LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # read topology and force field pair_style lj/sdk 15.0 bond_style harmonic angle_style sdk special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors neighbor 3.0 bin neigh_modify delay 5 timestep 5.0 #dump 1 all xtc 200 pegc12e8-1.xtc #dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 12.4188 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 8.7547 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 17.7479 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 26.7299 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 35.8941 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 45.1542 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s MPI task timings breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27 Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14 Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34 Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49 Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00 Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19 Other | | 0.2571 | | | 0.57 Nlocal: 20070 ave 20100 max 20040 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 20230.5 ave 20241 max 20220 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart