LAMMPS (6 Jan 2017) units real atom_style full dimension 3 boundary p p p lattice sc 3.1043 Lattice spacing in x,y,z = 3.1043 3.1043 3.1043 region simbox block -5 5 -5 5 -5 5 units lattice create_box 2 simbox bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/special/per/atom 2 extra/angle/per/atom 1 Created orthogonal box = (-15.5215 -15.5215 -15.5215) to (15.5215 15.5215 15.5215) 1 by 1 by 1 MPI processor grid molecule spce spce.mol Read molecule spce: 3 atoms with 2 types 2 bonds with 1 types 1 angles with 1 types 0 dihedrals with 0 types 0 impropers with 0 types pair_style lj/cut/coul/long 9.0 pair_modify tail yes bond_style harmonic angle_style harmonic kspace_style pppm 1.0e-6 mass 1 15.9994 mass 2 1.008 pair_coeff 1 1 0.1553 3.166 pair_coeff 1 2 0.0 0.0 pair_coeff 2 2 0.0 0.0 bond_coeff 1 554.13 1.0 angle_coeff 1 45.769 109.47 create_atoms 0 box mol spce 32537 Created 3000 atoms thermo 1 thermo_style custom step temp ke pe etotal press timestep 2.0 run_style verlet neighbor 3.0 bin neigh_modify every 1 delay 3 check yes fix rigid all shake 1.0e-4 100 0 b 1 a 1 t 1 2 mol spce 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # of frozen angles velocity all create 298.0 32537 dist gaussian rot yes mom yes run 0 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317) G vector (1/distance) = 0.374976 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.000401319 estimated relative force accuracy = 1.20856e-06 using double precision FFTs 3d grid and FFT values/proc = 185193 110592 Neighbor list info ... update every 1 steps, delay 3 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Memory usage per processor = 29.3859 Mbytes Step Temp KinEng PotEng TotEng Press 0 298 1775.6745 785.58069 2561.2552 29045.156 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3000 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 3000 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12632 ave 12632 max 12632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.08408e+06 ave 1.08408e+06 max 1.08408e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1084078 Ave neighs/atom = 361.359 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 velocity all scale 298.0 fix nve all nve dump 1 all custom 1 all.lammpstrj id x y z vx vy vz type dump_modify 1 sort id run 1 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317) G vector (1/distance) = 0.374976 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.000401319 estimated relative force accuracy = 1.20856e-06 using double precision FFTs 3d grid and FFT values/proc = 185193 110592 Memory usage per processor = 31.0365 Mbytes Step Temp KinEng PotEng TotEng Press 0 298 1775.6745 785.58069 2561.2552 29045.156 1 228.34642 1360.634 607.89386 1968.5278 26721.491 Loop time of 0.05232 on 1 procs for 1 steps with 3000 atoms Performance: 3.303 ns/day, 7.267 hours/ns, 19.113 timesteps/s 99.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022952 | 0.022952 | 0.022952 | 0.0 | 43.87 Bond | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00 Kspace | 0.022668 | 0.022668 | 0.022668 | 0.0 | 43.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.8705e-05 | 9.8705e-05 | 9.8705e-05 | 0.0 | 0.19 Output | 0.0062771 | 0.0062771 | 0.0062771 | 0.0 | 12.00 Modify | 0.00030398 | 0.00030398 | 0.00030398 | 0.0 | 0.58 Other | | 1.812e-05 | | | 0.03 Nlocal: 3000 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12632 ave 12632 max 12632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.08408e+06 ave 1.08408e+06 max 1.08408e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1084078 Ave neighs/atom = 361.359 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 write_restart end.restart PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317) G vector (1/distance) = 0.374976 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.000401319 estimated relative force accuracy = 1.20856e-06 using double precision FFTs 3d grid and FFT values/proc = 185193 110592 dump 2 all custom 1 rst.lammpstrj id x y z vx vy vz type dump_modify 2 sort id run 0 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317) G vector (1/distance) = 0.374976 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.000401319 estimated relative force accuracy = 1.20856e-06 using double precision FFTs 3d grid and FFT values/proc = 185193 110592 Memory usage per processor = 32.687 Mbytes Step Temp KinEng PotEng TotEng Press 1 228.34642 1360.634 607.89386 1968.5278 26722.071 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3000 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 3000 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12633 ave 12633 max 12633 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.08416e+06 ave 1.08416e+06 max 1.08416e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1084159 Ave neighs/atom = 361.386 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00