186 lines
8.2 KiB
Groff
186 lines
8.2 KiB
Groff
LAMMPS (19 May 2017)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
|
|
|
|
# Initialization
|
|
units metal
|
|
boundary p p p
|
|
atom_style atomic
|
|
|
|
# create simulation box and system
|
|
lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0
|
|
Lattice spacing in x,y,z = 5.90327 6.26136 5.11238
|
|
region mdbox block 0 3 0.0 14.0 0 84 units lattice
|
|
region system block 0 3 1.1 13.1 0 84 units lattice
|
|
create_box 2 mdbox
|
|
Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44)
|
|
1 by 1 by 4 MPI processor grid
|
|
create_atoms 1 region system
|
|
Created 48384 atoms
|
|
|
|
# Define atoms mass and force field
|
|
mass * 63.54
|
|
pair_style eam/alloy
|
|
pair_coeff * * Cu_Mishin1.eam Cu Cu
|
|
|
|
# Delete a plane of atoms along the z direction to generate a partial dislocation
|
|
region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
|
|
delete_atoms region dislocation_atoms
|
|
Deleted 76 atoms, new total = 48308
|
|
region quarter_up block 0 3 7 11 0 84 units lattice
|
|
group middle region quarter_up
|
|
16080 atoms in group middle
|
|
|
|
# specify simulation parameters
|
|
timestep 0.004
|
|
|
|
# Relax configuration using conjugate gradient
|
|
#min_style cg
|
|
#minimize 1.0e-4 1.0e-6 100 1000
|
|
|
|
# Setup calculations
|
|
compute 1 all cnp/atom 3.086
|
|
compute 2 all cna/atom 3.086
|
|
compute 3 all centro/atom fcc
|
|
compute 4 all coord/atom cutoff 3.086
|
|
dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4
|
|
|
|
### Set up thermo display
|
|
thermo 10
|
|
thermo_style custom step atoms temp press pe ke etotal
|
|
|
|
# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
|
|
fix 1 all nve
|
|
fix 2 all langevin 50 1 0.1 699483
|
|
fix 3 all setforce NULL 0.0 NULL
|
|
fix 4 middle setforce 0.0 0.0 0.0
|
|
run 100
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 7.50679
|
|
ghost atom cutoff = 7.50679
|
|
binsize = 3.75339, bins = 5 24 115
|
|
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
|
(1) pair eam/alloy, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
(2) compute cnp/atom, occasional
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
(3) compute cna/atom, occasional
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
(4) compute centro/atom, occasional
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
(5) compute coord/atom, occasional
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
|
|
Step Atoms Temp Press PotEng KinEng TotEng
|
|
0 48308 0 -3388.0911 -169746.07 0 -169746.07
|
|
10 48308 7.35092 -3091.0864 -169715.96 45.900393 -169670.05
|
|
20 48308 9.9162268 -2822.7045 -169678.51 61.918604 -169616.59
|
|
30 48308 12.351316 -2726.7195 -169666.35 77.123716 -169589.23
|
|
40 48308 13.302856 -2703.586 -169662.9 83.06529 -169579.83
|
|
50 48308 12.782228 -2706.8662 -169662.36 79.814401 -169582.55
|
|
60 48308 12.198179 -2772.4206 -169670.02 76.167503 -169593.86
|
|
70 48308 10.663322 -2841.3384 -169677.48 66.583595 -169610.9
|
|
80 48308 9.1169804 -2932.3896 -169687.85 56.927974 -169630.92
|
|
90 48308 7.2905076 -3029.9433 -169699.09 45.523167 -169653.56
|
|
100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89
|
|
Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms
|
|
|
|
Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s
|
|
31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 9.8764 | 9.9587 | 10.021 | 1.6 | 91.36
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.1232 | 0.18385 | 0.26683 | 12.1 | 1.69
|
|
Output | 0.45385 | 0.45451 | 0.45634 | 0.2 | 4.17
|
|
Modify | 0.25026 | 0.2537 | 0.25744 | 0.5 | 2.33
|
|
Other | | 0.04949 | | | 0.45
|
|
|
|
Nlocal: 12077 ave 12096 max 12020 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
|
Nghost: 14204 ave 14261 max 14109 min
|
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
|
Neighs: 814050 ave 818584 max 809212 min
|
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
|
FullNghs: 1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min
|
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
|
|
Total # of neighbors = 6512400
|
|
Ave neighs/atom = 134.81
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
unfix 4
|
|
run 200
|
|
Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
|
|
Step Atoms Temp Press PotEng KinEng TotEng
|
|
100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89
|
|
110 48308 15.260795 -2793.119 -169677.24 95.290993 -169581.95
|
|
120 48308 18.548656 -2433.1584 -169624.79 115.82096 -169508.97
|
|
130 48308 22.15831 -2276.626 -169604.28 138.36025 -169465.92
|
|
140 48308 24.393841 -2208.1771 -169596.16 152.31929 -169443.84
|
|
150 48308 24.797558 -2173.3145 -169591.43 154.84016 -169436.59
|
|
160 48308 24.73371 -2188.909 -169593.08 154.44148 -169438.64
|
|
170 48308 24.128467 -2220.3404 -169596.96 150.66225 -169446.29
|
|
180 48308 22.975708 -2275.1244 -169602.72 143.46422 -169459.26
|
|
190 48308 21.936324 -2348.3762 -169610.59 136.97413 -169473.61
|
|
200 48308 20.516249 -2432.8447 -169619.98 128.10694 -169491.87
|
|
210 48308 19.000566 -2510.2915 -169628.58 118.64276 -169509.93
|
|
220 48308 17.490407 -2597.299 -169638.24 109.21307 -169529.03
|
|
230 48308 16.062482 -2684.1203 -169648.31 100.29687 -169548.01
|
|
240 48308 14.360342 -2768.2313 -169657.7 89.668411 -169568.03
|
|
250 48308 12.802315 -2852.6965 -169666.99 79.939831 -169587.05
|
|
260 48308 11.258205 -2944.4533 -169677.52 70.298142 -169607.23
|
|
270 48308 9.6159129 -3038.6304 -169688.06 60.043393 -169628.02
|
|
280 48308 7.972425 -3129.0826 -169698.03 49.781176 -169648.25
|
|
290 48308 6.3752377 -3219.2054 -169708.23 39.808067 -169668.42
|
|
300 48308 4.7374688 -3306.1468 -169718.27 29.58156 -169688.69
|
|
Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms
|
|
|
|
Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s
|
|
31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 20.221 | 20.423 | 20.57 | 3.1 | 88.73
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.27748 | 0.42603 | 0.62832 | 21.4 | 1.85
|
|
Output | 1.5454 | 1.5473 | 1.5529 | 0.3 | 6.72
|
|
Modify | 0.48886 | 0.49773 | 0.50842 | 1.1 | 2.16
|
|
Other | | 0.1221 | | | 0.53
|
|
|
|
Nlocal: 12077 ave 12096 max 12020 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
|
Nghost: 14204 ave 14261 max 14109 min
|
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
|
Neighs: 814094 ave 818584 max 809212 min
|
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
|
FullNghs: 1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 1 0 2
|
|
|
|
Total # of neighbors = 6514094
|
|
Ave neighs/atom = 134.845
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:35
|