LAMMPS (19 May 2017) units real atom_style full read_data data.spce orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) 2 by 2 by 1 MPI processor grid reading atoms ... 4500 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 3000 bonds reading angles ... 1500 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors pair_style lj/cut/coul/long 12.0 12.0 kspace_style pppm 1.0e-4 pair_coeff 1 1 0.15535 3.166 pair_coeff * 2 0.0000 0.0000 bond_style harmonic angle_style harmonic dihedral_style none improper_style none bond_coeff 1 1000.00 1.000 angle_coeff 1 100.0 109.47 special_bonds lj/coul 0.0 0.0 1.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 2 = max # of special neighbors neighbor 2.0 bin fix 1 all shake 0.0001 20 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 # make certain that shake constraints are satisfied run 0 post no PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0319435 estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 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) = 10.6 | 10.61 | 10.61 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16692.358 0 -16692.358 -1289.8319 Loop time of 4.5e-06 on 4 procs for 0 steps with 4500 atoms group one molecule 1 2 6 atoms in group one # the following section shows equivalences between using the force/tally compute and other computes and thermo keywords # compute pairwise force between two molecules and everybody compute fpa one group/group all pair yes kspace no boundary no # tally pairwise force between two molecules and the all molecules compute c1 one force/tally all # tally the force of all with all (should be zero) compute c2 all force/tally all # collect per atom data. only reduce over the first group. compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] # determine magnitude of force variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) # round to 10**-10 absolute precision. variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 variable all equal round(1e10*c_c2)*1e-10 velocity all create 300 432567 dist uniform timestep 2.0 # v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all thermo 10 run 50 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0319435 estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.59 | 11.6 Mbytes Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0 Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s 31.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5075 | 3.6114 | 3.7489 | 4.7 | 83.67 Bond | 8.6e-05 | 0.00010525 | 0.000141 | 0.0 | 0.00 Kspace | 0.2581 | 0.39489 | 0.49723 | 14.2 | 9.15 Neigh | 0.19826 | 0.19888 | 0.19918 | 0.1 | 4.61 Comm | 0.034639 | 0.037137 | 0.038938 | 0.9 | 0.86 Output | 0.025465 | 0.025997 | 0.027558 | 0.6 | 0.60 Modify | 0.044022 | 0.044175 | 0.044407 | 0.1 | 1.02 Other | | 0.003593 | | | 0.08 Nlocal: 1125 ave 1148 max 1097 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 12212.5 ave 12269 max 12162 min Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 650496 ave 675112 max 631353 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 2601983 Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 Total wall time: 0:00:04