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lammps/examples/HEAT/log.lj_hex
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# heat flux
variable J equal 0.15
# timestep
variable dt equal 0.007
# cutoff radius for shifted LJ-potential
variable rc equal 3.0
# simulation time for the production run
variable tprod equal 5000
# total number of timesteps
variable Nprod equal floor(${tprod}/${dt})
variable Nprod equal floor(5000/${dt})
variable Nprod equal floor(5000/0.007)
# equilibrated steady state configuration
read_data "data.lj"
orthogonal box = (-5.28998 -5.28998 -10.58) to (5.28998 5.28998 10.58)
2 by 2 by 8 MPI processor grid
reading atoms ...
2000 atoms
reading velocities ...
2000 velocities
# use LJ shifted force pair style
pair_style lj/sf ${rc}
pair_style lj/sf 3
# with coefficients eps = 1, sigma = 1, and rc = 3.0
pair_coeff 1 1 1.0 1.0 ${rc}
pair_coeff 1 1 1.0 1.0 3
# increase neigbor skin because of the large timestep
neighbor 0.8 bin
# options used for fix ave/time; sample the quantities every 10 steps
variable Nsamp equal 10
variable Nrepeat equal floor(${Nprod}/${Nsamp})
variable Nrepeat equal floor(714285/${Nsamp})
variable Nrepeat equal floor(714285/10)
variable Nevery equal ${Nsamp}*${Nrepeat}
variable Nevery equal 10*${Nrepeat}
variable Nevery equal 10*71428
# box dimensions
variable Lz equal zhi-zlo
variable Lx equal xhi-xlo
variable Ly equal yhi-ylo
# reservoir width in z-direction
variable delta equal 2.
# specify z-extents of both reservoirs
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
variable zlo_Thi equal -21.16/4.-${delta}/2.
variable zlo_Thi equal -21.16/4.-2/2.
variable zhi_Thi equal ${zlo_Thi}+${delta}
variable zhi_Thi equal -6.29+${delta}
variable zhi_Thi equal -6.29+2
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
variable zlo_Tlo equal -6.29+${Lz}/2.
variable zlo_Tlo equal -6.29+21.16/2.
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
variable zhi_Tlo equal 4.29+${delta}
variable zhi_Tlo equal 4.29+2
# resolution for fix ave/spatial
variable dz equal ${Lz}/60
variable dz equal 21.16/60
# compute per-atom kinetic energy and temperature, respectively
# NOTE: In this example we ignored the centre of mass (com) velocities
# of the individual bins for simplicity. However, we took that
# into account for the publication.
compute ke all ke/atom
variable T atom c_ke/1.5
# specify the reservoirs
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
region Thi_region block INF INF INF INF -6.29 ${zhi_Thi}
region Thi_region block INF INF INF INF -6.29 -4.29
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
region Tlo_region block INF INF INF INF 4.29 ${zhi_Tlo}
region Tlo_region block INF INF INF INF 4.29 6.29
# compute the temperature of the individual region
compute cTlo all temp/region Tlo_region
compute cThi all temp/region Thi_region
# calculate the energy flux from the specified heat flux
variable F equal ${J}*${Lx}*${Ly}*2.
variable F equal 0.15*${Lx}*${Ly}*2.
variable F equal 0.15*10.57996*${Ly}*2.
variable F equal 0.15*10.57996*10.57996*2.
# use fix ehex to create the gradient
# hot reservoir
fix fHi all ehex 1 +${F} region Thi_region hex
fix fHi all ehex 1 +33.58066608048 region Thi_region hex
# cold reservoir
fix fLo all ehex 1 -${F} region Tlo_region hex
fix fLo all ehex 1 -33.58066608048 region Tlo_region hex
# use velocity Verlet for integration
fix fNVEGrad all nve
# calculate the centre of mass velocity of the entire box (vcmx, vcmy, vcmz)
variable vcmx equal "vcm(all,x)"
variable vcmy equal "vcm(all,y)"
variable vcmz equal "vcm(all,z)"
variable vcm2 equal v_vcmx*v_vcmx+v_vcmy*v_vcmy+v_vcmz*v_vcmz
# specify the timestep
timestep ${dt}
timestep 0.007
# frequency for console output
thermo 10000
# print timestep, temperature, total energy and v_com^2 to console
thermo_style custom step temp etotal v_vcm2
# calculate spatial average of temperature
compute cchT all chunk/atom bin/1d z lower ${dz}
compute cchT all chunk/atom bin/1d z lower 0.352666666666667
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
fix fchT all ave/chunk 10 71428 ${Nevery} cchT v_T file out.Tlj_hex
fix fchT all ave/chunk 10 71428 714280 cchT v_T file out.Tlj_hex
# compute the total energy
compute cKe all ke
compute cPe all pe
variable E equal c_cKe+c_cPe
