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) 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 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 ... 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 pe/tally only called from pair style (../compute_pe_tally.cpp:75) WARNING: Compute pe/tally only called from pair style (../compute_pe_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 = 8.44413 Mbytes Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911 Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms 100.0% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 7.168 ns/day 3.348 hours/ns 41.482 timesteps/s MPI task timings breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94 Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02 Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43 Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33 Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48 Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87 Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80 Other | | 0.001719 | | | 0.14 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 = 2601984 Ave neighs/atom = 578.219 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 Total wall time: 0:00:01