245 lines
10 KiB
Groff
245 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 ehex 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 = 0.000 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 0.925673 on 8 procs for 1000 steps with 8000 atoms
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Performance: 466687.339 tau/day, 1080.295 timesteps/s
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98.5% 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 | 0.5071 | 0.52493 | 0.5485 | 1.7 | 56.71
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Neigh | 0.23405 | 0.23912 | 0.24396 | 0.7 | 25.83
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Comm | 0.084007 | 0.10338 | 0.12987 | 4.9 | 11.17
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Output | 0.00030358 | 0.00048259 | 0.0017229 | 0.0 | 0.05
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Modify | 0.035045 | 0.043306 | 0.051758 | 3.2 | 4.68
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Other | | 0.01446 | | | 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 ehex 1 100.0 region hot
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fix cold all ehex 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) = 3.406 | 3.406 | 3.406 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 1.3537291 1.6418772 1.1875127
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3000 1.3615152 1.6451299 1.1769094
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4000 1.3612129 1.5281727 1.2022419
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5000 1.3552182 1.6672955 1.2212864
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6000 1.3643442 1.6072213 1.2390567
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7000 1.3665773 1.6909819 1.1466611
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8000 1.375741 1.6144274 1.1691231
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9000 1.3701136 1.8238424 1.136342
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10000 1.3563004 1.8059065 1.1547129
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11000 1.3794051 1.692299 1.0515688
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Loop time of 10.4087 on 8 procs for 10000 steps with 8000 atoms
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Performance: 415036.696 tau/day, 960.733 timesteps/s
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98.8% 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 | 4.2937 | 5.0957 | 5.741 | 23.2 | 48.96
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Neigh | 2.1995 | 2.4735 | 2.7099 | 13.0 | 23.76
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Comm | 0.81056 | 1.5944 | 2.6024 | 51.8 | 15.32
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Output | 0.00049738 | 0.00074599 | 0.0021147 | 0.0 | 0.01
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Modify | 0.92166 | 1.0638 | 1.1348 | 7.9 | 10.22
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Other | | 0.1804 | | | 1.73
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Nlocal: 1000 ave 1105 max 883 min
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Histogram: 1 1 2 0 0 0 0 0 2 2
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Nghost: 2319.38 ave 2502 max 2114 min
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Histogram: 1 3 0 0 0 0 0 0 0 4
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Neighs: 27387.9 ave 32453 max 21803 min
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Histogram: 2 2 0 0 0 0 0 0 0 4
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Total # of neighbors = 219103
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Ave neighs/atom = 27.387875
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Neighbor list builds = 1696
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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.ehex
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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) = 3.656 | 3.657 | 3.658 Mbytes
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Step Temp Temp_hot Temp_cold dTemp_step dTemp
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11000 1.3794051 1.6903393 1.0515688 0 0
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12000 1.3799777 1.8004888 1.1032219 0.63860014 0
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13000 1.3733605 1.7823094 1.0553582 0.65827891 0.65827891
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14000 1.3749743 1.7852256 1.1674016 0.68463005 0.67145448
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15000 1.3863795 1.8538127 1.0056247 0.73524813 0.69271903
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16000 1.3731955 1.7518546 1.0741458 0.74810775 0.70656621
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17000 1.3771856 1.9016869 1.0090502 0.73999567 0.7132521
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18000 1.3766032 1.7616195 1.1142155 0.73769104 0.71732526
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19000 1.3815934 1.7791247 1.1406987 0.73617832 0.72001855
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20000 1.3725543 1.8637436 1.0799364 0.73435569 0.7218107
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21000 1.3817369 1.8808771 1.0642524 0.76702329 0.72683432
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22000 1.3968704 1.840287 1.072304 0.82496419 0.7366473
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23000 1.3895558 1.9427293 1.0766665 0.75363908 0.73819201
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24000 1.3900493 1.9883976 1.1081017 0.86394774 0.74867166
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25000 1.3838912 1.8853041 1.0795751 0.83043902 0.75496145
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26000 1.3912105 1.9330259 1.1070335 0.79880182 0.75809291
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27000 1.3891151 1.8548451 1.0676153 0.81856523 0.7621244
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28000 1.3942624 1.9796706 1.1251407 0.81762456 0.76559316
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29000 1.3819302 1.8619138 1.0495292 0.78627491 0.76680973
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30000 1.3968366 1.883107 1.1004588 0.83902548 0.77082172
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31000 1.3822489 1.8220413 1.0322271 0.7550338 0.76999077
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Loop time of 23.253 on 8 procs for 20000 steps with 8000 atoms
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Performance: 371564.581 tau/day, 860.103 timesteps/s
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98.9% 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 | 8.0778 | 10.624 | 13.006 | 62.2 | 45.69
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Neigh | 4.358 | 5.32 | 6.1917 | 35.5 | 22.88
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Comm | 1.5574 | 4.6136 | 8.0947 | 127.6 | 19.84
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Output | 0.0025729 | 0.0027796 | 0.0041615 | 1.0 | 0.01
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Modify | 2.0737 | 2.2922 | 2.4432 | 9.2 | 9.86
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Other | | 0.4005 | | | 1.72
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Nlocal: 1000 ave 1121 max 857 min
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Histogram: 2 0 1 1 0 0 0 0 1 3
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Nghost: 2299.75 ave 2541 max 2067 min
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Histogram: 3 1 0 0 0 0 0 0 2 2
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Neighs: 27487.2 ave 33361 max 20651 min
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Histogram: 2 1 1 0 0 0 0 0 0 4
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Total # of neighbors = 219898
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Ave neighs/atom = 27.48725
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Neighbor list builds = 3474
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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: 3.45
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Total wall time: 0:00:34
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