Dear Lammps users,
Hi, I am trying to calculate thermal conductivity of single layer graphene (100 x 11 x 0.34 nm) using M-P NEMD method. Please find the copied input/output scripts below (highlighted numbers are ‘exchanged energy’, ‘delta T’, and ‘thermal conductivity’, respectively). I am getting exceptionally small exchanged energy between the coldest and hottest slabs, which results in very low thermal conductivity, around 40 W/m-K. Please let me know if you find anything suspicious. Thanks.
Best Regards,
-------input script----------------------------------------------------------------
variable T equal 300
variable V equal vol
variable dt equal 0.001
#variable p equal 1000 # correlation length
#variable s equal 5 # sample interval
#variable d equal $p*$s # dump interval
convert from LAMMPS real units to SI
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable eV2J equal 1.602e-19
variable A2m equal 1.0e-10
variable ps2s equal 1.0e-12
variable convert equal {eV2J}*{eV2J}/{ps2s}/{A2m}
variable alat equal 2.46
setup problem
units metal
boundary p p p
atom_style atomic
lattice custom ${alat} a1 0.86603 0.5 0 a2 0.86603 -0.5 0 a3 0 0 10 basis 0.33333 0.33333 0 basis 0.66667 0.66667 0
region box block 0 1000 0 110 -50 50 units box
create_box 1 box
region tf block INF INF INF INF -5 5 units box
create_atoms 1 region tf
mass 1 12
pair_style tersoff
pair_coeff * * /home/kpark39/programs/lammps-1Feb14/potentials/SiC_1994.tersoff C
neighbor 2.0 bin
neigh_modify delay 5
timestep ${dt}
dump 1 all cfg 10000 dump.config.*.cfg mass type xs ys zs vx vy vz x y z
1st equilibration run
velocity all create $T 4928459 mom yes rot yes dist gaussian units box
fix 1 all npt temp $T $T 1 iso 0 0 0.1 drag 1
thermo 1000
run 50000
write_restart restart.NPT20k.equil
unfix 1
#velocity all scale $t
2nd equilibration run
compute ke all ke/atom
units of Kb = J/K, units of ke = eV or J, so temp becomes K
variable temp atom c_ke*{eV2J}/(1.5*{kB})
fix 1 all nve
fix 2 all ave/spatial 10 100 1000 x lower 5 v_temp file profile.mp units box
fix 3 all thermal/conductivity 10 x 190 swap 2
fix 4 all temp/berendsen 300 300 100
variable tdiff equal f_2[96][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff
thermo 1000
dump 2 all cfg 10000 dump.config.*.cfg mass type xs ys zs vx vy vz x y z v_temp
run 50000
unfix 4
thermal conductivity calculation
fix 3 all thermal/conductivity 10 x 190 swap 2
fix ave all ave/time 1 1 1000 v_tdiff ave running file ave.dat
variable K equal f_3*{eV2J}*1000/2/(110*3.4)/{A2m}/{dt}/100000/{ps2s}/f_ave
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave v_K
thermo 1000
run 100000
-------output script----------------------------------------------------------------
LAMMPS (1 Feb 2014)
Lattice spacing in x,y,z = 4.26087 2.46 24.6
Created orthogonal box = (0 0 -50) to (1000 110 50)
16 by 2 by 2 MPI processor grid
Created 42255 atoms
Setting up run …
Memory usage per processor = 2.04764 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -182631.38 0 -180992.85 28749.175 11000000
1000 1674.1317 -223215.2 0 -214071.49 -43.559921 11573511
2000 1443.4808 -225168.02 0 -217284.07 3.7486431 11231479
3000 1270.692 -226736.2 0 -219795.98 0.71739626 10904871
.
.
.
.
Total # of neighbors = 806268
Ave neighs/atom = 19.081
Neighbor list builds = 1035
Dangerous builds = 22
System init for write_restart …
Setting up run …
Memory usage per processor = 4.21604 Mbytes
Step Temp E_pair TotEng 3 tdiff
50000 299.66342 -234816.49 -233179.8 0 0
51000 298.48589 -234809.4 -233179.14 26.991906 132.34869
52000 300.24937 -234818.29 -233178.4 48.134262 216.23663
53000 300.35156 -234817.94 -233177.49 67.511275 253.24118
54000 300.65795 -234818.65 -233176.53 86.98012 273.35123
55000 300.92432 -234819.46 -233175.88 104.72854 278.42473
56000 299.14405 -234809.44 -233175.59 122.06699 284.53212
57000 299.67826 -234811.71 -233174.94 139.3028 300.54634
.
.
.
.
Total # of neighbors = 806524
Ave neighs/atom = 19.0871
Neighbor list builds = 550
Dangerous builds = 0
Setting up run …
Memory usage per processor = 4.33457 Mbytes
Step Temp E_pair TotEng 3 tdiff ave K
100000 306.93395 -234827.59 -233151.19 0 460.32424 460.32424 0
101000 307.6306 -234831.05 -233150.85 9.3210409 459.66693 459.99558 0.43398195
102000 307.84754 -234831.72 -233150.33 18.620655 441.17254 453.72124 0.87895524
103000 307.32652 -234828.09 -233149.55 28.463156 446.35555 451.87982 1.3490282
104000 308.20542 -234831.94 -233148.59 38.011678 446.43801 450.79145 1.8059357
105000 308.46388 -234832.33 -233147.57 47.386046 467.22107 453.52972 2.2377194
106000 308.23792 -234830.44 -233146.92 56.758293 460.10769 454.46943 2.6747646
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.
.
.
.
193000 323.04911 -234840.79 -233076.37 835.50758 507.25976 474.51753 37.710218
194000 322.08415 -234834.39 -233075.24 844.18327 502.84934 474.81576 38.077859
195000 322.99552 -234838.66 -233074.54 853.05529 470.6863 474.77275 38.481529
196000 322.15434 -234833.62 -233074.09 862.24385 482.1616 474.84892 38.889787
197000 323.03706 -234837.66 -233073.31 870.78038 479.84933 474.89995 39.270591
198000 322.63209 -234834.51 -233072.37 879.81093 488.43577 475.03667 39.666431
199000 322.23855 -234831.55 -233071.56 888.75904 489.39559 475.18026 40.05775
200000 321.5094 -234826.35 -233070.34 897.6081 479.46705 475.2227 40.452978
Loop time of 513.501 on 64 procs for 100000 steps with 42255 atoms
Pair time () = 233.329 (45.4388)
Neigh time () = 0.946099 (0.184245)
Comm time () = 175.881 (34.2514)
Outpt time () = 0.464756 (0.0905072)
Other time (%) = 102.88 (20.035)
Nlocal: 660.234 ave 1333 max 0 min
Histogram: 12 6 5 5 4 3 7 6 5 11
Nghost: 646.625 ave 1287 max 22 min
Histogram: 2 1 1 10 24 11 8 5 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 64 0 0 0 0 0 0 0 0 0
FullNghs: 12612.3 ave 25399 max 0 min
Histogram: 12 7 4 5 4 2 8 5 7 10
Total # of neighbors = 807186
Ave neighs/atom = 19.1027
Neighbor list builds = 1273
Dangerous builds = 0