LAMMPS (21 Aug 2015-ICMS) using 1 OpenMP thread(s) per MPI task units real atom_style full read_data data.spce orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) 1 by 1 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 group one molecule 1 2 6 atoms in group one # the following section shows equivalences between using the pe/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 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 c_c2 thermo 10 run 50 PPPM initialization ... 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 = 8000 3375 WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7 -> bins = 6 6 6 Memory usage per processor = 16.7648 Mbytes Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0 Loop time of 4.11825 on 1 procs for 50 steps with 4500 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 2.098 ns/day 11.440 hours/ns 12.141 timesteps/s MPI task timings breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5286 | 3.5286 | 3.5286 | 0.0 | 85.68 Bond | 6.1274e-05 | 6.1274e-05 | 6.1274e-05 | 0.0 | 0.00 Kspace | 0.1937 | 0.1937 | 0.1937 | 0.0 | 4.70 Neigh | 0.31454 | 0.31454 | 0.31454 | 0.0 | 7.64 Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.25 Output | 0.039355 | 0.039355 | 0.039355 | 0.0 | 0.96 Modify | 0.029273 | 0.029273 | 0.029273 | 0.0 | 0.71 Other | | 0.002351 | | | 0.06 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21131 ave 21131 max 21131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2601984 Ave neighs/atom = 578.219 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 Total wall time: 0:00:04