LAMMPS (2 Aug 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) using 1 OpenMP thread(s) per MPI task units real boundary p p p dimension 3 atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/coul/long 13.0 14 kspace_style pppm 1.0e-3 read_data S1.data orthogonal box = (-116.54 -116.579 -116.441) to (116.5 116.461 116.599) 1 by 2 by 2 MPI processor grid reading atoms ... 180060 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom reading bonds ... 120040 bonds reading angles ... 60060 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_coeff 2 2 0 0 #H,H pair_coeff 2 3 0 1.594 #H,O pair_modify mix arithmetic neighbor 2 bin neigh_modify every 1 delay 0 check yes region surface block -31.502748 31.629252 -31.417480 31.7605180 -26.523444 26.601556 units box #region surface block -115.020424 114.979576 -115.058968 114.941032 -114.921227 115.078773 units box group water type 2 3 180000 atoms in group water group owater type 3 60000 atoms in group owater #group ions type 2 4 6 7 10 11 group sulphate type 4 5 50 atoms in group sulphate minimize 1.0e-4 1.0e-6 10000 100000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.130748 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.362294 estimated relative force accuracy = 0.00109104 using double precision FFTs 3d grid and FFT values/proc = 21689 11664 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 binsize = 8, bins = 30 30 30 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) = 73.02 | 73.22 | 73.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6025.2895 45089.23 39063.941 5881.9397 339 0 -389787.48 15764.613 -374022.87 -408.55645 Loop time of 105.14 on 4 procs for 339 steps with 180060 atoms 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 39063.9406572 -373988.265569 -374022.869539 Force two-norm initial, final = 13513.2 249.737 Force max component initial, final = 312.591 61.8899 Final line search alpha, max atom move = 0.00159107 0.0984709 Iterations, force evaluations = 339 454 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.73 | 79.596 | 81.541 | 19.2 | 75.70 Bond | 0.95784 | 0.97413 | 0.98669 | 1.1 | 0.93 Kspace | 17.292 | 19.245 | 21.116 | 39.3 | 18.30 Neigh | 3.045 | 3.0456 | 3.0467 | 0.0 | 2.90 Comm | 0.63278 | 0.63537 | 0.63902 | 0.3 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.644 | | | 1.56 Nlocal: 45015 ave 45258 max 44851 min Histogram: 1 1 0 0 1 0 0 0 0 1 Nghost: 35537.5 ave 35671 max 35441 min Histogram: 2 0 0 0 0 0 1 0 0 1 Neighs: 5.58158e+06 ave 5.65959e+06 max 5.49431e+06 min Histogram: 1 0 0 0 1 0 1 0 0 1 Total # of neighbors = 22326332 Ave neighs/atom = 123.994 Ave special neighs/atom = 2.00044 Neighbor list builds = 15 Dangerous builds = 0 velocity all create 348.0 12345678 dist uniform fix 1 water shake 1e-5 500 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 60000 = # of frozen angles fix 2 all npt temp 348.0 348.0 100.0 iso 70 70 1000 #thermo 100 #thermo_style multi timestep 1.0 dump 1 all xyz 100 dump1.xyz dump_modify 1 element Ca H O OS S reset_timestep 0 run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.130748 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.362294 estimated relative force accuracy = 0.00109104 using double precision FFTs 3d grid and FFT values/proc = 21689 11664 Per MPI rank memory allocation (min/avg/max) = 78.35 | 78.55 | 78.75 