type/ave/delta/count) on step 0 2 1.01212 0.677128 1584 2 96.2954 10.096 528 Per MPI rank memory allocation (min/avg/max) = 11.04 | 12.01 | 12.48 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 -10815.5 69720.116 1.1179105 358.96789 143.89384 565.43667 0 0 16018.647 -57997.644 -98.483661 -140321.85 -181591.51 2772.4091