LAMMPS (11 Sep 2015-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task ########################################################## # Units, BC, Forcefield Parameters and Initialization # ########################################################## #newton off #package gpu force/neigh 0 1 -1 units real boundary p p p atom_style full #sphere bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 10 12 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data pmma_water15x15_minimized.data orthogonal box = (-75 -75 -81.5512) to (75 75 81.5512) 8 by 10 by 10 MPI processor grid reading atoms ... 363681 atoms reading velocities ... 363681 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 24 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom reading bonds ... 258246 bonds reading angles ... 193950 angles reading dihedrals ... 119700 dihedrals reading impropers ... 3150 impropers 4 = max # of 1-2 neighbors 11 = max # of 1-3 neighbors 22 = max # of 1-4 neighbors 26 = max # of special neighbors special_bonds charmm neighbor 2.0 multi neigh_modify delay 0 every 1 check yes ################################################################### # GROUPS AND REGION based on region and positions # ################################################################### group pmma type 3 4 5 6 7 8 9 10 47565 atoms in group pmma group water type 1 2 316116 atoms in group water region anchored block INF INF INF INF -2.5 2.5 units box group anchoredH_gross region anchored 11522 atoms in group anchoredH_gross group anchoredH_net subtract anchoredH_gross water 11484 atoms in group anchoredH_net group pgroup subtract all anchoredH_net 352197 atoms in group pgroup group dilation subtract all anchoredH_net 352197 atoms in group dilation group mobile_pmma subtract pmma anchoredH_net 36081 atoms in group mobile_pmma ######################################################## # Make center slab of PMMA immobile # ######################################################### velocity anchoredH_net zero angular velocity anchoredH_net zero linear neigh_modify exclude group anchoredH_net anchoredH_net delete_bonds anchoredH_net multi PPPM initialization ... G vector (1/distance) = 0.214057 grid = 60 60 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0364502 estimated relative force accuracy = 0.000109769 using double precision FFTs 3d grid and FFT values/proc = 1859 360 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7 -> bins = 22 22 24 258246 total bonds, 248078 turned on, 10168 turned off 193950 total angles, 177397 turned on, 16553 turned off 119700 total dihedrals, 100399 turned on, 19301 turned off 3150 total impropers, 2618 turned on, 532 turned off ######################################################## fix 1 pgroup shake 1e-6 500 0 m 1.0 a 15 166 = # of size 2 clusters 2562 = # of size 3 clusters 4449 = # of size 4 clusters 105372 = # of frozen angles ######################################################### compute t0 pgroup temp fix b3 water npt temp 300.0 300.0 200.0 z 1.0 1.0 2000.0 dilate dilation fix_modify b3 temp t0 WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349) compute t01 water temp fix b4 mobile_pmma nvt temp 300.0 300.0 200.0 compute t1 all pressure t0 ######################################################### # Outputs # ######################################################### thermo 1000 thermo_style custom step c_b4_temp c_t01 zlo zhi vol c_t1 c_t1[3] ######################################################## timestep 2.0 run 1000 #2500000 PPPM initialization ... G vector (1/distance) = 0.214057 grid = 60 60 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0364502 estimated relative force accuracy = 0.000109769 using double precision FFTs 3d grid and FFT values/proc = 1859 360 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) Memory usage per processor = 19.6447 Mbytes Step b4_temp t01 Zlo Zhi Volume t1 t1[3] 0 292.64785 253.05203 -81.551232 81.551232 3669805.4 -384.17608 -476.43523 1000 297.50169 291.6526 -80.66764 80.66764 3630043.8 -92.255784 -194.9796 Loop time of 19.6318 on 800 procs for 1000 steps with 363681 atoms Performance: 8.802 ns/day, 2.727 hours/ns, 50.938 timesteps/s 99.6% CPU use with 800 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9428 | 6.1496 | 7.0182 | 15.2 | 31.32 Bond | 0.001493 | 0.029886 | 0.19012 | 32.5 | 0.15 Kspace | 8.7607 | 9.6039 | 10.849 | 12.1 | 48.92 Neigh | 1.9082 | 1.9166 | 1.9242 | 0.2 | 9.76 Comm | 0.75401 | 0.79772 | 0.84038 | 1.7 | 4.06 Output | 0.0069442 | 0.0071199 | 0.0085936 | 0.1 | 0.04 Modify | 0.94222 | 0.99711 | 1.0473 | 2.3 | 5.08 Other | | 0.1299 | | | 0.66 Nlocal: 454.601 ave 501 max 400 min Histogram: 5 26 50 105 120 154 197 103 28 12 Nghost: 8441.18 ave 8725 max 8034 min Histogram: 16 62 83 68 44 63 81 192 161 30 Neighs: 259546 ave 303179 max 216941 min Histogram: 11 41 94 125 143 128 127 88 33 10 Total # of neighbors = 207637033 Ave neighs/atom = 570.932 Ave special neighs/atom = 3.14504 Neighbor list builds = 119 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:24