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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
#LAMMPS input script
#in.GD
#see README for details
###############################################################################
#initialize variables
clear
using 1 OpenMP thread(s) per MPI task
#frequency for outputting info (timesteps)
variable dump_rate equal 50
variable thermo_rate equal 10
#equilibration time (timesteps)
variable equil equal 1000
#stabilization time (timesteps to reach steady-state)
variable stabil equal 1000
#data collection time (timesteps)
variable run equal 2000
#length of pipe
variable L equal 30
#width of pipe
variable d equal 20
#flux (mass/sigma*tau)
variable J equal 0.1
#simulation box dimensions
variable Lx equal 100
variable Ly equal 40
#bulk fluid density
variable dens equal 0.8
#lattice spacing for wall atoms
variable aWall equal 1.0 #1.7472
#timestep
variable ts equal 0.001
#temperature
variable T equal 2.0
#thermostat damping constant
variable tdamp equal ${ts}*100
variable tdamp equal 0.001*100
units lj
dimension 2
atom_style atomic
###############################################################################
#create box
#create lattice with the spacing aWall
variable rhoWall equal ${aWall}^(-2)
variable rhoWall equal 1^(-2)
lattice sq ${rhoWall}
lattice sq 1
Lattice spacing in x,y,z = 1 1 1
#modify input dimensions to be multiples of aWall
variable L1 equal round($L/${aWall})*${aWall}
variable L1 equal round(30/${aWall})*${aWall}
variable L1 equal round(30/1)*${aWall}
variable L1 equal round(30/1)*1
variable d1 equal round($d/${aWall})*${aWall}
variable d1 equal round(20/${aWall})*${aWall}
variable d1 equal round(20/1)*${aWall}
variable d1 equal round(20/1)*1
variable Ly1 equal round(${Ly}/${aWall})*${aWall}
variable Ly1 equal round(40/${aWall})*${aWall}
variable Ly1 equal round(40/1)*${aWall}
variable Ly1 equal round(40/1)*1
variable Lx1 equal round(${Lx}/${aWall})*${aWall}
variable Lx1 equal round(100/${aWall})*${aWall}
variable Lx1 equal round(100/1)*${aWall}
variable Lx1 equal round(100/1)*1
#create simulation box
variable lx2 equal ${Lx1}/2
variable lx2 equal 100/2
variable ly2 equal ${Ly1}/2
variable ly2 equal 40/2
region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box
region simbox block -50 ${lx2} -${ly2} ${ly2} 0 0.1 units box
region simbox block -50 50 -${ly2} ${ly2} 0 0.1 units box
region simbox block -50 50 -20 ${ly2} 0 0.1 units box
region simbox block -50 50 -20 20 0 0.1 units box
create_box 2 simbox
Created orthogonal box = (-50 -20 0) to (50 20 0.1)
1 by 1 by 1 MPI processor grid
#####################################################################
#set up potential
mass 1 1.0 #fluid atoms
mass 2 1.0 #wall atoms
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 1.12246
pair_coeff 2 2 0.0 0.0
neigh_modify exclude type 2 2
timestep ${ts}
timestep 0.001
#####################################################################
#create atoms
#create wall atoms everywhere
create_atoms 2 box
Created 4000 atoms
#define region which is "walled off"
variable dhalf equal ${d1}/2
variable dhalf equal 20/2
variable Lhalf equal ${L1}/2
variable Lhalf equal 30/2
region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box
region walltop block -15 ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box
region walltop block -15 15 ${dhalf} EDGE -0.1 0.1 units box
region walltop block -15 15 10 EDGE -0.1 0.1 units box
region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box
region wallbot block -15 ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box
region wallbot block -15 15 EDGE -${dhalf} -0.1 0.1 units box
region wallbot block -15 15 EDGE -10 -0.1 0.1 units box
region outsidewall union 2 walltop wallbot side out
#remove wall atoms outside wall region
group outside region outsidewall
3349 atoms in group outside
delete_atoms group outside
Deleted 3349 atoms, new total = 651
#remove wall atoms that aren't on edge of wall region
variable x1 equal ${Lhalf}-${aWall}
variable x1 equal 15-${aWall}
variable x1 equal 15-1
variable y1 equal ${dhalf}+${aWall}
variable y1 equal 10+${aWall}
variable y1 equal 10+1
