1LAMMPS (31 Jul 2019) 2 using 1 OpenMP thread(s) per MPI task 3# Initialization 4units metal 5boundary p p p 6atom_style full 7processors * * 1 # domain decomposition over x and y 8 9# System and atom definition 10# we use 2 atom types so that inter- and intra-layer 11# interactions can be specified separately 12read_data hBN_AB_stack_2L_noH_equi_300K.data 13 orthogonal box = (0 0 0) to (43.38 42.5773 100) 14 1 by 1 by 1 MPI processor grid 15 reading atoms ... 16 1360 atoms 17 reading velocities ... 18 1360 velocities 19 0 = max # of 1-2 neighbors 20 0 = max # of 1-3 neighbors 21 0 = max # of 1-4 neighbors 22 1 = max # of special neighbors 23 special bonds CPU = 0.000251532 secs 24 read_data CPU = 0.00451231 secs 25mass 1 10.8110 # boron mass (g/mole) | membrane 26mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate 27mass 3 10.8110 # boron mass (g/mole) | membrane 28mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate 29# Separate atom groups 30group membrane type 1 2 31680 atoms in group membrane 32group adsorbate type 3 4 33680 atoms in group adsorbate 34 35######################## Potential defition ######################## 36pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 37#################################################################### 38pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical 39Reading potential file BNC.tersoff with DATE: 2013-03-21 40pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range 41pair_coeff 1 3 coul/shield 0.70 42pair_coeff 1 4 coul/shield 0.69498201415576216335 43pair_coeff 2 3 coul/shield 0.69498201415576216335 44pair_coeff 2 4 coul/shield 0.69 45#################################################################### 46# Neighbor update settings 47neighbor 2.0 bin 48neigh_modify every 1 49neigh_modify delay 0 50neigh_modify check yes 51 52#### Simulation settings #### 53timestep 0.001 54#velocity adsorbate create 300.0 12345 55fix subf membrane setforce 0.0 0.0 0.0 56fix thermostat all nve 57 58compute 0 all pair tersoff 59compute 1 all pair coul/shield ecoul 60compute 2 all pair ilp/graphene/hbn 61variable Tersoff equal c_0 62variable Ecoul equal c_1 63variable ILP equal c_2 64variable Evdw equal c_2[1] 65variable Erep equal c_2[2] 66 67############################ 68 69# Output 70thermo 100 71thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp 72thermo_modify lost warn #ignore 73 74#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu 75#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes 76 77###### Run molecular dynamics ###### 78run 1000 79Neighbor list info ... 80 update every 1 steps, delay 0 steps, check yes 81 max neighbors/atom: 2000, page size: 100000 82 master list distance cutoff = 18 83 ghost atom cutoff = 18 84 binsize = 9, bins = 5 5 12 85 5 neighbor lists, perpetual/occasional/extra = 5 0 0 86 (1) pair tersoff, perpetual, skip from (4) 87 attributes: full, newton on 88 pair build: skip 89 stencil: none 90 bin: none 91 (2) pair ilp/graphene/hbn, perpetual 92 attributes: full, newton on, ghost 93 pair build: full/bin/ghost 94 stencil: full/ghost/bin/3d 95 bin: standard 96 (3) pair coul/shield, perpetual, skip from (5) 97 attributes: half, newton on 98 pair build: skip 99 stencil: none 100 bin: none 101 (4) neighbor class addition, perpetual, copy from (2) 102 attributes: full, newton on 103 pair build: copy 104 stencil: none 105 bin: none 106 (5) neighbor class addition, perpetual, half/full from (4) 107 attributes: half, newton on 108 pair build: halffull/newton 109 stencil: none 110 bin: none 111Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes 112Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 113 0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474 114 100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973 115 200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462 116 300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528 117 400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389 118 500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351 119 600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503 120 700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596 121 800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554 122 900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392 123 1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228 124Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms 125 126Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s 12799.9% CPU use with 1 MPI tasks x 1 OpenMP threads 128 129MPI task timing breakdown: 130Section | min time | avg time | max time |%varavg| %total 131--------------------------------------------------------------- 132Pair | 206.9 | 206.9 | 206.9 | 0.0 | 99.94 133Bond | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.00 134Neigh | 0 | 0 | 0 | 0.0 | 0.00 135Comm | 0.081397 | 0.081397 | 0.081397 | 0.0 | 0.04 136Output | 0.00036597 | 0.00036597 | 0.00036597 | 0.0 | 0.00 137Modify | 0.033408 | 0.033408 | 0.033408 | 0.0 | 0.02 138Other | | 0.01615 | | | 0.01 139 140Nlocal: 1360 ave 1360 max 1360 min 141Histogram: 1 0 0 0 0 0 0 0 0 0 142Nghost: 7840 ave 7840 max 7840 min 143Histogram: 1 0 0 0 0 0 0 0 0 0 144Neighs: 249628 ave 249628 max 249628 min 145Histogram: 1 0 0 0 0 0 0 0 0 0 146FullNghs: 253390 ave 253390 max 253390 min 147Histogram: 1 0 0 0 0 0 0 0 0 0 148 149Total # of neighbors = 253390 150Ave neighs/atom = 186.316 151Ave special neighs/atom = 0 152Neighbor list builds = 0 153Dangerous builds = 0 154Total wall time: 0:03:27 155