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 ######################################################### balance 1.05 shift xyz 20 1.05 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 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 iteration count = 16 initial/final max atoms/proc = 582 797 initial/final imbalance factor = 1.26978 1.73886 x cuts: 0 0.158854 0.299479 0.434896 0.591146 0.794271 1 y cuts: 0 0.115625 0.215625 0.296875 0.384375 0.465625 0.553125 0.640625 0.746875 0.871875 1 z cuts: 0 0.110795 0.201705 0.28125 0.355114 0.434659 0.508523 0.588068 0.667614 0.764205 0.877841 1 ################################################################### # 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 = 3276 832 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) 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] ######################################################## timestep 2.0 fix bal water balance 500 1.05 shift xyz 20 1.05 dump 2 colloid image 500 ./660procs/cpu.*.jpg type type zoom 1.5 subbox yes 0.02 dump_modify 2 adiam 11 5 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 = 3276 832 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:442) Memory usage per processor = 254.325 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 500 298.49359 298.40136 -78.909348 78.909348 3550920.7 104.97604 -95.360968 45.217686 60.302143 67.045553 1000 300.29046 298.16593 -78.888553 78.888553 3549984.9 -44.06474 -176.05688 45.174979 60.285288 67.006891 1500 297.4946 298.41964 -78.821075 78.821075 3546948.4 144.6112 -152.4279 45.14917 60.318315 66.835903 2000 298.80071 298.05089 -78.795666 78.795666 3545805 23.634669 -91.425901 45.220801 60.412718 66.825254 Loop time of 174.021 on 660 procs for 2000 steps with 302509 atoms Performance: 1.986 ns/day, 12.085 hours/ns, 11.493 timesteps/s 95.6% CPU use with 660 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5021 | 16.598 | 27.516 | 113.5 | 9.54 Bond | 0.0037603 | 0.091526 | 0.65288 | 56.5 | 0.05 Kspace | 17.107 | 34.481 | 47.732 | 85.9 | 19.81 Neigh | 46.612 | 47.807 | 48.32 | 4.2 | 27.47 Comm | 38.339 | 40.931 | 47.077 | 23.7 | 23.52 Output | 0.41217 | 0.41268 | 0.41575 | 0.0 | 0.24 Modify | 25.986 | 27.827 | 29.556 | 10.1 | 15.99 Other | | 5.873 | | | 3.37 Nlocal: 458.347 ave 775 max 0 min Histogram: 36 4 9 12 120 113 176 114 50 26 Nghost: 221204 ave 237151 max 210667 min Histogram: 49 104 117 94 87 65 57 51 28 8 Neighs: 257259 ave 448656 max 0 min Histogram: 38 10 12 19 118 125 170 100 50 18 Total # of neighbors = 169791234 Ave neighs/atom = 561.277 Ave special neighs/atom = 3.37658 Neighbor list builds = 254 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:03:00