region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box
region insideTop block -14 ${x1} ${y1} EDGE -0.1 0.1 units box
region insideTop block -14 14 ${y1} EDGE -0.1 0.1 units box
region insideTop block -14 14 11 EDGE -0.1 0.1 units box
region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box
region insideBot block -14 ${x1} EDGE -${y1} -0.1 0.1 units box
region insideBot block -14 14 EDGE -${y1} -0.1 0.1 units box
region insideBot block -14 14 EDGE -11 -0.1 0.1 units box
region insideWall union 2 insideTop insideBot
group insideWall region insideWall
551 atoms in group insideWall
delete_atoms group insideWall
Deleted 551 atoms, new total = 100
#define new lattice, to give correct fluid density
#y lattice const must be a multiple of aWall
variable atrue equal ${dens}^(-1/2)
variable atrue equal 0.8^(-1/2)
variable ay equal round(${atrue}/${aWall})*${aWall}
variable ay equal round(1.11803398874989/${aWall})*${aWall}
variable ay equal round(1.11803398874989/1)*${aWall}
variable ay equal round(1.11803398874989/1)*1
#choose x lattice const to give correct density
variable ax equal (${ay}*${dens})^(-1)
variable ax equal (1*${dens})^(-1)
variable ax equal (1*0.8)^(-1)
#change Lx to be multiple of ax
variable Lx1 equal round(${Lx}/${ax})*${ax}
variable Lx1 equal round(100/${ax})*${ax}
variable Lx1 equal round(100/1.25)*${ax}
variable Lx1 equal round(100/1.25)*1.25
variable lx2 equal ${Lx1}/2
variable lx2 equal 100/2
change_box all x final -${lx2} ${lx2} units box
change_box all x final -50 ${lx2} units box
change_box all x final -50 50 units box
orthogonal box = (-50 -20 0) to (50 20 0.1)
#define new lattice
lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0
lattice custom 0.8 a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0
lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0
lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 1 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0
Lattice spacing in x,y,z = 1.25 1 1
#fill in rest of box with bulk particles
variable delta equal 0.001
variable Ldelt equal ${Lhalf}+${delta}
variable Ldelt equal 15+${delta}
variable Ldelt equal 15+0.001
variable dDelt equal ${dhalf}-${delta}
variable dDelt equal 10-${delta}
variable dDelt equal 10-0.001
region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box
region left block EDGE -15.001 EDGE EDGE -0.1 0.1 units box
region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box
region right block 15.001 EDGE EDGE EDGE -0.1 0.1 units box
region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box
region pipe block -15.001 ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box
region pipe block -15.001 15.001 -${dDelt} ${dDelt} -0.1 0.1 units box
region pipe block -15.001 15.001 -9.999 ${dDelt} -0.1 0.1 units box
region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 units box
region bulk union 3 left pipe right
create_atoms 1 region bulk
Created 2675 atoms
group bulk type 1
2675 atoms in group bulk
group wall type 2
100 atoms in group wall
#remove atoms that are too close to wall
delete_atoms overlap 0.9 bulk wall
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 72 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Deleted 0 atoms, new total = 2775
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude group wall wall
velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
velocity bulk create 2 78915 dist gaussian rot yes mom yes loop geom
#####################################################################
#set up PUT
#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
#average number of particles per box, Evans and Morriss used 2.0
variable NperBox equal 8.0
#calculate box sizes
variable boxSide equal sqrt(${NperBox}/${dens})
variable boxSide equal sqrt(8/${dens})
variable boxSide equal sqrt(8/0.8)
variable nX equal round(lx/${boxSide})
variable nX equal round(lx/3.16227766016838)
variable nY equal round(ly/${boxSide})
variable nY equal round(ly/3.16227766016838)
variable dX equal lx/${nX}
variable dX equal lx/32
variable dY equal ly/${nY}
variable dY equal ly/13
#temperature of fluid (excluding wall)
compute myT bulk temp
#profile-unbiased temperature of fluid
compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY}
compute myTp bulk temp/profile 1 1 0 xy 32 ${nY}
compute myTp bulk temp/profile 1 1 0 xy 32 13
#thermo setup
thermo ${thermo_rate}
thermo 10
thermo_style custom step c_myT c_myTp etotal press
#dump initial configuration
# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz
# dump 56 wall custom 1 wall.init.lammpstrj id type x y z
# dump_modify 55 sort id
# dump_modify 56 sort id
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 72 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step c_myT c_myTp TotEng Press
0 2 2.0555109 0.77892922 7.3417096
Loop time of 9.53674e-07 on 1 procs for 0 steps with 2775 atoms
314.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 2775 ave 2775 max 2775 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 510 ave 510 max 510 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 26406 ave 26406 max 26406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 26406
Ave neighs/atom = 9.51568
Neighbor list builds = 0
Dangerous builds = 0
# undump 55
# undump 56
#####################################################################
#equilibrate without GD
fix nvt bulk nvt temp $T $T ${tdamp}
fix nvt bulk nvt temp 2 $T ${tdamp}
fix nvt bulk nvt temp 2 2 ${tdamp}
fix nvt bulk nvt temp 2 2 0.1
fix_modify nvt temp myTp
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1395)
fix 2 bulk enforce2d
run ${equil}
run 1000
Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes
Step c_myT c_myTp TotEng Press
0 2 2.0555109 0.77892922 7.3417096
10 1.9173594 1.9390034 0.77876976 7.6702228
20 1.7033394 1.6974676 0.77977799 8.5614784
30 1.5026161 1.4723993 0.78456655 9.4308258
40 1.4880481 1.4591602 0.79486693 9.6134304
50 1.6192437 1.6150635 0.81109069 9.2592835
60 1.7404087 1.7583444 0.82955456 8.952392
70 1.7757591 1.8006606 0.8452778 8.9717917
80 1.7573847 1.7813629 0.85769389 9.1936368
90 1.7491183 1.7726908 0.86882429 9.3712357
100 1.7798944 1.8079583 0.88029084 9.3871755
110 1.8440582 1.8793133 0.89259397 9.2582848
120 1.9191606 1.9673434 0.90533438 9.0680574
130 1.9883299 2.0484299 0.91755461 8.88117
140 2.0463366 2.1111872 0.92818114 8.7184178
150 2.0953769 2.167849 0.93639789 8.5713408
160 2.1442147 2.2216228 0.94145082 8.4082835
170 2.1797848 2.2631458 0.94246877 8.2767903
180 2.1863476 2.2700986 0.93873326 8.2311689
190 2.1832866 2.2710551 0.93003012 8.1959062
200 2.1937154 2.2868403 0.91642537 8.0842007
210 2.2022708 2.2915142 0.89824533 7.9575312
220 2.1884715 2.2770564 0.87677613 7.9000591
230 2.1671124 2.2496063 0.85409501 7.8673156
240 2.1560417 2.2379998 0.83167878 7.8003228
250 2.1421449 2.2240624 0.81004723 7.7491508
260 2.1172164 2.1971044 0.78931978 7.7457415
270 2.0856847 2.1672998 0.76956352 7.7719788
280 2.0670685 2.1449303 0.75073364 7.7524614
290 2.0639481 2.1428374 0.73258016 7.6727716
300 2.055776 2.1361719 0.7147669 7.6095248
310 2.038425 2.1209353 0.69722853 7.5797085
320 2.0203023 2.1066031 0.68006634 7.5521081
330 2.0118478 2.1039797 0.66330302 7.4877535
340 2.0159442 2.1096258 0.64673694 7.3761703
350 2.0166408 2.1075061 0.63020017 7.2788
360 2.0059407 2.0806316 0.61387618 7.2263941
370 1.9964281 2.0642074 0.59814148 7.1728041
380 1.9918446 2.0567527 0.58303017 7.101597
390 1.992835 2.0548138 0.56852431 7.0084774
400 2.0012934 2.0615016 0.55438401 6.8865948
410 2.0084291 2.073418 0.54034073 6.7697478
420 2.007464 2.0786717 0.52617041 6.6849032
430 1.9983712 2.0704366 0.51188183 6.6323103
440 1.9884651 2.0588515 0.49765394 6.5868356
450 1.982221 2.0467396 0.4837102 6.5311681
460 1.9738673 2.031238 0.47021649 6.4882783
470 1.9574246 2.0060447 0.45740021 6.4814923
480 1.9361065 1.9734507 0.44557947 6.4995199
490 1.9251024 1.9562469 0.43506067 6.4858343
500 1.9279545 1.9572145 0.42577835 6.4274765
510 1.9267504 1.9570246 0.41755013 6.3927027
520 1.9093405 1.9393872 0.41031829 6.4281888
530 1.8820555 1.9060756 0.40432569 6.5099401
540 1.86537 1.8912682 0.3999087 6.55843
550 1.8694252 1.9043192 0.39717519 6.5337875
560 1.8835224 1.9294105 0.39589322 6.4760141
570 1.8898719 1.9462433 0.39573596 6.4520041
580 1.8887698 1.9472764 0.39649878 6.4602989
