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 of hBN 11# so that inter- and intra-layer 12# interactions can be specified separately 13read_data hBN_AA_prime_stack_2L_noH.data 14 orthogonal box = (0 0 0) to (43.38 42.5773 100) 15 1 by 1 by 1 MPI processor grid 16 reading atoms ... 17 1360 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 = 0.000375509 secs 23 read_data CPU = 0.00181293 secs 24mass 1 10.8110 # boron mass (g/mole) | membrane 25mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate 26mass 3 10.8110 # boron mass (g/mole) | membrane 27mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate 28# Separate atom groups 29group layer1 molecule 1 30680 atoms in group layer1 31group layer2 molecule 2 32680 atoms in group layer2 33 34######################## Potential defition ######################## 35pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 36#################################################################### 37pair_coeff * * tersoff BNC.tersoff B N B N # chemical 38Reading potential file BNC.tersoff with DATE: 2013-03-21 39pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range 40pair_coeff 1 3 coul/shield 0.70 41pair_coeff 1 4 coul/shield 0.69498201415576216335 42pair_coeff 2 3 coul/shield 0.69498201415576216335 43pair_coeff 2 4 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 tersoff 57compute 1 all pair coul/shield ecoul 58compute 2 all pair ilp/graphene/hbn 59variable Tersoff equal c_0 # Tersoff energy 60variable Ecoul equal c_1 # Coulomb energy 61variable EILP equal c_2 # total interlayer energy 62variable Evdw equal c_2[1] # attractive energy 63variable Erep equal c_2[2] # repulsive energy 64 65############# Output ############### 66thermo 100 67thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp 68thermo_modify lost warn 69 70###### Run molecular dynamics ###### 71run 1000 72Neighbor list info ... 73 update every 1 steps, delay 0 steps, check yes 74 max neighbors/atom: 2000, page size: 100000 75 master list distance cutoff = 18 76 ghost atom cutoff = 18 77 binsize = 9, bins = 5 5 12 78 4 neighbor lists, perpetual/occasional/extra = 4 0 0 79 (1) pair tersoff, perpetual 80 attributes: full, newton on 81 pair build: full/bin 82 stencil: full/bin/3d 83 bin: standard 84 (2) pair ilp/graphene/hbn, perpetual 85 attributes: full, newton on, ghost 86 pair build: full/bin/ghost 87 stencil: full/ghost/bin/3d 88 bin: standard 89 (3) pair coul/shield, perpetual, skip from (4) 90 attributes: half, newton on 91 pair build: skip 92 stencil: none 93 bin: none 94 (4) neighbor class addition, perpetual, half/full from (1) 95 attributes: half, newton on 96 pair build: halffull/newton 97 stencil: none 98 bin: none 99Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes 100Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 101 0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300 102 100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947 103 200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191 104 300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162 105 400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051 106 500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824 107 600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004 108 700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859 109 800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415 110 900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017 111 1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339 112Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms 113 114Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s 11599.9% CPU use with 1 MPI tasks x 1 OpenMP threads 116 117MPI task timing breakdown: 118Section | min time | avg time | max time |%varavg| %total 119--------------------------------------------------------------- 120Pair | 211.4 | 211.4 | 211.4 | 0.0 | 99.94 121Bond | 0.00018859 | 0.00018859 | 0.00018859 | 0.0 | 0.00 122Neigh | 0 | 0 | 0 | 0.0 | 0.00 123Comm | 0.082034 | 0.082034 | 0.082034 | 0.0 | 0.04 124Output | 0.00037289 | 0.00037289 | 0.00037289 | 0.0 | 0.00 125Modify | 0.027928 | 0.027928 | 0.027928 | 0.0 | 0.01 126Other | | 0.0159 | | | 0.01 127 128Nlocal: 1360 ave 1360 max 1360 min 129Histogram: 1 0 0 0 0 0 0 0 0 0 130Nghost: 7836 ave 7836 max 7836 min 131Histogram: 1 0 0 0 0 0 0 0 0 0 132Neighs: 249560 ave 249560 max 249560 min 133Histogram: 1 0 0 0 0 0 0 0 0 0 134FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min 135Histogram: 1 0 0 0 0 0 0 0 0 0 136 137Total # of neighbors = 1005040 138Ave neighs/atom = 739 139Ave special neighs/atom = 0 140Neighbor list builds = 0 141Dangerous builds = 0 142Total wall time: 0:03:31 143