104 lines
3.9 KiB
Groff
104 lines
3.9 KiB
Groff
LAMMPS (30 Nov 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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# Generate tip
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units metal
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dimension 3
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boundary p p p
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atom_style atomic
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variable xm equal 10
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variable ym equal 10
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variable zm equal 5
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lattice diamond 5.481 # Si-Si
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Lattice spacing in x,y,z = 5.4810000 5.4810000 5.4810000
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region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm}
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region recbox block 0.0 10 0.0 ${ym} 0.0 ${zm}
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region recbox block 0.0 10 0.0 10 0.0 ${zm}
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region recbox block 0.0 10 0.0 10 0.0 5
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create_box 1 recbox
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.810000 54.810000 27.405000)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 region recbox units box
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Created 4000 atoms
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create_atoms CPU = 0.001 seconds
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mass * 28.0855
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pair_style tersoff shift 0.05
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pair_coeff * * Si.tersoff Si
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Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
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thermo_style custom step cpu etotal pe ke temp
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thermo 100
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thermo_modify flush yes norm no lost warn
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thermo_modify line one format float %20.15g
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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke temp
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:693)
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thermo_modify lost warn
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.2
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ghost atom cutoff = 5.2
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binsize = 2.6, bins = 22 22 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.127 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -18183.755 -18338.829 155.0734 300
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100 -18183.651 -18249.335 65.684288 127.07071
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200 -18183.643 -18241.96 58.317656 112.81946
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300 -18183.675 -18265.042 81.367616 157.41117
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400 -18183.661 -18257.198 73.536882 142.26208
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500 -18183.669 -18261.964 78.295204 151.46738
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600 -18183.665 -18258.552 74.886287 144.8726
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700 -18183.662 -18256.924 73.261529 141.7294
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800 -18183.67 -18263.155 79.484227 153.76763
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900 -18183.663 -18259.152 75.488804 146.03821
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1000 -18183.667 -18261.116 77.448767 149.82989
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Loop time of 2.63101 on 4 procs for 1000 steps with 4000 atoms
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Performance: 32.839 ns/day, 0.731 hours/ns, 380.082 timesteps/s
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99.6% CPU use with 4 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 | 2.4651 | 2.5025 | 2.5216 | 1.4 | 95.11
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.093127 | 0.11216 | 0.14937 | 6.5 | 4.26
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Output | 0.000129 | 0.00016075 | 0.000253 | 0.0 | 0.01
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Modify | 0.008488 | 0.0086423 | 0.008735 | 0.1 | 0.33
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Other | | 0.007586 | | | 0.29
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1470.00 ave 1470 max 1470 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 28000.0 ave 28000 max 28000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 112000
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Ave neighs/atom = 28.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:02
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