590 1.8945125 1.9550624 0.39810844 6.4470226
600 1.9106571 1.9735939 0.40045321 6.3971026
610 1.9273243 1.98509 0.40330026 6.3474421
620 1.9351802 1.9888986 0.4064498 6.3340566
630 1.9337889 1.9846794 0.40981479 6.3610556
640 1.9257018 1.9757153 0.4134641 6.4184721
650 1.9204429 1.9718256 0.41750942 6.4679594
660 1.9220449 1.9701963 0.42202455 6.4919724
670 1.9230578 1.9707406 0.4270412 6.5178484
680 1.9204554 1.9740485 0.43255127 6.5572507
690 1.9201811 1.9762854 0.43847123 6.5869126
700 1.9271511 1.9867455 0.44474356 6.5882669
710 1.9418851 2.0042477 0.45120727 6.558573
720 1.9544547 2.0186724 0.4576061 6.5338329
730 1.9687971 2.0326169 0.46367507 6.4988775
740 1.9830308 2.0466267 0.46920367 6.4618136
750 1.9936981 2.0526606 0.47397868 6.4367349
760 2.0008431 2.0535449 0.47786748 6.4249001
770 1.9982133 2.0483219 0.48085757 6.4504786
780 1.9841544 2.0311693 0.48306488 6.5200512
790 1.9683122 2.0158738 0.48475632 6.5959263
800 1.9604618 2.003224 0.48619405 6.6392559
810 1.9629155 2.0075077 0.48756075 6.6406486
820 1.9683056 2.0110554 0.48883443 6.6269424
830 1.975409 2.0189161 0.48995399 6.6030215
840 1.9897264 2.035016 0.4907852 6.5485575
850 2.0094338 2.0555358 0.49104505 6.4719926
860 2.0217589 2.0643603 0.49040437 6.4233305
870 2.0147718 2.0641627 0.48866908 6.4491964
880 1.9883859 2.0324092 0.48592007 6.5488061
890 1.9625853 2.0028776 0.48263002 6.6452734
900 1.9520401 1.9889124 0.47925524 6.6808078
910 1.9559583 1.9952984 0.47597346 6.6573059
920 1.9657244 2.0083503 0.47268726 6.6073704
930 1.969288 2.0152339 0.4692054 6.5780416
940 1.9652206 2.0116384 0.4654438 6.5769812
950 1.9567495 1.9960693 0.46147541 6.5942022
960 1.9418452 1.980858 0.45753557 6.6369454
970 1.9247196 1.9585585 0.45390337 6.6888821
980 1.9128262 1.9481721 0.45090045 6.7198221
990 1.9167211 1.9451096 0.44869731 6.6912394
1000 1.935529 1.9662384 0.44728238 6.6079829
Loop time of 1.307 on 1 procs for 1000 steps with 2775 atoms
Performance: 66105.601 tau/day, 765.111 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.7676 | 0.7676 | 0.7676 | 0.0 | 58.73
Neigh | 0.088947 | 0.088947 | 0.088947 | 0.0 | 6.81
Comm | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.72
Output | 0.019547 | 0.019547 | 0.019547 | 0.0 | 1.50
Modify | 0.39755 | 0.39755 | 0.39755 | 0.0 | 30.42
Other | | 0.02394 | | | 1.83
Nlocal: 2775 ave 2775 max 2775 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 527 ave 527 max 527 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24332 ave 24332 max 24332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24332
Ave neighs/atom = 8.76829
Neighbor list builds = 38
Dangerous builds = 0
#####################################################################
#initialize the COM velocity and run to achieve steady-state
#calculate velocity to add: V=J/rho_total
variable Vadd equal $J*lx*ly/count(bulk)
variable Vadd equal 0.1*lx*ly/count(bulk)
#first remove any COM velocity, then add back the streaming velocity
velocity bulk zero linear
velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no
velocity bulk set 0.149532710280374 0.0 0.0 units box sum yes mom no
fix GD bulk flow/gauss 1 0 0 #energy yes
#fix_modify GD energy yes
run ${stabil}
run 1000
Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes
Step c_myT c_myTp TotEng Press
1000 1.9466974 1.9662384 0.45804438 6.615449
1010 1.9605467 1.9815754 0.45717241 6.5545496
1020 1.9560139 1.9823875 0.45660431 6.5672421
1030 1.9348326 1.9691606 0.45633148 6.6463667
1040 1.9167809 1.9449522 0.45657707 6.7139486
1050 1.9193541 1.943342 0.45767968 6.7014054
1060 1.9410751 1.9720491 0.45967742 6.6150379
1070 1.9658493 1.9964883 0.46221539 6.5178418
1080 1.9767205 2.0074304 0.46491236 6.4768594
1090 1.9714544 2.0003054 0.46759126 6.5026957
1100 1.9647035 1.9927455 0.4703109 6.5400181
1110 1.9657667 1.9959656 0.47317481 6.5519094
1120 1.9706062 1.9980802 0.476185 6.5512675
1130 1.9747655 2.0062292 0.47932281 6.554091
1140 1.9761245 2.0075076 0.48248327 6.5670381
1150 1.9744197 2.0073027 0.48562483 6.5914441
1160 1.9722698 2.0046687 0.48874207 6.6165575
1170 1.9692145 2.0013845 0.49187442 6.6438115
1180 1.9665609 1.9970724 0.49508053 6.6693821
