LAMMPS (28 Mar 2023 - Development) using 1 OpenMP thread(s) per MPI task units real dimension 3 boundary p p p atom_style full pair_style lj/cut/coul/long 10.0 bond_style harmonic angle_style harmonic read_data data.spce Reading data file ... orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533) 1 by 1 by 1 MPI processor grid reading atoms ... 8640 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 5760 bonds reading angles ... 2880 angles 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 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds read_data CPU = 0.048 seconds molecule h2omol H2O.txt Read molecule template h2omol: 1 molecules 0 fragments 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### pair_coeff 1 1 0.1502629 3.1169 pair_coeff 1 2 0.0341116368 2.04845 pair_coeff 2 2 0.00774378 0.98 bond_coeff 1 176.864 0.9611 angle_coeff 1 42.1845 109.4712 kspace_style pppm 1.0e-4 fix mywidom all widom 10 20 0 29494 298 mol h2omol fix 2 all nvt temp 298.0 298.0 100.0 neighbor 2.0 bin neigh_modify delay 10 every 2 check yes #run variables timestep 0.5 thermo 10 thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3] run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.2690183 grid = 24 24 24 stencil order = 5 estimated absolute RMS force accuracy = 0.024843102 estimated relative force accuracy = 7.4814263e-05 using double precision KISS FFT 3d grid and FFT values/proc = 29791 13824 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule WARNING: Fix widom using full_energy option (src/MC/fix_widom.cpp:320) 0 atoms in group FixWidom:widom_exclusion_group:mywidom 0 atoms in group FixWidom:rotation_gas_atoms:mywidom WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:654) Neighbor list info ... update: every = 2 steps, delay = 10 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 8 8 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.0447118 0 0 82468.116 10 -29718 -32598.944 111.87604 -498.88935 82468.116 1.0447118 200.15526 1.6274344e-147 82468.116 20 -29698.227 -32625.357 113.6696 -3120.7115 82468.116 1.0447118 -1.0295764 5.6893637 82468.116 30 -29668.463 -33188.922 136.71037 -8129.0179 82468.116 1.0447118 5.5971294 7.856256e-05 82468.116 40 -29654.066 -34017.797 169.45726 -5730.6427 82468.116 1.0447118 128.14313 1.0550462e-94 82468.116 50 -29627.714 -33214.549 139.28799 -3954.0179 82468.116 1.0447118 122.28545 2.0851209e-90 82468.116 60 -29602.616 -32995.039 131.73836 -8099.2136 82468.116 1.0447118 -1.4752191 12.07497 82468.116 70 -29591.096 -33872.451 166.25834 -7065.2821 82468.116 1.0447118 17.210054 2.3911575e-13 82468.116 80 -29553.631 -32971.209 132.7152 -3535.4257 82468.116 1.0447118 11.148921 6.6631697e-09 82468.116 90 -29530.109 -33346.146 148.18857 -5312.6414 82468.116 1.0447118 51.783293 1.055658e-38 82468.116 100 -29505.327 -34074.801 177.4469 -5991.0034 82468.116 1.0447118 32.415523 1.6878187e-24 82468.116 Loop time of 55.4401 on 1 procs for 100 steps with 8640 atoms Performance: 0.078 ns/day, 308.000 hours/ns, 1.804 timesteps/s, 15.584 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4117 | 5.4117 | 5.4117 | 0.0 | 9.76 Bond | 0.029451 | 0.029451 | 0.029451 | 0.0 | 0.05 Kspace | 0.73758 | 0.73758 | 0.73758 | 0.0 | 1.33 Neigh | 1.4296 | 1.4296 | 1.4296 | 0.0 | 2.58 Comm | 0.018593 | 0.018593 | 0.018593 | 0.0 | 0.03 Output | 0.00069303 | 0.00069303 | 0.00069303 | 0.0 | 0.00 Modify | 47.81 | 47.81 | 47.81 | 0.0 | 86.24 Other | | 0.002525 | | | 0.00 Nlocal: 8640 ave 8640 max 8640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23534 ave 23534 max 23534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.27356e+06 ave 3.27356e+06 max 3.27356e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3273560 Ave neighs/atom = 378.88426 Ave special neighs/atom = 2 Neighbor list builds = 220 Dangerous builds = 0 Total wall time: 0:00:55