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) 4 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) = 3.067 | 3.068 | 3.07 Mbytes Step c_myT c_myTp TotEng Press 0 2 2.0555109 0.77892922 7.3417096 Loop time of 4.35114e-06 on 4 procs for 0 steps with 2775 atoms 114.9% CPU use with 4 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 | | 4.351e-06 | | |100.00 Nlocal: 693.75 ave 800 max 578 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 266.25 ave 325 max 198 min Histogram: 1 1 0 0 0 0 0 0 0 2 Neighs: 6601.5 ave 8000 max 5147 min Histogram: 2 0 0 0 0 0 0 0 0 2 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) = 3.13 | 3.131 | 3.132 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 0.474418 on 4 procs for 1000 steps with 2775 atoms Performance: 182118.045 tau/day, 2107.848 timesteps/s 98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13953 | 0.19068 | 0.23764 | 10.4 | 40.19 Neigh | 0.016439 | 0.022345 | 0.027069 | 3.2 | 4.71 Comm | 0.018215 | 0.068071 | 0.12178 | 18.6 | 14.35 Output | 0.011982 | 0.012633 | 0.013047 | 0.4 | 2.66 Modify | 0.14494 | 0.15597 | 0.16628 | 2.4 | 32.88 Other | | 0.02472 | | | 5.21 Nlocal: 693.75 ave 800 max 584 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 255.5 ave 323 max 192 min Histogram: 2 0 0 0 0 0 0 0 1 1 Neighs: 6083 ave 7384 max 4742 min Histogram: 2 0 0 0 0 0 0 0 0 2 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) = 3.13 | 3.131 | 3.132 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 0.482133 on 4 procs for 1000 steps with 2775 atoms Performance: 179203.608 tau/day, 2074.116 timesteps/s 98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1081 | 0.18228 | 0.23471 | 12.7 | 37.81 Neigh | 0.011443 | 0.019967 | 0.025651 | 4.1 | 4.14 Comm | 0.01639 | 0.073615 | 0.15634 | 21.8 | 15.27 Output | 0.011851 | 0.012603 | 0.013287 | 0.5 | 2.61 Modify | 0.14306 | 0.16634 | 0.18018 | 3.6 | 34.50 Other | | 0.02733 | | | 5.67 Nlocal: 693.75 ave 797 max 590 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 259 ave 320 max 195 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 6101 ave 7360 max 4853 min Histogram: 2 0 0 0 0 0 0 0 0 2 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) = 5.138 | 5.139 | 5.14 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 0.50110509 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 2.059074 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 0.53922057 6.7130909 3220 2.0102377 2.0554701 0.53219251 6.6919069 3230 2.0017671 2.0505068 0.52386898 6.6867054 3240 1.9854941 2.0308454 0.51458792 6.7051085 3250 1.9767009 2.0187664 0.50486785 6.6916859 3260 1.9771733 2.0186148 0.49510722 6.6424305 3270 1.974003 2.0136039 0.48556819 6.6078903 3280 1.9627665 1.9989122 0.47654147 6.6067904 3290 1.9491247 1.9826248 0.46834866 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 0.43206391 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 0.46976378 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 2.0545962 0.48076561 6.5633282 3570 1.9637165 2.0335394 0.4816783 6.6519124 3580 1.9407948 2.0067763 0.48212405 6.7605224 3590 1.9226532 1.9825887 0.48252299 6.8486041 3600 1.9135067 1.9700999 0.48328348 6.8977858 3610 1.9157516 1.9720028 0.48470695 6.8977759 3620 1.9328644 2.0001154 0.48688777 6.8361569 3630 1.9568208 2.0243053 0.48963933 6.7442107 3640 1.9824587 2.0569223 0.49259173 6.6452535 3650 1.9934906 2.0686356 0.49529038 6.6020218 3660 1.9996281 2.0747054 0.4973223 6.5808904 3670 2.0038801 2.0772777 0.49838833 6.5691351 3680 1.9941342 2.0712365 0.49826732 6.6088107 3690 1.9762631 2.0486045 0.49689108 6.6739002 3700 1.9667284 2.0349391 0.4943899 6.7010265 3710 1.9615089 2.0168112 0.49093735 6.7040384 3720 1.9613068 2.0147489 0.48673788 6.6813041 3730 1.9731234 2.0290151 0.48175561 6.6096757 3740 1.9829764 2.0461907 0.47575173 6.5424752 3750 1.9792839 2.0454423 0.46852709 6.5237753 3760 1.9599692 2.0287014 0.46022484 6.5616271 3770 1.935975 2.0000948 0.45138016 6.6136471 3780 1.9236713 1.9834802 0.44262435 6.6187463 3790 1.9268004 1.9875324 0.43430112 6.5632772 3800 1.932601 1.9872595 0.42649563 6.4984764 3810 1.9322506 1.9814946 0.41928855 6.4617054 3820 1.9245737 1.9712821 0.4128224 6.4613779 3830 1.9148568 1.9555602 0.40721003 6.4774474 3840 1.9049961 1.9457058 0.40261179 6.5029211 3850 1.8915137 1.9265199 0.39914961 6.5483592 3860 1.8784768 1.9058055 0.39700153 6.5962113 3870 1.8755236 1.9045158 0.39632768 6.6079033 3880 1.8841415 1.9140314 0.39710037 6.577707 3890 1.8958027 1.9331149 0.39918951 6.5359785 3900 1.9064085 1.948805 0.40238576 6.499859 3910 1.9185092 1.9675733 0.40647523 6.4610682 3920 1.9342595 1.9933225 0.41115392 6.4122308 3930 1.9482664 2.0076139 0.41603495 6.3736841 3940 1.9557759 2.0161573 0.42084462 6.3636708 3950 1.9573687 2.016612 0.42540421 6.3804124 3960 1.9486354 1.9998027 0.42974612 6.4404944 3970 1.936214 1.9807209 0.43412037 6.5176788 3980 1.9274292 1.9595259 0.43885103 6.5846212 3990 1.9233082 1.953436 0.44425085 6.6354276 4000 1.9289166 1.9522097 0.45042645 6.6513835 Loop time of 0.998413 on 4 procs for 2000 steps with 2775 atoms Performance: 173074.634 tau/day, 2003.179 timesteps/s 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25646 | 0.3672 | 0.47947 | 15.7 | 36.78 Neigh | 0.027925 | 0.039163 | 0.050221 | 4.5 | 3.92 Comm | 0.032807 | 0.14565 | 0.27684 | 25.4 | 14.59 Output | 0.025572 | 0.032272 | 0.035355 | 2.2 | 3.23 Modify | 0.31519 | 0.35781 | 0.375 | 4.1 | 35.84 Other | | 0.05632 | | | 5.64 Nlocal: 693.75 ave 805 max 582 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 255.5 ave 312 max 199 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 6091.5 ave 7423 max 4780 min Histogram: 2 0 0 0 0 0 0 0 0 2 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: 0:00:01