1190 1.9625031 1.9908427 0.49843816 6.7002606
1200 1.960528 1.993084 0.50203044 6.7237076
1210 1.9649156 1.9981485 0.50587066 6.7217755
1220 1.9788059 2.0134511 0.50987442 6.6833452
1230 1.9952283 2.0343101 0.51379781 6.6340278
1240 2.0039391 2.0494196 0.51730872 6.6129751
1250 2.0019006 2.0526773 0.52014603 6.6320217
1260 1.9974025 2.0528914 0.52221385 6.6601786
1270 1.9953949 2.0561121 0.5234754 6.6796142
1280 1.9893864 2.0470375 0.5238632 6.7140134
1290 1.9694951 2.019253 0.5235093 6.798442
1300 1.9473901 1.9965919 0.52280384 6.8863369
1310 1.9511151 2.006161 0.52203882 6.8700917
1320 1.979341 2.0388959 0.52106938 6.7529595
1330 2.0073235 2.0720045 0.51935291 6.6297731
1340 2.0202482 2.0841419 0.51624273 6.55803
1350 2.0177489 2.0669046 0.51142591 6.5401753
1360 2.0069274 2.04717 0.50505824 6.5506533
1370 1.994854 2.0311383 0.49743042 6.5633001
1380 1.9793176 2.0077184 0.48890503 6.5859072
1390 1.9580907 1.9839831 0.48004316 6.6288992
1400 1.9415542 1.9594192 0.47143599 6.6534105
1410 1.9405188 1.9591825 0.46353105 6.620549
1420 1.9504784 1.9730647 0.45640199 6.5471784
1430 1.9594158 1.9819854 0.44995052 6.4802874
1440 1.9615108 1.9863792 0.44406411 6.44391
1450 1.9544127 1.9806249 0.43873409 6.4484818
1460 1.9384927 1.9614953 0.43408605 6.4905259
1470 1.9214711 1.9425515 0.43035972 6.5390434
1480 1.9170761 1.9300809 0.42775046 6.5409502
1490 1.9242904 1.9385731 0.42631007 6.5005057
1500 1.9307133 1.9446119 0.4258836 6.4660754
1510 1.9303576 1.9435389 0.42633976 6.4616415
1520 1.9248382 1.9408306 0.42765441 6.4832059
1530 1.9120794 1.9278123 0.42986958 6.5380951
1540 1.899122 1.9125029 0.4331459 6.5987181
1550 1.9030956 1.9187821 0.43765067 6.6012019
1560 1.9182961 1.9453782 0.44330842 6.5674222
1570 1.9272863 1.9613129 0.44971962 6.5619794
1580 1.931679 1.9698134 0.45643436 6.5780809
1590 1.9336692 1.9728684 0.46314752 6.6035675
1600 1.938895 1.9823104 0.46964519 6.6138411
1610 1.9510838 1.9937914 0.47568807 6.5916989
1620 1.9685387 2.0087314 0.48102339 6.5424432
1630 1.9894416 2.0295715 0.48539861 6.4757743
1640 1.9982699 2.0426949 0.48860411 6.4512418
1650 1.9901677 2.0363837 0.49062424 6.4879985
1660 1.9814216 2.0291326 0.49172203 6.5248034
1670 1.9812111 2.0293629 0.49218297 6.5253876
1680 1.9903906 2.0408376 0.49211747 6.4852787
1690 2.0015983 2.0538843 0.4914581 6.4325081
1700 2.009727 2.0503407 0.49011163 6.3878577
1710 2.0167822 2.0531002 0.4881688 6.3477054
1720 2.0189021 2.0445033 0.48564798 6.3273063
1730 2.0129713 2.0354734 0.48270666 6.3385541
1740 2.0048763 2.0199836 0.47950943 6.3587586
1750 1.9994843 2.0085942 0.47624908 6.3694119
1760 1.9940025 2.0072098 0.47305283 6.3816295
1770 1.9817431 1.9974066 0.46994486 6.4224295
1780 1.965171 1.9805421 0.4670779 6.4832371
1790 1.9474078 1.9662605 0.46466823 6.5516524
1800 1.9286009 1.9507751 0.46292015 6.6263366
1810 1.9168087 1.9437961 0.46199899 6.6759834
1820 1.9107555 1.9306323 0.46204129 6.7029857
1830 1.9135569 1.930819 0.46316484 6.6949737
1840 1.9345342 1.9553413 0.46532704 6.6178988
1850 1.9630349 1.9929548 0.46822932 6.5137866
1860 1.9820746 2.0188839 0.47135068 6.4489028
1870 1.9834959 2.0217145 0.47427805 6.4552721
1880 1.9731564 2.0120293 0.47692755 6.5100251
1890 1.9653605 2.0070624 0.47943307 6.5594235
1900 1.9630631 2.0095488 0.48192185 6.5912876
1910 1.9556778 2.0035006 0.48443107 6.6437189
1920 1.9408788 1.9828296 0.48710124 6.7228731
1930 1.9292393 1.9732376 0.49025327 6.7880112
1940 1.9263081 1.9708942 0.49416086 6.8162477
1950 1.9358375 1.976323 0.49899895 6.7946964
1960 1.9520543 1.9936542 0.50485961 6.7467481
1970 1.9709064 2.0108957 0.51165586 6.6909455
1980 1.9940026 2.0375428 0.51918913 6.6250463
1990 2.0171261 2.0646948 0.52705638 6.5649879
2000 2.0302713 2.0802515 0.53472229 6.5470853
Loop time of 1.34877 on 1 procs for 1000 steps with 2775 atoms
Performance: 64058.154 tau/day, 741.414 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77091 | 0.77091 | 0.77091 | 0.0 | 57.16
Neigh | 0.085835 | 0.085835 | 0.085835 | 0.0 | 6.36
Comm | 0.0093472 | 0.0093472 | 0.0093472 | 0.0 | 0.69
Output | 0.019047 | 0.019047 | 0.019047 | 0.0 | 1.41
Modify | 0.43949 | 0.43949 | 0.43949 | 0.0 | 32.58
