244 lines
10 KiB
Groff
244 lines
10 KiB
Groff
LAMMPS (4 May 2022)
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using 1 OpenMP thread(s) per MPI task
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# sample LAMMPS input script for thermal conductivity of liquid LJ
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# use fix heat to add/subtract energy from 2 regions
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# settings
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variable x equal 10
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variable y equal 10
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variable z equal 20
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variable rho equal 0.6
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variable t equal 1.35
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variable rc equal 2.5
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#variable rho equal 0.85
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#variable t equal 0.7
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#variable rc equal 3.0
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# setup problem
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units lj
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atom_style atomic
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lattice fcc ${rho}
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lattice fcc 0.6
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Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
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region box block 0 $x 0 $y 0 $z
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region box block 0 10 0 $y 0 $z
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region box block 0 10 0 10 0 $z
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region box block 0 10 0 10 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
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2 by 1 by 4 MPI processor grid
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create_atoms 1 box
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Created 8000 atoms
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using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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velocity all create $t 87287
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velocity all create 1.35 87287
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1
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# heat layers
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region hot block INF INF INF INF 0 1
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region cold block INF INF INF INF 10 11
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compute Thot all temp/region hot
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compute Tcold all temp/region cold
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# 1st equilibration run
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fix 1 all nvt temp $t $t 0.5
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fix 1 all nvt temp 1.35 $t 0.5
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fix 1 all nvt temp 1.35 1.35 0.5
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thermo 100
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run 1000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 14 14 27
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.35 -4.1241917 0 -2.0994448 -3.1961612
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100 1.1819832 -3.7640881 0 -1.991335 0.53985757
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200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
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300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
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400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
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500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
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600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
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700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
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800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
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900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
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1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
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Loop time of 0.944921 on 8 procs for 1000 steps with 8000 atoms
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Performance: 457180.899 tau/day, 1058.289 timesteps/s
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98.4% CPU use with 8 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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Pair | 0.53036 | 0.5381 | 0.55265 | 1.0 | 56.95
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Neigh | 0.24246 | 0.24602 | 0.25063 | 0.5 | 26.04
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Comm | 0.092773 | 0.10258 | 0.11364 | 2.3 | 10.86
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Output | 0.0003103 | 0.0004958 | 0.0017848 | 0.0 | 0.05
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Modify | 0.033332 | 0.043019 | 0.054672 | 3.7 | 4.55
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Other | | 0.0147 | | | 1.56
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Nlocal: 1000 ave 1020 max 982 min
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Histogram: 1 0 2 1 0 1 1 1 0 1
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Nghost: 2299.5 ave 2331 max 2268 min
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Histogram: 1 1 1 1 0 0 0 3 0 1
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Neighs: 27122 ave 28382 max 26337 min
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Histogram: 2 0 2 1 1 0 0 1 0 1
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Total # of neighbors = 216976
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Ave neighs/atom = 27.122
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Neighbor list builds = 162
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Dangerous builds = 0
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velocity all scale $t
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velocity all scale 1.35
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unfix 1
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# 2nd equilibration run
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fix 1 all nve
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fix hot all heat 1 100.0 region hot
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fix cold all heat 1 -100.0 region cold
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thermo_style custom step temp c_Thot c_Tcold
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thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
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thermo 1000
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run 10000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.156 | 3.156 | 3.156 Mbytes
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Step Temp Temp_hot Temp_cold
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1000 1.35 1.431295 1.2955644
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2000 1.3518468 1.5562602 1.154905
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3000 1.3477229 1.5890075 1.2395414
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4000 1.3487175 1.5491615 1.2019696
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5000 1.3594394 1.5780597 1.1824492
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6000 1.3583923 1.541735 1.1675586
