5fd323fe32
- flatten directory structure - remove CPU time and reduce excess precision from output - delete redundant and unused files - regenerate reference outputs
128 lines
5.2 KiB
Groff
128 lines
5.2 KiB
Groff
LAMMPS (31 Jul 2019)
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using 1 OpenMP thread(s) per MPI task
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data Bi_gr_AB_stack_2L_noH.data
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orthogonal box = (0 0 0) to (42.6 41.8117 100)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1360 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000290871 secs
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read_data CPU = 0.00159073 secs
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group layer1 molecule 1
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680 atoms in group layer1
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group layer2 molecule 2
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680 atoms in group layer2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
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####################################################################
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pair_coeff * * rebo CH.rebo C C # chemical
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Reading potential file CH.rebo with DATE: 2018-7-3
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pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345
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compute 0 all pair rebo
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compute 1 all pair ilp/graphene/hbn
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variable REBO equal c_0 # REBO energy
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variable ILP equal c_1 # total interlayer energy
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variable Evdw equal c_1[1] # attractive energy
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variable Erep equal c_1[2] # repulsive energy
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############################
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# Output
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thermo 100
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thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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fix thermostat all nve
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 5 5 12
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair rebo, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) pair ilp/graphene/hbn, perpetual, copy from (1)
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attributes: full, newton on, ghost
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
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Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
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0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
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100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
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200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
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300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
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400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
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500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
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600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
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700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
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800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
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900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
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1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
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Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
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Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 149.75 | 149.75 | 149.75 | 0.0 | 99.91
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Bond | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.086328 | 0.086328 | 0.086328 | 0.0 | 0.06
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Output | 0.00036383 | 0.00036383 | 0.00036383 | 0.0 | 0.00
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Modify | 0.028636 | 0.028636 | 0.028636 | 0.0 | 0.02
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Other | | 0.01708 | | | 0.01
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Nlocal: 1360 ave 1360 max 1360 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7964 ave 7964 max 7964 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1037000
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Ave neighs/atom = 762.5
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:02:30
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