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 # ########################################################## units real boundary p p p atom_style full #sphere bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style hybrid lj/charmm/coul/long 10 12 colloid 100.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data pmma_water_colloid1_minimized.data orthogonal box = (-75 -75 -79.0324) to (75 75 79.0324) 6 by 10 by 11 MPI processor grid WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:476) reading atoms ... 302509 atoms reading velocities ... 302509 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 ... 217464 bonds reading angles ... 173559 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 one 100000 page 1000000 comm_modify mode multi ######################################################### # Add Colloidal Carbon # ######################################################### pair_coeff 1 11 colloid 57.86 3.47 100.0 0.0 52.3 pair_coeff 2 11 colloid 105.21 3.47 100.0 0.0 63.3 pair_coeff 3 11 colloid 84.45 3.47 100.0 0.0 62.8 pair_coeff 4 11 colloid 48.26 3.47 100.0 0.0 64.96 pair_coeff 5 11 colloid 63.84 3.47 100.0 0.0 65.0 pair_coeff 6 11 colloid 75.34 3.47 100.0 0.0 65.3 pair_coeff 7 11 colloid 50.47 3.47 100.0 0.0 60.3 pair_coeff 8 11 colloid 41.79 3.47 100.0 0.0 60.3 pair_coeff 9 11 colloid 93.45 3.47 100.0 0.0 62.8 pair_coeff 10 11 colloid 85.31 3.47 100.0 0.0 62.5 ################################################################### # 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 254943 atoms in group water group colloid type 11 1 atoms in group colloid region anchored block INF INF INF INF -2.5 2.5 units box group anchoredH_gross region anchored 11721 atoms in group anchoredH_gross group anchoredH_net subtract anchoredH_gross water 11627 atoms in group anchoredH_net group pgroup subtract all anchoredH_net 290882 atoms in group pgroup group dilation subtract all anchoredH_net 290882 atoms in group dilation group mobile_pmma subtract pmma anchoredH_net 35938 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) = 0.213045 grid = 60 60 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0351393 estimated relative force accuracy = 0.000105821 using double precision FFTs 3d grid and FFT values/proc = 1980 360 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) Neighbor list info ... 3 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 100000, page size: 1000000 master list distance cutoff = 102 ghost atom cutoff = 102 binsize = 7 -> bins = 22 22 23 217464 total bonds, 207210 turned on, 10254 turned off 173559 total angles, 156873 turned on, 16686 turned off 119700 total dihedrals, 100260 turned on, 19440 turned off 3150 total impropers, 2620 turned on, 530 turned off ######################################################### # Make Fullerene rigid # ######################################################### velocity colloid zero angular velocity colloid zero linear ######################################################## fix 1 pgroup shake 1e-6 500 0 m 1.0 a 15 172 = # of size 2 clusters 2585 = # of size 3 clusters 4398 = # of size 4 clusters 84981 = # of frozen angles ######################################################### compute t00 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 t00 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 fix b5 colloid nve compute com1 colloid com compute t1 all pressure t00 ######################################################### # Outputs # ######################################################### thermo 500 thermo_style custom step c_b4_temp c_t01 zlo zhi vol c_t1 c_t1[3] c_com1[1] c_com1[2] c_com1[3] #c_t1[1] c_t1[2] c_t1[3] restart 1000000 ./restart.* ######################################################## timestep 2.0 run 2000 PPPM initialization ... G vector (1/distance) = 0.213045 grid = 60 60 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0351393 estimated relative force accuracy = 0.000105821 using double precision FFTs 3d grid and FFT values/proc = 1980 360 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) Memory usage per processor = 232.811 Mbytes Step b4_temp t01 Zlo Zhi Volume t1 t1[3] com1[1] com1[2] com1[3] 0 299.15727 296.86626 -79.032419 79.032419 3556458.8 -27.556366 2.9283129 45.173312 60.280687 67.079637 500 298.58135 298.227 -78.910588 78.910588 3550976.5 -74.365306 -250.96153 45.213992 60.304604 67.054841 1000 302.50496 299.07291 -78.877126 78.877126 3549470.7 115.31404 93.312534 45.203375 60.280098 66.988138 1500 300.57252 299.54968 -78.868804 78.868804 3549096.2 220.55472 182.86347 45.184325 60.276215 66.976149 2000 297.58343 297.47564 -78.843635 78.843635 3547963.6 171.33721 133.99684 45.191128 60.298444 66.93063 Loop time of 161.933 on 660 procs for 2000 steps with 302509 atoms Performance: 2.134 ns/day, 11.245 hours/ns, 12.351 timesteps/s 95.3% CPU use with 660 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9206 | 17.19 | 26.076 | 134.8 | 10.62 Bond | 0.0038195 | 0.10219 | 1.0043 | 56.6 | 0.06 Kspace | 16.967 | 31.233 | 46.095 | 110.8 | 19.29 Neigh | 38.252 | 40.516 | 41.272 | 6.2 | 25.02 Comm | 35.871 | 40.052 | 50.997 | 30.7 | 24.73 Output | 0.017467 | 0.018699 | 0.021924 | 0.2 | 0.01 Modify | 24.875 | 26.858 | 30.237 | 22.6 | 16.59 Other | | 5.963 | | | 3.68 Nlocal: 458.347 ave 591 max 0 min Histogram: 69 9 10 7 10 9 14 21 93 418 Nghost: 217669 ave 230666 max 199302 min Histogram: 10 26 42 61 70 105 120 118 68 40 Neighs: 257141 ave 356965 max 0 min Histogram: 73 11 16 6 17 18 15 53 290 161 Total # of neighbors = 169712901 Ave neighs/atom = 561.018 Ave special neighs/atom = 3.37658 Neighbor list builds = 250 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:47