242 lines
14 KiB
Groff
242 lines
14 KiB
Groff
LAMMPS (4 May 2022)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
|
# Green-Kubo method via compute heat/flux and fix ave/correlate
|
|
|
|
# settings
|
|
|
|
variable x equal 10
|
|
variable y equal 10
|
|
variable z equal 10
|
|
|
|
variable rho equal 0.6
|
|
variable t equal 1.35
|
|
variable rc equal 2.5
|
|
|
|
#variable rho equal 0.85
|
|
#variable t equal 0.7
|
|
#variable rc equal 3.0
|
|
|
|
variable p equal 200 # correlation length
|
|
variable s equal 10 # sample interval
|
|
variable d equal $p*$s # dump interval
|
|
variable d equal 200*$s
|
|
variable d equal 200*10
|
|
|
|
# setup problem
|
|
|
|
units lj
|
|
atom_style atomic
|
|
|
|
lattice fcc ${rho}
|
|
lattice fcc 0.6
|
|
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
|
region box block 0 $x 0 $y 0 $z
|
|
region box block 0 10 0 $y 0 $z
|
|
region box block 0 10 0 10 0 $z
|
|
region box block 0 10 0 10 0 10
|
|
create_box 1 box
|
|
Created orthogonal box = (0 0 0) to (18.820721 18.820721 18.820721)
|
|
2 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 4000 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 18.820721)
|
|
create_atoms CPU = 0.001 seconds
|
|
mass 1 1.0
|
|
|
|
velocity all create $t 87287
|
|
velocity all create 1.35 87287
|
|
|
|
pair_style lj/cut ${rc}
|
|
pair_style lj/cut 2.5
|
|
pair_coeff 1 1 1.0 1.0
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 0 every 1
|
|
|
|
# 1st equilibration run
|
|
|
|
fix 1 all nvt temp $t $t 0.5
|
|
fix 1 all nvt temp 1.35 $t 0.5
|
|
fix 1 all nvt temp 1.35 1.35 0.5
|
|
thermo 100
|
|
run 1000
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 2.8
|
|
ghost atom cutoff = 2.8
|
|
binsize = 1.4, bins = 14 14 14
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.108 | 3.108 | 3.108 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
|
|
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
|
|
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
|
|
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
|
|
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
|
|
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
|
|
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
|
|
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
|
|
800 1.3489121 -3.7082852 0 -1.6854229 0.86438061
|
|
900 1.3708803 -3.6966168 0 -1.6408103 0.921415
|
|
1000 1.3640742 -3.7075319 0 -1.6619322 0.86651332
|
|
Loop time of 0.508902 on 8 procs for 1000 steps with 4000 atoms
|
|
|
|
Performance: 848886.657 tau/day, 1965.015 timesteps/s
|
|
98.2% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.25474 | 0.26957 | 0.27746 | 1.4 | 52.97
|
|
Neigh | 0.11684 | 0.12283 | 0.13178 | 1.3 | 24.14
|
|
Comm | 0.07187 | 0.089583 | 0.10975 | 3.5 | 17.60
|
|
Output | 0.00026594 | 0.00041865 | 0.0014818 | 0.0 | 0.08
|
|
Modify | 0.016091 | 0.017624 | 0.018502 | 0.7 | 3.46
|
|
Other | | 0.008882 | | | 1.75
|
|
|
|
Nlocal: 500 ave 510 max 479 min
|
|
Histogram: 1 0 0 0 0 2 1 1 0 3
|
|
Nghost: 1519 ave 1539 max 1509 min
|
|
Histogram: 2 0 4 0 0 0 0 1 0 1
|
|
Neighs: 13553.8 ave 14051 max 12567 min
|
|
Histogram: 1 0 0 0 1 0 2 1 1 2
|
|
|
|
Total # of neighbors = 108430
|
|
Ave neighs/atom = 27.1075
|
|
Neighbor list builds = 155
|
|
Dangerous builds = 0
|
|
|
|
velocity all scale $t
|
|
velocity all scale 1.35
|
|
|
|
unfix 1
|
|
|
|
# thermal conductivity calculation
|
|
|
|
reset_timestep 0
|
|
|
|
compute myKE all ke/atom
|
|
compute myPE all pe/atom
|
|
compute myStress all stress/atom NULL virial
|
|
compute flux all heat/flux myKE myPE myStress
