LAMMPS (23 Oct 2017) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task # created by fftool print "Methane in TIP4P water" Methane in TIP4P water units real boundary p p p atom_style full bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 0.5 read_data data.lmp orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438) 1 by 2 by 2 MPI processor grid reading atoms ... 5 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom reading bonds ... 4 bonds reading angles ... 6 angles 4 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 3 = max # of 1-4 neighbors 4 = max # of special neighbors pair_style lj/cut/coul/long 8.0 10.0 pair_modify tail no kspace_style pppm 1.0e-4 pair_coeff 1 1 0.0660 3.5000 # C4H C4H pair_coeff 1 2 0.0445 2.9580 # C4H H pair_coeff 2 2 0.0300 2.5000 # H H variable TK equal 300.0 variable PBAR equal 1.0 neighbor 2.0 bin timestep 1.0 velocity all create ${TK} 12345 velocity all create 300 12345 thermo_style multi thermo 500 fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 fix TPSTAT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 1000 fix TPSTAT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 1000 fix TPSTAT all npt temp 300 300 100 iso 1 ${PBAR} 1000 fix TPSTAT all npt temp 300 300 100 iso 1 1 1000 run 10000 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.089259 grid = 2 2 2 stencil order = 5 estimated absolute RMS force accuracy = 0.0309227 estimated relative force accuracy = 9.31229e-05 using double precision FFTs 3d grid and FFT values/proc = 252 2 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 5 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) = 6.446 | 6.591 | 7.025 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 3.7455 KinEng = 3.5770 Temp = 300.0000 PotEng = 0.1685 E_bond = 0.0000 E_angle = 0.1685 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 8.4090 Volume = 19438.0383 ---------------- Step 500 ----- CPU = 0.2469 (sec) ---------------- TotEng = 5.1614 KinEng = 3.7878 Temp = 317.6808 PotEng = 1.3736 E_bond = 0.7006 E_angle = 0.6730 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -35.9304 Volume = 19489.7733 ---------------- Step 1000 ----- CPU = 0.4993 (sec) ---------------- TotEng = 7.8794 KinEng = 3.7972 Temp = 318.4709 PotEng = 4.0822 E_bond = 3.7626 E_angle = 0.3197 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -116.0194 Volume = 19741.8188 ---------------- Step 1500 ----- CPU = 0.7374 (sec) ---------------- TotEng = 8.1464 KinEng = 4.7622 Temp = 399.4065 PotEng = 3.3842 E_bond = 3.0479 E_angle = 0.3364 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -129.4207 Volume = 20582.2328 ---------------- Step 2000 ----- CPU = 1.0045 (sec) ---------------- TotEng = 8.7702 KinEng = 5.3082 Temp = 445.1965 PotEng = 3.4620 E_bond = 1.9452 E_angle = 1.5168 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -92.4347 Volume = 23450.8739 ---------------- Step 2500 ----- CPU = 1.1562 (sec) ---------------- TotEng = 7.5634 KinEng = 5.7967 Temp = 486.1716 PotEng = 1.7667 E_bond = 1.5521 E_angle = 0.2146 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -41.5219 Volume = 30773.9823 ---------------- Step 3000 ----- CPU = 1.3072 (sec) ---------------- TotEng = 5.7809 KinEng = 3.6598 Temp = 306.9435 PotEng = 2.1211 E_bond = 1.2360 E_angle = 0.8852 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 3.5872 Volume = 45261.6945 ---------------- Step 3500 ----- CPU = 1.4763 (sec) ---------------- TotEng = 4.3415 KinEng = 2.0775 Temp = 174.2399 PotEng = 2.2640 E_bond = 1.5760 E_angle = 0.6880 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -2.1749 Volume = 67665.1803 ---------------- Step 4000 ----- CPU = 1.6518 (sec) ---------------- TotEng = 6.0633 KinEng = 3.1661 Temp = 265.5442 PotEng = 2.8972 E_bond = 1.5034 E_angle = 1.3939 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -7.6295 Volume = 91551.2012 ---------------- Step 