Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/KAPPA/log.langevin.1Feb14
9a302200ab7defficient_neuronet

Last Change
Raw File

log.langevin.1Feb14
View Options

LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
variable tlo equal 1.0
variable thi equal 1.70
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
#variable tlo equal 0.3
#variable thi equal 1.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# heat layers
region hot block INF INF INF INF 0 1
region cold block INF INF INF INF 10 11
compute Thot all temp/region hot
compute Tcold all temp/region cold
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Memory usage per processor = 2.14238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419994 -3.7155648 0 -1.7028172 0.82925677
900 1.3562214 -3.6965608 0 -1.662483 0.88908144
1000 1.3732016 -3.7100024 0 -1.6504575 0.83982823
Loop time of 0.862126 on 8 procs for 1000 steps with 8000 atoms
Pair time (%) = 0.482831 (56.0047)
Neigh time (%) = 0.221903 (25.739)
Comm time (%) = 0.104307 (12.0989)
Outpt time (%) = 0.000301003 (0.0349141)
Other time (%) = 0.0527841 (6.12256)
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
fix 1 all nve
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
variable tdiff equal c_Thot-c_Tcold
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo 1000
run 10000
Memory usage per processor = 2.60014 Mbytes
Step Temp Thot Tcold hot cold tdiff
1000 1.35 1.4312938 1.2955632 0 0 0.13573057
2000 1.360018 1.493833 1.108937 -0.12327246 0.1384129 0.38489598
3000 1.3375537 1.6938591 1.0191771 -0.21101663 0.26135778 0.67468203
4000 1.3233024 1.6026443 1.1480306 -0.26177493 0.34439263 0.45461365
5000 1.3107386 1.711679 1.05711 -0.31795111 0.42339093 0.65456895
6000 1.297964 1.6472939 0.95469459 -0.36994548 0.48890072 0.69259932
7000 1.3062638 1.5806629 1.080306 -0.43385121 0.56448283 0.50035689
8000 1.3062755 1.6415159 1.0407288 -0.48697483 0.62125026 0.60078705
9000 1.2850239 1.6253774 1.0574621 -0.50398307 0.66921986 0.56791525
10000 1.3035594 1.5362476 1.0681602 -0.56218263 0.71574454 0.46808735
11000 1.2973176 1.6350179 1.0433547 -0.61814256 0.75532475 0.59166313
Loop time of 11.3468 on 8 procs for 10000 steps with 8000 atoms
Pair time (%) = 4.81454 (42.4309)
Neigh time (%) = 2.27955 (20.0899)
Comm time (%) = 1.88988 (16.6557)
Outpt time (%) = 0.000712395 (0.00627838)
Other time (%) = 2.36209 (20.8173)
Nlocal: 1000 ave 1135 max 867 min
Histogram: 2 0 2 0 0 0 0 2 1 1
Nghost: 2314.38 ave 2559 max 2067 min
Histogram: 1 1 2 0 0 0 0 2 0 2
Neighs: 27392.4 ave 33962 max 20582 min
Histogram: 2 0 2 0 0 0 0 1 1 2
Total # of neighbors = 219139
Ave neighs/atom = 27.3924
Neighbor list builds = 1666
Dangerous builds = 0
# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation
compute ke all ke/atom
variable temp atom c_ke/1.5
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
fix ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp file profile.langevin units reduced
run 20000
Memory usage per processor = 2.60106 Mbytes
Step Temp Thot Tcold hot cold tdiff ave
11000 1.2973176 1.6350179 1.0433547 0 0 0.59166313 0
12000 1.3039677 1.6419813 1.0477757 -0.046382646 0.056968333 0.5942056 0.59568325
13000 1.3110256 1.5869209 1.0158888 -0.094090387 0.10445821 0.57103213 0.57629599
14000 1.293218 1.6629496 1.1121109 -0.11375822 0.15128701 0.55083862 0.5707904
15000 1.2811676 1.6722435 1.0942864 -0.14415448 0.20239116 0.57795712 0.5695191
16000 1.2791266 1.5765255 1.1007618 -0.2014815 0.2427606 0.47576367 0.56997652
17000 1.2622984 1.6433371 1.0358679 -0.22929967 0.29997963 0.60746917 0.56431552
18000 1.2795857 1.7006846 1.0702476 -0.29495954 0.3304481 0.630437 0.57298103
19000 1.2794851 1.5796065 1.0383562 -0.3325748 0.3825079 0.54125035 0.567257
20000 1.3013271 1.6682287 1.0624636 -0.40206115 0.42100016 0.60576507 0.57276102
21000 1.277446 1.5408233 1.0275158 -0.43012499 0.48360636 0.51330753 0.57340191
22000 1.3031703 1.6370721 1.0356931 -0.51126428 0.52836134 0.60137903 0.57578211
23000 1.2719643 1.4882391 0.98769817 -0.55845167 0.61243478 0.50054093 0.57457152
24000 1.2931956 1.5814171 1.0586513 -0.60691503 0.63563787 0.52276581 0.57294037
25000 1.2846646 1.7006525 1.0209227 -0.64068901 0.67962894 0.67972988 0.57312421
26000 1.2711788 1.6697984 0.99699462 -0.67019827 0.73853772 0.67280381 0.57276936
27000 1.2732777 1.6285951 1.1302554 -0.70566156 0.76748898 0.49833966 0.57255348
28000 1.2831929 1.5938242 1.0977096 -0.75144205 0.81168035 0.49611462 0.57460785
29000 1.2792513 1.4854998 1.0013453 -0.79831201 0.86425474 0.4841545 0.57139895
30000 1.2677402 1.6009684 1.092679 -0.83584426 0.90606945 0.50828948 0.57156924
31000 1.2720929 1.5851445 1.0736744 -0.87730401 0.95644174 0.51147013 0.5717415
Loop time of 23.7017 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.6584 (40.7498)
Neigh time (%) = 4.57821 (19.3159)
Comm time (%) = 4.45101 (18.7793)
Outpt time (%) = 0.00194073 (0.00818813)
Other time (%) = 5.01215 (21.1468)
Nlocal: 1000 ave 1121 max 880 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Nghost: 2281.5 ave 2471 max 2073 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Neighs: 27428.1 ave 33179 max 21152 min
Histogram: 2 2 0 0 0 0 0 0 1 3
Total # of neighbors = 219425
Ave neighs/atom = 27.4281
Neighbor list builds = 3338
Dangerous builds = 0
c4science · Help