|
|
variable Jx equal c_flux[1]/vol
|
|
variable Jy equal c_flux[2]/vol
|
|
variable Jz equal c_flux[3]/vol
|
|
|
|
fix 1 all nve
|
|
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
|
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
|
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
|
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
|
|
|
variable scale equal $s*dt/$t/$t/vol
|
|
variable scale equal 10*dt/$t/$t/vol
|
|
variable scale equal 10*dt/1.35/$t/vol
|
|
variable scale equal 10*dt/1.35/1.35/vol
|
|
variable k11 equal trap(f_JJ[3])*${scale}
|
|
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
|
|
variable k22 equal trap(f_JJ[4])*${scale}
|
|
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
|
|
variable k33 equal trap(f_JJ[5])*${scale}
|
|
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
|
|
variable kappa equal (v_k11+v_k22+v_k33)/3.0
|
|
|
|
thermo $d
|
|
thermo 2000
|
|
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 v_kappa
|
|
thermo_modify colname v_Jx Jx colname v_Jy Jy colname v_Jz Jz colname v_k11 kappa_11 colname v_k22 kappa_22 colname v_k33 kappa_33 colname v_kappa kappa
|
|
|
|
run 100000
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes
|
|
Step Temp Jx Jy Jz kappa_11 kappa_22 kappa_33 kappa
|
|
0 1.35 0.012561273 -0.087295611 -0.037041124 0.014429409 0.69689289 0.12547278 0.27893169
|
|
2000 1.3455113 -0.034571206 -0.17570902 -0.057218308 -1.6110148 7.9287556 8.5035767 4.9404392
|
|
4000 1.3477761 -0.029528723 0.018790489 0.056107464 7.698411 1.9459053 9.9605272 6.5349478
|
|
6000 1.3411436 -0.20281149 0.2184806 0.036024028 4.6533075 1.6223216 3.7246529 3.3334273
|
|
8000 1.3561682 0.12038719 0.034930957 0.12173601 4.6450263 1.9032849 2.7566363 3.1016492
|
|
10000 1.3397694 -0.14241489 -0.10956496 0.053088086 6.4191535 3.1582257 2.2786677 3.9520156
|
|
12000 1.3410756 0.0033462395 0.14337321 0.16381733 5.9663779 1.6774436 1.7442075 3.129343
|
|
14000 1.3484928 0.0080419803 -0.080232102 0.039035519 4.9483626 1.6210893 1.6103343 2.7265954
|
|
16000 1.3414836 -0.11063045 -0.031557643 0.032060333 6.1381241 1.438198 1.5831541 3.0531587
|
|
18000 1.3488617 0.15908507 -0.021418806 -0.13992507 5.9198613 1.1016464 1.2905478 2.7706852
|
|
20000 1.3535727 0.13217689 0.071933521 -0.028452943 6.3746606 1.003194 1.7007101 3.0261882
|
|
22000 1.3408534 -0.078953557 -0.0022323663 -0.22979033 5.0105241 1.1489328 1.720847 2.626768
|
|
24000 1.34722 0.074784199 -0.071218632 0.15238165 4.4835452 0.94086945 3.1603615 2.8615921
|
|
26000 1.3539218 0.052534363 0.10419096 0.1866213 4.2233104 1.3973253 3.2802881 2.9669746
|
|
28000 1.3510105 0.0080425673 -0.03723976 0.20758595 5.261917 1.1931088 3.498831 3.3179523
|
|
30000 1.3410807 -0.043957884 0.065683978 0.015386362 4.3815277 1.5000017 3.2237565 3.0350953
|
|
32000 1.34766 -0.060481287 0.17142383 0.034367135 4.0974942 1.1637027 3.3771953 2.8794641
|
|
34000 1.3417583 -0.10055844 0.050237668 0.06974988 4.1478021 1.0235517 2.9440249 2.7051263
|
|
36000 1.3468728 0.09375756 -0.17875264 -0.063513807 4.4412987 0.71084371 3.4316313 2.8612579
|
|
38000 1.3496868 -0.038635804 0.117965 0.018050271 4.962332 0.41701129 3.4690212 2.9494548
|
|
40000 1.3403452 -0.092158116 0.14432655 -0.062258229 4.9980486 0.3762815 3.1688552 2.8477284
|
|
42000 1.3498661 0.085807945 0.010256385 -0.002956898 4.8200626 0.29278287 3.094633 2.7358261
|
|
44000 1.3564084 -0.07415163 -0.051327929 -0.18457986 4.7070907 0.3358167 3.0741797 2.7056957
|
|
46000 1.3435866 -0.013911463 0.081813372 0.022628846 4.6043718 0.3682401 2.9956189 2.6560769
