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lammps/examples/HEAT/log.lj_ehex
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log.lj_ehex
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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 +${F} region Thi_region
fix fHi all ehex 1 +33.58066608048 region Thi_region
# cold reservoir
fix fLo all ehex 1 -${F} region Tlo_region
fix fLo all ehex 1 -33.58066608048 region Tlo_region
# 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_ehex
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_ehex
fix fchT all ave/chunk 10 71428 ${Nevery} cchT v_T file out.Tlj_ehex
fix fchT all ave/chunk 10 71428 714280 cchT v_T file out.Tlj_ehex
# 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_ehex
fix fE all ave/time 10 1000 10000 v_E file out.Elj_ehex
# 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 0.72399955 -4.1075876 6.3569796e-30
20000 0.72200145 -4.1076527 9.4131743e-30
30000 0.7189538 -4.1076266 9.9917978e-30
40000 0.72493542 -4.1075882 1.2907194e-29
50000 0.71651186 -4.1076193 1.6114353e-29
60000 0.73095328 -4.107638 1.6281247e-29
70000 0.70276229 -4.1074716 1.5732538e-29
80000 0.71186017 -4.1075456 1.9714873e-29
90000 0.7277987 -4.1076333 1.9683783e-29
100000 0.74378417 -4.1076831 2.008245e-29
110000 0.7066978 -4.1074049 1.8623846e-29
120000 0.72500229 -4.1075844 2.117713e-29
130000 0.72008927 -4.1076012 2.3931505e-29
140000 0.72772233 -4.1076511 2.1582564e-29
150000 0.73860983 -4.1077211 2.4705578e-29
160000 0.72961264 -4.1074785 2.7170029e-29
170000 0.71734552 -4.1074323 2.4675122e-29
180000 0.70571153 -4.1074453 2.2384488e-29
190000 0.72598398 -4.1076489 2.6149518e-29
200000 0.71654285 -4.1075445 2.2884041e-29
210000 0.70521682 -4.1075104 2.1544528e-29
220000 0.72901276 -4.107639 2.2758013e-29
230000 0.73245466 -4.1075811 2.4878827e-29
240000 0.71163454 -4.1074882 2.072386e-29
250000 0.72347298 -4.1075939 2.0114174e-29
260000 0.71577745 -4.1075268 1.8020948e-29
270000 0.71563876 -4.1075331 1.726083e-29
280000 0.71472187 -4.1076037 1.5702905e-29
290000 0.71640897 -4.1075095 1.3652432e-29
300000 0.71189676 -4.1074701 1.3273904e-29
310000 0.73110074 -4.1075712 1.2920349e-29
320000 0.73650669 -4.107631 1.3923757e-29
330000 0.69674914 -4.1074138 1.4152976e-29
340000 0.72631298 -4.1077512 1.386547e-29
350000 0.72730004 -4.1077609 1.6375273e-29
360000 0.73133088 -4.1076599 1.4915012e-29
370000 0.71990302 -4.1075023 1.4387132e-29
380000 0.70764996 -4.1075914 1.4723241e-29
390000 0.7255125 -4.1077323 1.6664958e-29
400000 0.7326785 -4.1077028 1.5203345e-29
410000 0.71953373 -4.1075658 2.0232789e-29
420000 0.71143005 -4.107548 2.229431e-29
430000 0.74033148 -4.1076115 2.657992e-29
440000 0.7267839 -4.1077112 2.9458629e-29
450000 0.71505305 -4.107557 2.9103833e-29
460000 0.7089713 -4.1075146 3.3253897e-29
470000 0.72444212 -4.1076379 3.1465484e-29
480000 0.72079711 -4.1075868 2.8388782e-29
490000 0.71267656 -4.1074868 3.2128913e-29
500000 0.70974489 -4.1076207 3.5271604e-29
510000 0.7053828 -4.1074928 3.7845378e-29
520000 0.71396356 -4.107609 3.520462e-29
530000 0.71637729 -4.1075377 3.131853e-29
540000 0.72648522 -4.1075216 2.9893315e-29
550000 0.7012357 -4.1074612 2.9823982e-29
560000 0.71040667 -4.1074729 2.9340227e-29
570000 0.73041709 -4.1074866 3.398074e-29
580000 0.71814185 -4.107633 3.4865255e-29
590000 0.72128126 -4.1074578 3.6128155e-29
600000 0.72342897 -4.107554 3.1929655e-29
610000 0.71695081 -4.1075492 3.110134e-29
620000 0.7144036 -4.1076465 3.734556e-29
630000 0.74624251 -4.1076366 3.9372399e-29
640000 0.72448733 -4.1076427 4.0683832e-29
650000 0.71347763 -4.1075844 4.2153755e-29
660000 0.72287745 -4.1075678 4.3130586e-29
670000 0.71618749 -4.1075379 4.1023799e-29
680000 0.71846662 -4.1075145 4.0775831e-29
690000 0.72276205 -4.1076277 4.6351083e-29
700000 0.71712649 -4.1077598 4.6374261e-29
710000 0.71280668 -4.1074476 4.8082341e-29
714285 0.72291151 -4.1075743 4.8273006e-29
Loop time of 170.968 on 32 procs for 714285 steps with 2000 atoms
Performance: 2526790.532 tau/day, 4177.894 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 | 68.213 | 77.684 | 85.031 | 57.6 | 45.44
Neigh | 8.8658 | 9.609 | 10.196 | 14.8 | 5.62
Comm | 49.931 | 56.883 | 67.495 | 60.5 | 33.27
Output | 0.013727 | 0.014771 | 0.014943 | 0.2 | 0.01
Modify | 20.448 | 22.358 | 25.099 | 32.3 | 13.08
Other | | 4.419 | | | 2.58
Nlocal: 62.5 ave 69 max 55 min
Histogram: 2 1 3 5 3 4 2 8 2 2
Nghost: 1371 ave 1405 max 1338 min
Histogram: 2 4 6 4 0 3 4 3 1 5
Neighs: 6007.94 ave 6893 max 5323 min
Histogram: 4 6 3 3 5 2 1 2 2 4
Total # of neighbors = 192254
Ave neighs/atom = 96.127
Neighbor list builds = 40326
Dangerous builds = 0
Total wall time: 0:02:50
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