4500 ----- CPU = 1.8244 (sec) ---------------- TotEng = 8.3688 KinEng = 5.2437 Temp = 439.7869 PotEng = 3.1251 E_bond = 1.0204 E_angle = 2.1047 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -13.6797 Volume = 102214.4143 ---------------- Step 5000 ----- CPU = 1.9894 (sec) ---------------- TotEng = 3.1652 KinEng = 1.3594 Temp = 114.0167 PotEng = 1.8058 E_bond = 0.7695 E_angle = 1.0363 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -10.0163 Volume = 83140.8948 ---------------- Step 5500 ----- CPU = 2.1507 (sec) ---------------- TotEng = 5.0765 KinEng = 1.5941 Temp = 133.6959 PotEng = 3.4825 E_bond = 2.0367 E_angle = 1.4458 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -14.2654 Volume = 39152.4893 ---------------- Step 6000 ----- CPU = 2.2942 (sec) ---------------- TotEng = 6.1935 KinEng = 2.6886 Temp = 225.4936 PotEng = 3.5049 E_bond = 1.6534 E_angle = 1.8516 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 49.2442 Volume = 17668.4335 ---------------- Step 6500 ----- CPU = 2.4682 (sec) ---------------- TotEng = 6.9176 KinEng = 3.0931 Temp = 259.4197 PotEng = 3.8245 E_bond = 2.3209 E_angle = 1.5036 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 191.6118 Volume = 11972.0945 ---------------- Step 7000 ----- CPU = 2.6354 (sec) ---------------- TotEng = 9.4724 KinEng = 5.3103 Temp = 445.3732 PotEng = 4.1622 E_bond = 1.7859 E_angle = 2.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 217.0317 Volume = 9869.2174 ---------------- Step 7500 ----- CPU = 2.7879 (sec) ---------------- TotEng = 10.5032 KinEng = 6.2725 Temp = 526.0759 PotEng = 4.2306 E_bond = 1.8803 E_angle = 2.3504 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = 59.5561 Volume = 8850.3610 ---------------- Step 8000 ----- CPU = 2.9668 (sec) ---------------- TotEng = 8.9537 KinEng = 4.0855 Temp = 342.6470 PotEng = 4.8683 E_bond = 3.1331 E_angle = 1.7352 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -100.2544 Volume = 8423.3186 ---------------- Step 8500 ----- CPU = 3.1197 (sec) ---------------- TotEng = 2.3669 KinEng = 1.1663 Temp = 97.8205 PotEng = 1.2005 E_bond = 0.5802 E_angle = 0.6203 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -84.2012 Volume = 8440.3070 ---------------- Step 9000 ----- CPU = 3.3071 (sec) ---------------- TotEng = 5.7029 KinEng = 4.0802 Temp = 342.2081 PotEng = 1.6226 E_bond = 0.8523 E_angle = 0.7704 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -172.7305 Volume = 8749.0284 ---------------- Step 9500 ----- CPU = 3.4513 (sec) ---------------- TotEng = 7.2859 KinEng = 4.1636 Temp = 349.2025 PotEng = 3.1223 E_bond = 1.9116 E_angle = 1.2108 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -144.5764 Volume = 10049.6149 ---------------- Step 10000 ----- CPU = 3.6310 (sec) ---------------- TotEng = 6.5406 KinEng = 3.2883 Temp = 275.7923 PotEng = 3.2522 E_bond = 2.2788 E_angle = 0.9734 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 0.0000 E_coul = 1.2040 E_long = -1.2040 Press = -35.4721 Volume = 13634.4038 Loop time of 3.6322 on 4 procs for 10000 steps with 5 atoms Performance: 237.873 ns/day, 0.101 hours/ns, 2753.154 timesteps/s 83.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011116 | 0.015578 | 0.027557 | 5.5 | 0.43 Bond | 0.008337 | 0.014866 | 0.030934 | 7.6 | 0.41 Kspace | 1.9965 | 2.0971 | 2.1442 | 4.1 | 57.74 Neigh | 0.0032039 | 0.016049 | 0.028834 | 10.0 | 0.44 Comm | 0.16148 | 0.25543 | 0.29864 | 11.1 | 7.03 Output | 0.0013779 | 0.0062095 | 0.020698 | 10.6 | 0.17 Modify | 0.88087 | 0.92723 | 0.97318 | 3.8 | 25.53 Other | | 0.2998 | | | 8.25 Nlocal: 1.25 ave 5 max 0 min Histogram: 3 0 0 0 0 0 0 0 0 1 Nghost: 21.25 ave 40 max 5 min Histogram: 1 0 0 0 2 0 0 0 0 1 Neighs: 2.5 ave 10 max 0 min Histogram: 3 0 0 0 0 0 0 0 0 1 Total # of neighbors = 10 Ave neighs/atom = 2 Ave special neighs/atom = 4 Neighbor list builds = 207 Dangerous builds = 0 Total wall time: 0:00:04