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 1 by 1 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 = 0.009 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 = 2197 512 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) = 6.962 | 6.962 | 6.962 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 0.61185377 0.95892928 13 67 74 7 0 0 200 0.54355177 1.1282424 19 61 76 15 0 0 300 0.4519957 1.0764688 20 60 85 26 1 0 400 0.41479389 0.99212685 24 56 92 36 0 0 500 0.37382446 0.99776674 28 52 98 46 0 0 600 0.34785337 1.1115081 28 52 109 57 0 0 700 0.34637618 1.0332262 28 52 120 68 0 0 800 0.21020932 1.1264036 29 51 125 74 0 0 900 0.21246108 1.1168609 30 50 131 81 0 0 1000 0.20997475 1.1201478 32 48 132 84 0 0 1100 0.1984165 1.0209092 31 49 144 95 0 0 1200 0.2061932 0.95880059 35 45 151 106 0 0 1300 0.17220376 0.980077 36 44 156 112 0 0 1400 0.15671143 0.93535342 37 43 161 118 0 0 1500 0.16174665 0.9495928 36 44 168 124 0 0 1600 0.11062965 0.94072924 40 40 164 124 0 0 1700 0.13002563 0.95010828 38 42 167 125 0 0 1800 0.14527814 0.93555342 37 43 172 129 0 0 1900 0.17627465 0.96682495 32 48 176 128 0 0 2000 0.16497265 0.95226954 33 47 180 133 0 0 Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms Performance: 115895.577 tau/day, 268.277 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45607 | 0.45607 | 0.45607 | 0.0 | 6.12 Bond | 0.0062385 | 0.0062385 | 0.0062385 | 0.0 | 0.08 Kspace | 2.3257 | 2.3257 | 2.3257 | 0.0 | 31.20 Neigh | 0.067103 | 0.067103 | 0.067103 | 0.0 | 0.90 Comm | 0.02577 | 0.02577 | 0.02577 | 0.0 | 0.35 Output | 0.00087047 | 0.00087047 | 0.00087047 | 0.0 | 0.01 Modify | 4.5664 | 4.5664 | 4.5664 | 0.0 | 61.25 Other | | 0.006848 | | | 0.09 Nlocal: 393.000 ave 393 max 393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 749.000 ave 749 max 749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5359.00 ave 5359 max 5359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5359 Ave neighs/atom = 13.636132 Ave special neighs/atom = 1.1908397 Neighbor list builds = 1489 Dangerous builds = 0 Total wall time: 0:00:07