Other | | 0.02415 | | | 1.79
Nlocal: 2775 ave 2775 max 2775 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 530 ave 530 max 530 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24404 ave 24404 max 24404 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24404
Ave neighs/atom = 8.79423
Neighbor list builds = 36
Dangerous builds = 0
#####################################################################
#collect data
#print the applied force and total flux to ensure conservation of Jx
variable Fapp equal f_GD[1]
compute vxBulk bulk reduce sum vx
compute vyBulk bulk reduce sum vy
variable invVol equal 1.0/(lx*ly)
variable jx equal c_vxBulk*${invVol}
variable jx equal c_vxBulk*0.00025
variable jy equal c_vyBulk*${invVol}
variable jy equal c_vyBulk*0.00025
variable curr_step equal step
variable p_Fapp format Fapp %.3f
variable p_jx format jx %.5g
variable p_jy format jy %.5g
fix print_vCOM all print ${dump_rate} "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy"
fix print_vCOM all print 50 "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy"
#compute IK1 pressure profile
#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627
#use profile-unbiased temperature to remove the streaming velocity
#from the kinetic part of the pressure
compute spa bulk stress/atom myTp
#for the pressure profile, use the same grid as the PUT
compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box
compute chunkX bulk chunk/atom bin/1d x lower 3.125 units box
#output pressure profile and other profiles
#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where
#V is the volume of a slice
fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite
fix profiles bulk ave/chunk 1 1 50 chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite
#compute velocity profile across the pipe with a finer grid
variable dYnew equal ${dY}/10
variable dYnew equal 3.07692307692308/10
compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box region pipe
compute chunkY bulk chunk/atom bin/1d y center 0.307692307692308 units box region pipe
fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY vx file Vy_profile ave running overwrite
fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy_profile ave running overwrite
#full trajectory
# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z
# dump_modify 7 sort id
run ${run}
run 2000
Per MPI rank memory allocation (min/avg/max) = 5.174 | 5.174 | 5.174 Mbytes
Step c_myT c_myTp TotEng Press
2000 2.0302713 2.0802515 0.53472229 6.5470853
2010 2.0303419 2.0806129 0.54177821 6.5808527
2020 2.0245167 2.0792991 0.54803523 6.6381758
2030 2.0169072 2.065404 0.55345227 6.7008962
2040 2.0052526 2.0513817 0.55818432 6.7755868
2050 1.9953625 2.0366564 0.56245299 6.8382569
2060 2.0003667 2.0462109 0.56649798 6.8390557
2070 2.0238288 2.0834553 0.57023651 6.7637821
2080 2.045765 2.1173867 0.5730944 6.6861321
2090 2.0563925 2.1370313 0.57430831 6.6422581
2100 2.0620437 2.1480293 0.57319824 6.6080678
2110 2.0584437 2.1473173 0.56913597 6.5969671
2120 2.0532825 2.1393006 0.56154606 6.5799417
2130 2.0450143 2.1234905 0.55009479 6.5616931
2140 2.0229537 2.1004507 0.53511912 6.5854627
2150 1.9832556 2.0554119 0.51812599 6.6700591
2160 1.9444027 2.0110758 0.50163049 6.7534263
2170 1.9267473 1.9904528 0.48759542 6.76469
2180 1.9262232 1.9809353 0.47662199 6.7188048
2190 1.9359331 1.9854626 0.46836289 6.6406985
2200 1.9530728 1.9971865 0.4620366 6.5409943
2210 1.9657099 2.0056761 0.45692542 6.4639397
2220 1.9661008 2.0046161 0.45253504 6.4388081
2230 1.9574696 1.9947839 0.44864257 6.4528687
2240 1.9522284 1.9922663 0.44518111 6.4584458
2250 1.9518203 1.9950044 0.44206844 6.4491722
2260 1.9527908 1.9989603 0.4391804 6.4377912
2270 1.9452231 1.9932538 0.43643529 6.4607516
2280 1.9249341 1.9759145 0.43392742 6.5320897
2290 1.9087464 1.960985 0.43186869 6.5875176
2300 1.9103289 1.964731 0.43039882 6.5765021
2310 1.9182062 1.9783814 0.4294628 6.5434488
2320 1.9204281 1.9796609 0.42889381 6.5351629
2330 1.916279 1.9720659 0.42866391 6.5562619
2340 1.9062866 1.9587628 0.42890166 6.6033936
2350 1.9024117 1.9566812 0.42979475 6.6297969
2360 1.908153 1.960687 0.43141898 6.6215148