# track the time evolution of the total energy
fix fE all ave/time ${Nsamp} 1000 10000 v_E file out.Elj_hex
fix fE all ave/time 10 1000 10000 v_E file out.Elj_hex
# production run
run ${Nprod}
run 714285
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 1.9 -> bins = 6 6 12
Memory usage per processor = 2.40563 Mbytes
Step Temp TotEng vcm2
0 0.72367949 -4.1076054 7.0171467e-30
10000 0.71696731 -4.1078382 1.1938548e-29
20000 0.71725882 -4.1080333 1.5504952e-29
30000 0.7228273 -4.1083683 1.403949e-29
40000 0.73478918 -4.1087812 1.446699e-29
50000 0.72841192 -4.1089089 1.3198991e-29
60000 0.74581896 -4.1093422 1.5059838e-29
70000 0.72063371 -4.109324 1.6171041e-29
80000 0.72009466 -4.1095719 1.6870537e-29
90000 0.73014429 -4.109994 1.571385e-29
100000 0.71327476 -4.1101323 1.5412564e-29
110000 0.72316493 -4.1104409 1.7709502e-29
120000 0.7234872 -4.1105344 1.7948787e-29
130000 0.72816899 -4.1109221 1.7741547e-29
140000 0.72506096 -4.1111987 1.9030371e-29
150000 0.72511673 -4.1114823 1.757343e-29
160000 0.73317551 -4.1116909 1.8994729e-29
170000 0.72082439 -4.1120083 1.865766e-29
180000 0.72626999 -4.112335 1.9148683e-29
190000 0.71326654 -4.1124685 1.8915793e-29
200000 0.74065832 -4.112821 1.9843217e-29
210000 0.71845086 -4.1131127 2.4402147e-29
220000 0.71791233 -4.1132362 2.2097117e-29
230000 0.7208125 -4.1135103 2.4606119e-29
240000 0.72909134 -4.1136773 2.2783022e-29
250000 0.71684431 -4.1140752 2.1670987e-29
260000 0.72213406 -4.1143319 1.8390834e-29
270000 0.72455866 -4.1146051 1.5318237e-29
280000 0.73251834 -4.114923 1.6228615e-29
290000 0.72332528 -4.1150291 1.8472989e-29
300000 0.72197256 -4.1153626 1.8294525e-29
310000 0.71912916 -4.1155306 1.6031831e-29
320000 0.71457342 -4.1158131 1.7531014e-29
330000 0.72421737 -4.1161772 1.9968319e-29
340000 0.72235101 -4.1163113 2.3190719e-29
350000 0.70988998 -4.1164748 2.5611335e-29
360000 0.71775456 -4.1169932 3.0014053e-29
370000 0.71679741 -4.1170966 3.0945259e-29
380000 0.70612966 -4.117342 2.9062249e-29
390000 0.70739305 -4.1177322 2.7053082e-29
400000 0.71295005 -4.1179697 2.4414341e-29
410000 0.72470924 -4.118195 2.1651938e-29
420000 0.70443619 -4.1186353 1.876675e-29
430000 0.72845824 -4.1189494 1.6850186e-29
440000 0.71062175 -4.119168 1.3962175e-29
450000 0.71550284 -4.1192887 1.9906124e-29
460000 0.71447701 -4.1196143 1.6312135e-29
470000 0.71361306 -4.1197326 1.5080229e-29
480000 0.72704141 -4.1202699 1.6559898e-29
490000 0.72221343 -4.1203799 1.582088e-29
500000 0.71244432 -4.1206248 1.1449744e-29
510000 0.70019538 -4.1208159 9.6577977e-30
520000 0.7093834 -4.1210854 9.2916455e-30
530000 0.71987196 -4.1213538 9.1536296e-30
540000 0.71955704 -4.121897 8.9426037e-30
550000 0.72739215 -4.1219256 7.885467e-30
560000 0.70927863 -4.122129 6.8477877e-30
570000 0.70617194 -4.1224777 5.700215e-30
580000 0.71925255 -4.1227138 5.5056496e-30
590000 0.71501495 -4.1230402 5.273532e-30
600000 0.71662363 -4.1233293 3.9763449e-30
610000 0.71711036 -4.123687 3.1692329e-30
620000 0.72296651 -4.1240099 2.4431085e-30
630000 0.71994644 -4.1240367 1.9069135e-30
640000 0.7086421 -4.1243122 1.5270107e-30
650000 0.70878259 -4.1245389 2.9144979e-30
660000 0.70731638 -4.1247635 3.1199575e-30
670000 0.7218969 -4.1252117 2.306873e-30
680000 0.71825558 -4.1254141 1.085262e-30
690000 0.71399204 -4.1256692 1.5706617e-30
700000 0.72094628 -4.1259655 2.058912e-30
710000 0.70106365 -4.1262688 3.8784102e-30
714285 0.70771156 -4.1262914 4.2318798e-30
Loop time of 170.167 on 32 procs for 714285 steps with 2000 atoms
Performance: 2538674.602 tau/day, 4197.544 timesteps/s
100.0% CPU use with 32 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 69.016 | 77.498 | 85.354 | 57.0 | 45.54
Neigh | 8.8368 | 9.5809 | 10.199 | 15.2 | 5.63
Comm | 49.229 | 56.994 | 66.176 | 59.6 | 33.49
Output | 0.013675 | 0.014766 | 0.014929 | 0.2 | 0.01
Modify | 19.558 | 21.817 | 24.56 | 35.3 | 12.82
Other | | 4.263 | | | 2.51
Nlocal: 62.5 ave 71 max 54 min
Histogram: 2 0 4 3 7 7 2 5 1 1
Nghost: 1381.91 ave 1426 max 1343 min
Histogram: 3 6 2 4 1 3 6 1 3 3
Neighs: 6004.25 ave 6872 max 5037 min
Histogram: 3 1 3 6 1 5 2 4 4 3
Total # of neighbors = 192136
Ave neighs/atom = 96.068
Neighbor list builds = 40221
Dangerous builds = 0
Total wall time: 0:02:50
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