133 lines
5.2 KiB
Groff
133 lines
5.2 KiB
Groff
LAMMPS (30 Apr 2019)
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using 1 OpenMP thread(s) per MPI task
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units metal
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kim_style init ex_sim_model_Si_mod_tersoff
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units metal
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newton on
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atom_style atomic
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atom_modify map array
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boundary p p p
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# temperatures
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variable tlo equal 1800.0
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variable thi equal 2400.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region myreg block 0 4 0 4 0 4
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create_box 1 myreg
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region myreg
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Created 512 atoms
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create_atoms CPU = 0.000393867 secs
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mass 1 28.06
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group Si type 1
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512 atoms in group Si
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velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
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velocity all create 2400 5287286 mom yes rot yes dist gaussian
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# make a vacancy
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group del id 300
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1 atoms in group del
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delete_atoms group del
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Deleted 1 atoms, new total = 511
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kim_style define Si
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Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff
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For Simulator : LAMMPS 12-Dec-2018
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Running on : LAMMPS 30 Apr 2019
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pair_style tersoff/mod
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pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV Si
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Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV with DATE: 2013-07-26
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thermo 10
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fix 1 all nve
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fix 2 all langevin ${thi} ${thi} 0.1 48278
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fix 2 all langevin 2400 ${thi} 0.1 48278
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fix 2 all langevin 2400 2400 0.1 48278
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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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 = 4.3
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ghost atom cutoff = 4.3
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binsize = 2.15, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/mod, 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) = 3.11 | 3.11 | 3.11 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2397.3877 -2363.0694 0 -2205.0272 15086.224
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10 1328.4035 -2289.1682 0 -2201.5963 29164.666
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20 1086.1557 -2254.4447 0 -2182.8424 31906.878
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30 1528.8439 -2270.2968 0 -2169.5113 21610.528
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40 1345.227 -2250.3915 0 -2161.7105 22146.886
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50 1300.3329 -2235.8593 0 -2150.1379 23557.875
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60 1546.1664 -2241.3019 0 -2139.3744 21648.774
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70 1662.2896 -2236.2369 0 -2126.6543 23958.738
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80 1631.7284 -2223.45 0 -2115.8821 28842.194
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90 1795.3629 -2225.2998 0 -2106.9447 29522.37
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100 1830.156 -2224.3733 0 -2103.7245 28805.09
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Loop time of 0.201725 on 1 procs for 100 steps with 511 atoms
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Performance: 42.831 ns/day, 0.560 hours/ns, 495.724 timesteps/s
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99.3% 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 | 0.19292 | 0.19292 | 0.19292 | 0.0 | 95.63
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Neigh | 0.0037313 | 0.0037313 | 0.0037313 | 0.0 | 1.85
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Comm | 0.00074744 | 0.00074744 | 0.00074744 | 0.0 | 0.37
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Output | 0.00026727 | 0.00026727 | 0.00026727 | 0.0 | 0.13
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Modify | 0.0036564 | 0.0036564 | 0.0036564 | 0.0 | 1.81
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Other | | 0.0004075 | | | 0.20
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Nlocal: 511 ave 511 max 511 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 970 ave 970 max 970 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: 9174 ave 9174 max 9174 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9174
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Ave neighs/atom = 17.953
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Neighbor list builds = 4
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Dangerous builds = 0
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Total wall time: 0:00:00
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