2370 1.9115944 1.9663337 0.43376668 6.6236491
2380 1.9086193 1.9637867 0.4367911 6.6529568
2390 1.9039907 1.9610268 0.44053991 6.6926343
2400 1.9034944 1.9609406 0.44508818 6.7193441
2410 1.9151521 1.9753641 0.4504458 6.7015957
2420 1.9314517 1.9925924 0.45644382 6.6669864
2430 1.9433933 2.0062001 0.46277215 6.6481527
2440 1.9504631 2.0087015 0.46917209 6.6475757
2450 1.9550092 2.0094957 0.47550077 6.6556459
2460 1.9609689 2.0147997 0.48170141 6.6568282
2470 1.9730726 2.0328127 0.48763131 6.6337545
2480 1.9838562 2.0466643 0.49303443 6.6143423
2490 1.9862031 2.0473388 0.49767532 6.6245587
2500 1.9817565 2.0455432 0.50152131 6.6573893
2510 1.9785788 2.0423176 0.50460561 6.6808042
2520 1.9823006 2.0505106 0.50696374 6.6726698
2530 1.9907178 2.0553736 0.50852885 6.6402082
2540 2.0005205 2.0690408 0.50919421 6.5966469
2550 2.0079727 2.0809816 0.50872954 6.5568419
2560 2.0133128 2.096271 0.50682742 6.5199915
2570 2.0141298 2.0990846 0.50314491 6.4951991
2580 2.0048768 2.0874319 0.49750096 6.5025454
2590 1.9876498 2.0638834 0.4900201 6.5333038
2600 1.9720479 2.0474479 0.48105263 6.5527157
2610 1.9596324 2.0355764 0.4710001 6.5547867
2620 1.9439039 2.0106405 0.46046644 6.5646889
2630 1.9321714 1.9924346 0.45021207 6.5589454
2640 1.9349378 1.9923889 0.44082833 6.5012762
2650 1.9448459 2.0069955 0.43251999 6.4228945
2660 1.9446852 2.0050346 0.42525857 6.3921645
2670 1.9325594 1.9884937 0.41913362 6.4169726
2680 1.9121687 1.9606084 0.41434428 6.4821267
2690 1.8923613 1.9339385 0.41105831 6.5517615
2700 1.8807238 1.9191801 0.40933203 6.5949447
2710 1.8797367 1.918758 0.40906826 6.6001309
2720 1.8852961 1.9225996 0.41005611 6.58191
2730 1.8937478 1.9357751 0.41204348 6.5541946
2740 1.9019279 1.9449374 0.41476104 6.5278575
2750 1.9134396 1.9614415 0.41800066 6.4890769
2760 1.9339551 1.9913779 0.42150554 6.4159805
2770 1.9597826 2.0220988 0.42487614 6.3232273
2780 1.9753466 2.0414907 0.42771704 6.2715489
2790 1.9720423 2.0402016 0.42976012 6.2949288
2800 1.9512893 2.0172711 0.43109201 6.3878056
2810 1.9232302 1.9870212 0.4320928 6.5101822
2820 1.9026913 1.959286 0.43326424 6.6024967
2830 1.9033802 1.9621601 0.43500785 6.6114274
2840 1.9214292 1.9833838 0.43733454 6.5508757
2850 1.9440563 2.0087358 0.43995473 6.4713496
2860 1.9589136 2.0211107 0.44250821 6.4232961
2870 1.9588429 2.022232 0.44477492 6.4355861
2880 1.9456751 2.0009513 0.44676532 6.5021746
2890 1.9269155 1.9782929 0.44877858 6.5926531
2900 1.9125262 1.9554653 0.45121196 6.6657808
2910 1.9187855 1.9572583 0.45438665 6.6589954
2920 1.9416112 1.9784518 0.45839212 6.5888253
2930 1.9613579 1.9975032 0.46305788 6.5317424
2940 1.9711529 2.0102501 0.46812715 6.5148943
2950 1.9707865 2.0133283 0.47345305 6.5389543
2960 1.9732526 2.0170219 0.47898306 6.5537092
2970 1.9871126 2.0282309 0.48465048 6.5273492
2980 1.9953449 2.0404164 0.49032615 6.5227325
2990 1.9909136 2.037246 0.49581423 6.5664662
3000 1.9872474 2.0307896 0.5011051 6.6060698
3010 1.9944885 2.0457308 0.5062755 6.6031811
3020 2.0103461 2.0599491 0.51116655 6.5654871
3030 2.0240275 2.077342 0.5154921 6.5358852
3040 2.0205953 2.0704954 0.51898871 6.5708937
3050 2.0032184 2.0463036 0.52167438 6.657741
3060 1.9889341 2.0265284 0.52385964 6.7329171
3070 1.9795143 2.0201081 0.52588914 6.7881407
3080 1.9713362 2.0123964 0.52797238 6.8362858
3090 1.9692592 2.0106467 0.53025538 6.8616268
3100 1.9722487 2.0259566 0.53277635 6.8689898
3110 1.9703322 2.0314028 0.53541462 6.895271
3120 1.9594359 2.0217586 0.53808512 6.954362
3130 1.9524729 2.0148628 0.5409094 6.9965233
3140 1.9630381 2.0260807 0.54400259 6.968082
3150 1.9902598 2.0549364 0.54720142 6.8698796
3160 2.029715 2.0923999 0.54995378 6.7193678
3170 2.0581544 2.1137995 0.55150021 6.6053728
3180 2.0590739 2.1156535 0.55123668 6.5919337
3190 2.0400682 2.0904721 0.54894762 6.6505757
3200 2.0211594 2.0682597 0.54484887 6.7046468
3210 2.012712 2.0573114 0.53922056 6.7130909
3220 2.0102377 2.0554701 0.53219251 6.6919068
3230 2.0017671 2.0505068 0.52386898 6.6867054
3240 1.9854941 2.0308454 0.51458791 6.7051085
3250 1.9767009 2.0187664 0.50486784 6.6916859
3260 1.9771733 2.0186148 0.49510721 6.6424305
3270 1.974003 2.0136039 0.48556818 6.6078903
