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add example input for compute cnp/atom

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This commit is contained in:
Axel Kohlmeyer
2017-05-31 00:43:53 -04:00
parent 85e917ae52
commit 2b3c124e61
3 changed files with 30245 additions and 0 deletions
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examples/USER/misc/cnp/Cu_Mishin1.eam Normal file
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examples/USER/misc/cnp/in.cnp Normal file
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# 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
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
create_atoms 1 region system
# 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
region quarter_up block 0 3 7 11 0 84 units lattice
group middle region quarter_up
# 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
unfix 4
run 200

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examples/USER/misc/cnp/log.31May17.cnp.g++.4 Normal file
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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