LAMMPS (10 Feb 2021) using 1 OpenMP thread(s) per MPI task # Charge regulation lammps for a polymer chain units lj atom_style full neighbor 3.0 bin read_data data.chreg-polymer Reading data file ... orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) 1 by 2 by 2 MPI processor grid reading atoms ... 160 atoms scanning bonds ... 1 = max bonds/atom reading bonds ... 79 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.016 seconds bond_style harmonic bond_coeff 1 100 1.122462 # K R0 velocity all create 1.0 8008 loop geom pair_style lj/cut/coul/long 1.122462 20 pair_coeff * * 1.0 1.0 1.122462 # charges kspace_style pppm 1.0e-3 pair_modify shift yes dielectric 1.0 ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### fix fnve all nve compute dtemp all temp compute_modify dtemp dynamic yes fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 thermo 100 # print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] timestep 0.005 run 2000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:339) G vector (1/distance) = 0.077106934 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00074388331 estimated relative force accuracy = 0.00074388331 using double precision FFTW3 3d grid and FFT values/proc = 1053 128 0 atoms in group FixChargeRegulation:exclusion_group:chareg1 0 atoms in group FixChargeRegulation:exclusion_group:chareg2 0 atoms in group FixChargeRegulation:exclusion_group:chareg3 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 23 ghost atom cutoff = 23 binsize = 11.5, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 6.878 | 6.935 | 6.992 Mbytes Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] 0 0.50528297 1 0 80 80 0 0 0 100 0.60223729 0.89547569 13 67 75 8 0 0 200 0.65253636 0.87662399 18 62 78 16 0 0 300 0.51550501 1.0542131 22 58 84 27 1 0 400 0.43566766 0.94557633 26 54 90 36 0 0 500 0.36269507 1.0386276 31 49 94 45 0 0 600 0.32430641 0.99903033 27 53 111 58 0 0 700 0.30255299 0.91225991 28 52 121 69 0 0 800 0.27189951 0.9747089 28 52 127 75 0 0 900 0.25495247 1.0747821 28 52 135 83 0 0 1000 0.25950416 0.95256449 32 48 134 86 0 0 1100 0.22561248 1.0102255 32 48 147 99 0 0 1200 0.1734754 0.99475154 33 47 157 110 0 0 1300 0.20081084 0.99873599 36 44 160 116 0 0 1400 0.14240417 0.99442152 36 44 164 121 1 0 1500 0.15314186 0.94559876 39 41 167 126 0 0 1600 0.13574107 1.0484195 43 37 164 127 0 0 1700 0.14477789 1.0105172 42 38 166 128 0 0 1800 0.13493107 1.0349667 41 39 171 132 0 0 1900 0.14849779 0.9994329 33 47 178 131 0 0 2000 0.14485171 0.99739608 34 46 183 137 0 0 Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms Performance: 270955.695 tau/day, 627.212 timesteps/s 94.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68 Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06 Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89 Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56 Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47 Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03 Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07 Other | | 0.007591 | | | 0.24 Nlocal: 100.000 ave 110 max 89 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 415.000 ave 418 max 411 min Histogram: 1 0 1 0 0 0 0 0 0 2 Neighs: 1360.75 ave 1872 max 1018 min Histogram: 1 1 0 0 1 0 0 0 0 1 Total # of neighbors = 5443 Ave neighs/atom = 13.607500 Ave special neighs/atom = 1.1700000 Neighbor list builds = 1492 Dangerous builds = 0 Total wall time: 0:00:03