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 521.91449 -389787.48 2.5434787 -203005.8 103.772 12655854 100 240.70073 -315843.7 21.993209 -229681.4 -548.79722 12648289 Loop time of 13.9506 on 4 procs for 100 steps with 180060 atoms Performance: 0.619 ns/day, 38.752 hours/ns, 7.168 timesteps/s 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3265 | 9.501 | 9.6851 | 5.4 | 68.10 Bond | 0.00020674 | 0.0005519 | 0.00076492 | 0.0 | 0.00 Kspace | 2.1629 | 2.3468 | 2.5207 | 10.9 | 16.82 Neigh | 0.64393 | 0.64468 | 0.64497 | 0.1 | 4.62 Comm | 0.12709 | 0.12892 | 0.12987 | 0.3 | 0.92 Output | 0.10088 | 0.10091 | 0.10098 | 0.0 | 0.72 Modify | 1.1555 | 1.1597 | 1.1633 | 0.3 | 8.31 Other | | 0.06806 | | | 0.49 Nlocal: 45015 ave 45259 max 44854 min Histogram: 1 1 0 0 1 0 0 0 0 1 Nghost: 35509.2 ave 35657 max 35401 min Histogram: 1 0 1 0 1 0 0 0 0 1 Neighs: 5.58072e+06 ave 5.6572e+06 max 5.49522e+06 min Histogram: 1 0 0 0 1 0 1 0 0 1 Total # of neighbors = 22322898 Ave neighs/atom = 123.975 Ave special neighs/atom = 2.00044 Neighbor list builds = 5 Dangerous builds = 0 unfix 2 fix 3 owater evaporate 100 9 surface 38277 molecule yes fix 4 all npt temp 348.0 348.0 100.0 iso 70 70 1000 compute allmol all chunk/atom molecule nchunk every compress yes compute watmol owater chunk/atom molecule nchunk every compress yes compute mols all reduce max c_allmol c_watmol thermo_style custom step pe temp atoms c_mols[*] thermo 100 thermo_modify lost warn run 1000 #for equib PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.130762 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.362146 estimated relative force accuracy = 0.00109059 using double precision FFTs 3d grid and FFT values/proc = 21689 11664 Per MPI rank memory allocation (min/avg/max) = 78.35 | 78.55 | 78.75 Mbytes Step PotEng Temp Atoms c_mols[1] c_mols[2] WARNING: One or more chunks do not contain all atoms in molecule (../compute_chunk_atom.cpp:1161) 100 -315821.81 240.70073 180060 9999 9999 200 -326904.82 286.01374 180042 9998 9998 300 -330464.59 314.92403 180024 9997 9997 400 -331686.81 335.063 180006 9996 9996 500 -334151.02 353.67335 179988 9995 9995 600 -336489.4 358.42022 179970 9994 9994 700 -340515.98 356.7316 179952 9993 9993 800 -345255.97 356.84949 179934 9992 9992 900 -349808.68 356.34511 179916 9991 9991 1000 -354401.71 356.24121 179898 9990 9990 1100 -358610.55 355.26899 179880 9989 9989 Loop time of 167.147 on 4 procs for 1000 steps with 179880 atoms Performance: 0.517 ns/day, 46.430 hours/ns, 5.983 timesteps/s 98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 104.4 | 107.92 | 110.49 | 22.1 | 64.57 Bond | 0.002227 | 0.0060787 | 0.0085549 | 3.0 | 0.00 Kspace | 27.978 | 30.543 | 34.058 | 41.6 | 18.27 Neigh | 11.987 | 11.991 | 11.996 | 0.1 | 7.17 Comm | 1.6143 | 1.6358 | 1.6597 | 1.3 | 0.98 Output | 1.4765 | 1.477 | 1.4783 | 0.1 | 0.88 Modify | 12.73 | 12.774 | 12.817 | 1.1 | 7.64 Other | | 0.7954 | | | 0.48 Nlocal: 44970 ave 45099 max 44858 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 36028.8 ave 36174 max 35756 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 5.76691e+06 ave 5.86587e+06 max 5.64294e+06 min Histogram: 1 0 0 1 0 0 0 0 1 1 Total # of neighbors = 23067631 Ave neighs/atom = 128.239 Ave special neighs/atom = 2.00044 Neighbor list builds = 76 Dangerous builds = 0 Total wall time: 0:04:55