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7000 1.3700321 1.6735877 1.1279114
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8000 1.3631993 1.6367675 1.0697225
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9000 1.3739201 1.6846211 1.1138829
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10000 1.3751455 1.8039471 1.1500399
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11000 1.3716416 1.833336 1.1267278
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Loop time of 11.4492 on 8 procs for 10000 steps with 8000 atoms
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Performance: 377320.435 tau/day, 873.427 timesteps/s
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98.7% CPU use with 8 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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Pair | 4.6062 | 5.3944 | 6.169 | 26.0 | 47.12
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Neigh | 2.3148 | 2.6122 | 2.8769 | 14.9 | 22.82
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Comm | 0.82337 | 1.7921 | 2.9417 | 59.6 | 15.65
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Output | 0.00052195 | 0.00073566 | 0.0020974 | 0.0 | 0.01
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Modify | 1.4086 | 1.4856 | 1.6791 | 9.2 | 12.98
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Other | | 0.1641 | | | 1.43
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Nlocal: 1000 ave 1131 max 878 min
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Histogram: 3 1 0 0 0 0 0 1 1 2
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Nghost: 2312.88 ave 2525 max 2114 min
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Histogram: 2 2 0 0 0 0 0 1 1 2
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Neighs: 27457 ave 33797 max 21031 min
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Histogram: 3 1 0 0 0 0 0 0 1 3
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Total # of neighbors = 219656
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Ave neighs/atom = 27.457
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Neighbor list builds = 1691
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Dangerous builds = 0
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# thermal conductivity calculation
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compute ke all ke/atom
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variable temp atom c_ke/1.5
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compute layers all chunk/atom bin/1d z lower 0.05 units reduced
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fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
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variable tdiff equal f_2[1][3]-f_2[11][3]
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fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
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variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave
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thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
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thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname v_tdiff dTemp_step colname f_ave dTemp
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run 20000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.406 | 3.407 | 3.408 Mbytes
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Step Temp Temp_hot Temp_cold dTemp_step dTemp
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11000 1.3716416 1.833336 1.1267278 0 0
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12000 1.3703433 1.7829467 1.1194444 0.66044316 0
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13000 1.3686734 1.8334366 1.1193477 0.71431978 0.71431978
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14000 1.3856987 1.8048077 1.1052708 0.73112558 0.72272268
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15000 1.3820117 1.7460559 1.110725 0.72927647 0.72490728
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16000 1.3911309 1.923603 1.1161499 0.77407515 0.73719925
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17000 1.3841301 1.7276486 1.0283807 0.77278638 0.74431667
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18000 1.3888918 1.7944951 1.0532944 0.75665895 0.74637372
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19000 1.3876032 1.838174 1.059715 0.71342263 0.74166642
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20000 1.3724644 1.8297128 1.1439176 0.77352223 0.7456484
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21000 1.3798921 1.7968403 1.0288381 0.70077132 0.74066206
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22000 1.3763952 1.8202225 1.0658157 0.75629111 0.74222496
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23000 1.3911378 1.8691478 1.018589 0.76094865 0.74392711
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24000 1.3867754 1.7826523 1.09347 0.80367344 0.74890597
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25000 1.385877 1.9029313 1.0815131 0.73559505 0.74788206
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26000 1.3791773 1.8904022 1.0151678 0.7729123 0.74966993
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27000 1.3800063 1.729283 1.127594 0.71473941 0.74734123
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28000 1.3757197 1.7823772 1.084523 0.73849831 0.74678855
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29000 1.3777555 1.8287284 1.0715132 0.70375514 0.74425717
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30000 1.3821118 1.7382856 1.1078333 0.79892499 0.74729427
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31000 1.3870476 1.8410063 1.1235958 0.76218423 0.74807795
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Loop time of 26.9314 on 8 procs for 20000 steps with 8000 atoms
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Performance: 320814.865 tau/day, 742.627 timesteps/s
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97.4% CPU use with 8 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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Pair | 8.5017 | 11.183 | 13.664 | 67.1 | 41.52
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Neigh | 4.5072 | 5.5343 | 6.4781 | 37.9 | 20.55
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Comm | 2.6028 | 5.7342 | 9.01 | 118.2 | 21.29
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Output | 0.0041722 | 0.0082705 | 0.0088616 | 1.7 | 0.03
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Modify | 3.7207 | 4.0439 | 4.4497 | 13.7 | 15.02
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Other | | 0.4277 | | | 1.59
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Nlocal: 1000 ave 1134 max 850 min
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Histogram: 2 1 0 1 0 0 0 1 0 3
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Nghost: 2307.75 ave 2561 max 2083 min
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Histogram: 4 0 0 0 0 0 0 0 2 2
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Neighs: 27561.1 ave 34071 max 19891 min
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Histogram: 2 1 1 0 0 0 0 0 1 3
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Total # of neighbors = 220489
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Ave neighs/atom = 27.561125
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Neighbor list builds = 3442
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Dangerous builds = 0
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print "Running average thermal conductivity: $(v_kappa:%.2f)"
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Running average thermal conductivity: 3.55
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Total wall time: 0:00:39
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