rename example folders
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Axel Kohlmeyer
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LAMMPS (18 Sep 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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# ***
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# Example input for including electronic stopping effects using fix electron/stopping/fit
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# Al lattice with a single incident Cu atom - multiple species simulation
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# ***
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units metal
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boundary p p p
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lattice fcc 4.0495
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Lattice spacing in x,y,z = 4.0495000 4.0495000 4.0495000
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region box block -10 10 -10 10 -10 10
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create_box 2 box
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Created orthogonal box = (-40.495000 -40.495000 -40.495000) to (40.495000 40.495000 40.495000)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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create_atoms CPU = 0.001 seconds
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pair_style eam/alloy
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pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
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Reading eam/alloy potential file ../../../../potentials/AlCu.eam.alloy with DATE: 2008-10-01
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mass 1 26.982
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mass 2 63.546
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velocity all create 300 42534 mom yes rot yes
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set atom 1 type 2
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Setting atom values ...
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1 settings made for type
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group pka id 1
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1 atoms in group pka
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velocity pka set 1120 1620 400
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fix 1 all nve
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fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
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fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
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thermo 5
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thermo_style custom step dt time temp pe ke f_3
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thermo_modify lost warn flush yes
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#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
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#dump_modify 0 first 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 = 8.6825
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ghost atom cutoff = 8.6825
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binsize = 4.34125, bins = 19 19 19
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eam/alloy, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 9.014 | 9.014 | 9.014 Mbytes
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Step Dt Time Temp PotEng KinEng f_3
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0 2.4879625e-05 0 53029.167 -106186.96 219339 0
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5 2.4881895e-05 0.00012440247 53019.542 -106184.2 219299.18 36.968257
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10 1.0341742e-05 0.00021830123 53006.803 -106159.67 219246.49 64.866388
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15 5.6752732e-06 0.00025836298 52996.09 -106127.26 219202.18 76.76618
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20 4.0862174e-06 0.00028301112 52987.566 -106099.31 219166.93 84.086114
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25 3.3676848e-06 0.00030179899 52980.99 -106077.67 219139.73 89.664821
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30 3.021773e-06 0.00031783944 52976.302 -106063.02 219120.33 94.427181
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35 2.8935472e-06 0.00033261879 52973.489 -106055.77 219108.7 98.814784
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40 2.9393606e-06 0.00034710883 52972.541 -106056.15 219104.78 103.11632
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45 3.1821803e-06 0.00036219854 52973.425 -106064.29 219108.43 107.59586
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50 3.7436309e-06 0.00037905755 52976.071 -106080.26 219119.38 112.60079
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55 5.0681667e-06 0.0003999252 52980.343 -106104.15 219137.05 118.79618
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60 1.0187808e-05 0.00043197649 52985.861 -106136.51 219159.87 128.3128
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65 1.8643099e-05 0.00052944037 52985.278 -106162.53 219157.46 157.25436
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70 1.8445045e-05 0.00060999223 52977.928 -106155.89 219127.06 181.17146
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75 2.4893021e-05 0.00072688076 52972.393 -106168.08 219104.17 215.8731
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80 7.3916674e-06 0.0008114874 52959.382 -106139.9 219050.35 240.98764
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85 4.1550998e-06 0.00084037284 52948.08 -106101.75 219003.6 249.55971
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90 2.976545e-06 0.00085843108 52938.032 -106065.55 218962.04 254.91754
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95 2.3728646e-06 0.00087196913 52929.045 -106032.38 218924.87 258.93348
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100 2.0139362e-06 0.00088304819 52921.106 -106002.82 218892.03 262.21943
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Loop time of 2.45676 on 4 procs for 100 steps with 32000 atoms
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Performance: 0.007 ns/day, 3388.559 hours/ns, 40.704 timesteps/s
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99.8% 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 | 2.2127 | 2.2257 | 2.2399 | 0.8 | 90.59
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Neigh | 0.095856 | 0.097842 | 0.10197 | 0.8 | 3.98
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Comm | 0.03626 | 0.054908 | 0.069787 | 6.3 | 2.23
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Output | 0.00088538 | 0.0011005 | 0.0017236 | 1.1 | 0.04
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Modify | 0.072449 | 0.072553 | 0.072611 | 0.0 | 2.95
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Other | | 0.004684 | | | 0.19
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Nlocal: 8000.00 ave 8033 max 7977 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Nghost: 12605.0 ave 12628 max 12572 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Neighs: 703998.0 ave 706570 max 702282 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Total # of neighbors = 2815992
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Ave neighs/atom = 87.999750
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Neighbor list builds = 5
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Dangerous builds = 3
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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