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) 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 # 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 = 8000 3375 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) = 26.54 | 26.54 | 26.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16692.358 0 -16692.358 -1289.8319 Loop time of 1e-06 on 1 procs for 0 steps with 4500 atoms group oxy type 1 1500 atoms in group oxy group hyd type 2 3000 atoms in group hyd # the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords # compute pairwise energy between all oxygen and all hydrogen compute epa oxy group/group hyd pair yes kspace no boundary no # tally pairwise energy between all oygen and all hydrogen compute c1 oxy pe/tally hyd # tally pairwise energy beween all atoms to compare with globals compute c2 all pe/tally all # collect per atom energies compute c3 all pe/atom pair # reduce over the first group only the per-atom data is storing VDW and Coulomb separately... compute oxy oxy reduce sum c_c1[1] c_c1[2] compute red all reduce sum c_c2[1] c_c2[2] c_c3 # ... thus to get the same as compute group/group, we need to add the two # ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group. variable epa equal 2.0*(c_oxy[1]+c_oxy[2]) # compute equivalent values to globals variable vdwl equal c_red[1] variable coul equal c_red[2] variable pe equal c_red[3] variable pair equal v_vdwl+v_coul variable eref equal epair-elong velocity all create 300 432567 dist uniform timestep 2.0 # c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value thermo_style custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair 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 = 8000 3375 WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) WARNING: Compute pe/tally only called from pair style (../compute_pe_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) = 29.08 | 29.08 | 29.08 Mbytes Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935 Loop time of 15.3339 on 1 procs for 50 steps with 4500 atoms Performance: 0.563 ns/day, 42.594 hours/ns, 3.261 timesteps/s 32.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.432 | 13.432 | 13.432 | 0.0 | 87.60 Bond | 0.000365 | 0.000365 | 0.000365 | 0.0 | 0.00 Kspace | 0.581 | 0.581 | 0.581 | 0.0 | 3.79 Neigh | 0.66081 | 0.66081 | 0.66081 | 0.0 | 4.31 Comm | 0.019908 | 0.019908 | 0.019908 | 0.0 | 0.13 Output | 0.57731 | 0.57731 | 0.57731 | 0.0 | 3.76 Modify | 0.058515 | 0.058515 | 0.058515 | 0.0 | 0.38 Other | | 0.003889 | | | 0.03 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 = 2601983 Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 Total wall time: 0:00:16