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 different molecule ids for each layer 11# so that inter- and intra-layer 12# interactions can be specified separately 13read_data gr_hBN_Cstack_2L_noH.data 14 orthogonal box = (0 0 0) to (44.583 42.9 100) 15 1 by 1 by 1 MPI processor grid 16 reading atoms ... 17 1440 atoms 18 0 = max # of 1-2 neighbors 19 0 = max # of 1-3 neighbors 20 0 = max # of 1-4 neighbors 21 1 = max # of special neighbors 22 special bonds CPU = 0.000282049 secs 23 read_data CPU = 0.00159025 secs 24mass 1 10.8110 # boron mass (g/mole) | membrane 25mass 2 14.0067 # nitrogen mass (g/mole) | membrane 26mass 3 12.0107 # carbon mass (g/mole) | adsorbate 27# Separate atom groups 28group hBN molecule 1 29720 atoms in group hBN 30group gr molecule 2 31720 atoms in group gr 32 33######################## Potential defition ######################## 34pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 35#################################################################### 36pair_coeff * * rebo CH.rebo NULL NULL C # chemical 37Reading potential file CH.rebo with DATE: 2018-7-3 38pair_coeff * * tersoff BNC.tersoff B N NULL # chemical 39Reading potential file BNC.tersoff with DATE: 2013-03-21 40pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range 41pair_coeff 1 1 coul/shield 0.70 42pair_coeff 1 2 coul/shield 0.69498201415576216335 43pair_coeff 2 2 coul/shield 0.69 44#################################################################### 45# Neighbor update settings 46neighbor 2.0 bin 47neigh_modify every 1 48neigh_modify delay 0 49neigh_modify check yes 50 51#### Simulation settings #### 52timestep 0.001 53velocity all create 300.0 12345 dist gaussian mom yes rot yes 54fix thermostat all nve 55 56compute 0 all pair rebo 57compute 1 all pair tersoff 58compute 2 all pair ilp/graphene/hbn 59compute 3 all pair coul/shield 60variable REBO equal c_0 61variable Tersoff equal c_1 62variable EILP equal c_2 # total interlayer energy 63variable Evdw equal c_2[1] # attractive energy 64variable Erep equal c_2[2] # repulsive energy 65variable Ecoul equal c_3 66 67############# Output ############## 68thermo 100 69thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp 70 71###### Run molecular dynamics ###### 72run 1000 73Neighbor list info ... 74 update every 1 steps, delay 0 steps, check yes 75 max neighbors/atom: 2000, page size: 100000 76 master list distance cutoff = 18 77 ghost atom cutoff = 18 78 binsize = 9, bins = 5 5 12 79 6 neighbor lists, perpetual/occasional/extra = 6 0 0 80 (1) pair rebo, perpetual, skip from (3) 81 attributes: full, newton on, ghost 82 pair build: skip/ghost 83 stencil: none 84 bin: none 85 (2) pair tersoff, perpetual, skip from (5) 86 attributes: full, newton on 87 pair build: skip 88 stencil: none 89 bin: none 90 (3) pair ilp/graphene/hbn, perpetual 91 attributes: full, newton on, ghost 92 pair build: full/bin/ghost 93 stencil: full/ghost/bin/3d 94 bin: standard 95 (4) pair coul/shield, perpetual, half/full from (2) 96 attributes: half, newton on 97 pair build: halffull/newton/skip 98 stencil: none 99 bin: none 100 (5) neighbor class addition, perpetual, copy from (3) 101 attributes: full, newton on 102 pair build: copy 103 stencil: none 104 bin: none 105 (6) neighbor class addition, perpetual, half/full from (5) 106 attributes: half, newton on 107 pair build: halffull/newton 108 stencil: none 109 bin: none 110Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes 111Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 112 0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300 113 100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347 114 200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042 115 300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194 116 400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706 117 500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121 118 600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561 119 700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921 120 800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494 121 900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783 122 1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466 123Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms 124 125Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 timesteps/s 12699.8% CPU use with 1 MPI tasks x 1 OpenMP threads 127 128MPI task timing breakdown: 129Section | min time | avg time | max time |%varavg| %total 130--------------------------------------------------------------- 131Pair | 152.52 | 152.52 | 152.52 | 0.0 | 99.91 132Bond | 0.00023174 | 0.00023174 | 0.00023174 | 0.0 | 0.00 133Neigh | 0 | 0 | 0 | 0.0 | 0.00 134Comm | 0.087147 | 0.087147 | 0.087147 | 0.0 | 0.06 135Output | 0.0004189 | 0.0004189 | 0.0004189 | 0.0 | 0.00 136Modify | 0.029972 | 0.029972 | 0.029972 | 0.0 | 0.02 137Other | | 0.02057 | | | 0.01 138 139Nlocal: 1440 ave 1440 max 1440 min 140Histogram: 1 0 0 0 0 0 0 0 0 0 141Nghost: 8180 ave 8180 max 8180 min 142Histogram: 1 0 0 0 0 0 0 0 0 0 143Neighs: 140400 ave 140400 max 140400 min 144Histogram: 1 0 0 0 0 0 0 0 0 0 145FullNghs: 280800 ave 280800 max 280800 min 146Histogram: 1 0 0 0 0 0 0 0 0 0 147 148Total # of neighbors = 280800 149Ave neighs/atom = 195 150Ave special neighs/atom = 0 151Neighbor list builds = 0 152Dangerous builds = 0 153Total wall time: 0:02:32 154