|
|
48000 1.350611 0.036512747 0.080481423 -0.22973181 4.5648715 0.32728516 3.8573343 2.916497
|
|
50000 1.3421783 0.057665789 0.075597141 0.17377918 4.4278473 0.5383886 3.5866168 2.8509509
|
|
52000 1.3473497 -0.11159587 -0.09688769 0.19876168 4.3876613 0.43408155 3.4786305 2.7667911
|
|
54000 1.3459495 -0.15341705 0.063996148 -0.0038254597 4.8434026 0.62047297 3.445187 2.9696875
|
|
56000 1.3545654 -0.082406034 0.089232864 -0.024355614 4.546051 0.7367607 3.3694561 2.8840893
|
|
58000 1.3577504 0.082844384 0.019500036 0.073721698 4.4061886 1.4575694 3.2754066 3.0463882
|
|
60000 1.348614 -0.16190321 -0.048576343 0.093820555 4.2946463 1.3416919 3.1159234 2.9174205
|
|
62000 1.3551143 0.097443296 -0.04420265 -0.25713945 4.1260882 1.2550603 3.063215 2.8147879
|
|
64000 1.346239 0.019198575 -0.095746619 0.18383922 4.5691519 1.2615165 2.9935539 2.9414074
|
|
66000 1.3535383 -0.0035547901 -0.1753318 0.014025292 4.5371394 1.0740671 2.9362916 2.8491661
|
|
68000 1.3421249 -0.18217113 0.077901408 0.04314081 5.1644747 1.0218342 2.9789097 3.0550729
|
|
70000 1.3446114 0.029565781 -0.13771336 0.050328878 5.4811405 1.0430806 2.9748623 3.1663612
|
|
72000 1.3692655 0.005711741 0.13966773 -0.062638787 5.3033385 1.1040582 2.7599218 3.0557729
|
|
74000 1.3405365 -0.054281977 0.038019086 -0.024980877 5.1246258 2.0782965 2.725331 3.3094177
|
|
76000 1.3644178 0.040847675 -0.051968108 -0.12259032 5.1218657 1.8504273 2.6804003 3.2175644
|
|
78000 1.353792 -0.093663092 0.018784967 -0.073871437 5.025196 1.7789709 2.5339006 3.1126891
|
|
80000 1.3520982 -0.09407101 0.010328039 0.0028841073 5.1410049 1.855057 2.6935895 3.2298838
|
|
82000 1.3447597 -0.11935066 -0.2184608 0.073543056 5.2645334 1.7883077 4.2012292 3.7513568
|
|
84000 1.3712151 -0.064367612 0.021246872 -0.033571866 5.0479674 1.8947341 4.3856536 3.7761184
|
|
86000 1.3453867 -0.029842112 -0.042297039 0.05422886 5.0667777 2.0365983 4.4542311 3.8525357
|
|
88000 1.3439543 -0.21625828 -0.028119372 -0.010320332 4.9946428 2.3095763 4.3429587 3.8823926
|
|
90000 1.3472579 0.058391002 0.037139373 0.03424008 5.0599004 2.8132794 4.4503426 4.1078408
|
|
92000 1.361788 0.028891114 0.072799744 -0.12035229 4.8759851 2.5130025 4.2747068 3.8878981
|
|
94000 1.3440566 0.043421348 0.049653856 -0.060444094 4.8884081 2.5072981 4.3105221 3.9020761
|
|
96000 1.3537566 0.088733517 -0.11449828 -0.049852036 4.8115085 2.4780963 4.2213579 3.8369876
|
|
98000 1.3373399 0.25457663 -0.041723778 0.00084565184 4.7163394 2.4100822 4.485536 3.8706525
|
|
100000 1.3487502 0.046333889 0.1247351 0.063467467 4.6563279 2.4049358 4.5742925 3.8785187
|
|
Loop time of 53.5266 on 8 procs for 100000 steps with 4000 atoms
|
|
|
|
Performance: 807074.833 tau/day, 1868.229 timesteps/s
|
|
98.9% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 29.794 | 30.392 | 31.376 | 8.7 | 56.78
|
|
Neigh | 12.248 | 12.475 | 12.79 | 4.5 | 23.31
|
|
Comm | 6.5584 | 7.5712 | 8.3818 | 19.5 | 14.14
|
|
Output | 0.016848 | 0.067296 | 0.074694 | 7.4 | 0.13
|
|
Modify | 2.0311 | 2.0593 | 2.1324 | 2.1 | 3.85
|
|
Other | | 0.9616 | | | 1.80
|
|
|
|
Nlocal: 500 ave 505 max 491 min
|
|
Histogram: 1 0 0 1 0 1 0 2 2 1
|
|
Nghost: 1529.88 ave 1548 max 1508 min
|
|
Histogram: 1 1 0 0 1 1 2 0 0 2
|
|
Neighs: 13569.8 ave 13906 max 13235 min
|
|
Histogram: 1 1 0 1 1 1 1 1 0 1
|
|
|
|
Total # of neighbors = 108558
|
|
Ave neighs/atom = 27.1395
|
|
Neighbor list builds = 16041
|
|
Dangerous builds = 0
|
|
|
|
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
|
Running average thermal conductivity: 3.88
|
|
Total wall time: 0:00:54
|