3280 1.9627665 1.9989122 0.47654147 6.6067904
3290 1.9491247 1.9826247 0.46834865 6.6186709
3300 1.9414093 1.9724941 0.4612122 6.6119543
3310 1.9433901 1.9715482 0.45518879 6.570612
3320 1.9518837 1.9872717 0.45010165 6.5057947
3330 1.9603874 1.9957995 0.44566728 6.4428221
3340 1.9615962 1.9945224 0.44167201 6.4099339
3350 1.955918 1.9882866 0.4380303 6.4070811
3360 1.9463445 1.9763654 0.43480086 6.4241178
3370 1.9411187 1.9683081 0.4320639 6.4296577
3380 1.9407224 1.9580074 0.42991627 6.4210217
3390 1.9402479 1.9530447 0.42850635 6.4170536
3400 1.9451337 1.9555771 0.42787382 6.3990336
3410 1.9475586 1.9612432 0.42797178 6.3953251
3420 1.9434927 1.960532 0.4286887 6.4210681
3430 1.9339054 1.9516935 0.43003682 6.4707071
3440 1.9234014 1.9464343 0.43214965 6.5248205
3450 1.9191846 1.9444777 0.43516361 6.5558451
3460 1.923218 1.9594606 0.43915611 6.5549213
3470 1.9328953 1.9792053 0.44397878 6.5327637
3480 1.9466227 1.9997841 0.44940599 6.4954965
3490 1.9672374 2.0323219 0.45511091 6.4358811
3500 1.9799622 2.0479841 0.46061029 6.4100217
3510 1.97942 2.0493411 0.46551964 6.4368108
3520 1.9725674 2.0389602 0.46976379 6.4892049
3530 1.9716429 2.0389798 0.47344292 6.5200899
3540 1.9789254 2.0486162 0.47659268 6.5198212
3550 1.9872455 2.0577517 0.47908145 6.5144586
3560 1.9808834 2.0545963 0.48076562 6.5633282
3570 1.9637165 2.0335394 0.4816783 6.6519124
3580 1.9407948 2.0067763 0.48212406 6.7605224
3590 1.9226532 1.9825887 0.482523 6.8486041
3600 1.9135067 1.9700999 0.48328349 6.8977859
3610 1.9157516 1.9720028 0.48470695 6.8977759
3620 1.9328644 2.0001154 0.48688778 6.8361569
3630 1.9568208 2.0243053 0.48963934 6.7442107
3640 1.9824587 2.0569223 0.49259174 6.6452535
3650 1.9934906 2.0686357 0.49529039 6.6020218
3660 1.9996281 2.0747054 0.49732231 6.5808905
3670 2.0038801 2.0772777 0.49838834 6.5691351
3680 1.9941342 2.0712365 0.49826732 6.6088108
3690 1.9762631 2.0486045 0.49689109 6.6739003
3700 1.9667284 2.034939 0.49438991 6.7010266
3710 1.9615089 2.0168112 0.49093736 6.7040385
3720 1.9613068 2.014749 0.48673789 6.6813041
3730 1.9731234 2.0290151 0.48175562 6.6096756
3740 1.9829764 2.0461907 0.47575174 6.5424752
3750 1.9792839 2.0454423 0.4685271 6.5237752
3760 1.9599692 2.0287015 0.46022485 6.5616271
3770 1.935975 2.0000948 0.45138017 6.6136471
3780 1.9236713 1.9834802 0.44262437 6.6187463
3790 1.9268004 1.9875324 0.43430113 6.5632772
3800 1.932601 1.9872595 0.42649564 6.4984765
3810 1.9322506 1.9814946 0.41928856 6.4617054
3820 1.9245737 1.9712821 0.4128224 6.461378
3830 1.9148568 1.9555602 0.40721003 6.4774474
3840 1.9049961 1.9457058 0.4026118 6.5029211
3850 1.8915137 1.9265199 0.39914962 6.5483592
3860 1.8784768 1.9058055 0.39700153 6.5962113
3870 1.8755236 1.9045158 0.39632769 6.6079033
3880 1.8841415 1.9140314 0.39710038 6.5777071
3890 1.8958027 1.9331148 0.39918951 6.5359786
3900 1.9064085 1.948805 0.40238576 6.4998591
3910 1.9185092 1.9675732 0.40647523 6.4610682
3920 1.9342595 1.9933225 0.41115392 6.4122308
3930 1.9482664 2.007614 0.41603495 6.373684
3940 1.9557759 2.0161573 0.42084462 6.3636707
3950 1.9573687 2.016612 0.42540421 6.3804123
3960 1.9486354 1.9998027 0.42974612 6.4404943
3970 1.936214 1.980721 0.43412037 6.5176787
3980 1.9274292 1.9595259 0.43885103 6.5846211
3990 1.9233082 1.953436 0.44425085 6.6354275
4000 1.9289165 1.9522097 0.45042645 6.6513836
Loop time of 2.49114 on 1 procs for 2000 steps with 2775 atoms
Performance: 69365.902 tau/day, 802.846 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4257 | 1.4257 | 1.4257 | 0.0 | 57.23
Neigh | 0.15501 | 0.15501 | 0.15501 | 0.0 | 6.22
Comm | 0.017206 | 0.017206 | 0.017206 | 0.0 | 0.69
Output | 0.034183 | 0.034183 | 0.034183 | 0.0 | 1.37
Modify | 0.81531 | 0.81531 | 0.81531 | 0.0 | 32.73
Other | | 0.04374 | | | 1.76
Nlocal: 2775 ave 2775 max 2775 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 517 ave 517 max 517 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24366 ave 24366 max 24366 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24366
Ave neighs/atom = 8.78054
Neighbor list builds = 72
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05
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