LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task #LAMMPS input script #in.GD #see README for details ############################################################################### #initialize variables clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) 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} -0.1 0.1 units box region simbox block -50 ${lx2} -${ly2} ${ly2} -0.1 0.1 units box region simbox block -50 50 -${ly2} ${ly2} -0.1 0.1 units box region simbox block -50 50 -20 ${ly2} -0.1 0.1 units box region simbox block -50 50 -20 20 -0.1 0.1 units box create_box 2 simbox Created orthogonal box = (-50 -20 -0.1) 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 using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) create_atoms CPU = 0.002 seconds #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 Changing box ... orthogonal box = (-50 -20 -0.1) 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 using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) create_atoms CPU = 0.002 seconds 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 System init for delete_atoms ... Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule 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 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 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 with time integration, atoms won't move (src/verlet.cpp:60) Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.104 | 3.104 Mbytes Step c_myT c_myTp TotEng Press 0 2 2.054601 0.77892922 7.3417096 Loop time of 6.85e-07 on 1 procs for 0 steps with 2775 atoms 146.0% 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 | | 6.85e-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 = 9.5156757 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 (src/fix_nh.cpp:1391) fix 2 bulk enforce2d run ${equil} run 1000 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes Step c_myT c_myTp TotEng Press 0 2 2.054601 0.77892922 7.3417096 10 1.9173668 1.9381538 0.77877698 7.6702283 20 1.7033651 1.6967466 0.7798044 8.5615039 30 1.5026644 1.4718046 0.78461914 9.4308883 40 1.4881235 1.4586031 0.79494919 9.6135307 50 1.6193439 1.6144665 0.81119835 9.2594114 60 1.7405127 1.7576881 0.82966956 8.9525458 70 1.7758506 1.7999706 0.84538866 8.9719793 80 1.7574736 1.7806782 0.85780732 9.1938511 90 1.7492232 1.7720284 0.86895259 9.3714617 100 1.7800292 1.807315 0.88044504 9.3874107 110 1.8442295 1.878681 0.89278276 9.2585436 120 1.9193695 1.9667163 0.90556381 9.0683654 130 1.9885753 2.0478097 0.91782871 8.8815507 140 2.04662 2.1105827 0.92850319 8.718882 150 2.0957046 2.1672706 0.93677238 8.5718869 160 2.144595 2.2210801 0.94188484 8.4089161 170 2.1802133 2.2626399 0.9429713 8.2775682 180 2.1868284 2.2696504 0.93931537 8.2321283 190 2.1838369 2.2706873 0.93069783 8.1970105 200 2.1943436 2.2865542 0.91717737 8.0854148 210 2.2029439 2.2912731 0.89906796 7.9589187 220 2.1891494 2.2768232 0.87764254 7.9016509 230 2.1677848 2.2493747 0.85497463 7.8690125 240 2.156695 2.2377486 0.83255207 7.8020978 250 2.142758 2.2237662 0.81090722 7.7510242 260 2.1177881 2.1967699 0.79016944 7.7477503 270 2.0862408 2.1669583 0.77040874 7.7740216 280 2.0676515 2.1446262 0.75157955 7.7544068 290 2.0645498 2.1425534 0.73343008 7.6746729 300 2.0563664 2.1358776 0.71562279 7.6114783 310 2.0390115 2.1198472 0.69809211 7.581719 320 2.0209035 2.1063385 0.68093855 7.5540946 330 2.012488 2.1037583 0.66418283 7.4896097 340 2.0166095 2.1094212 0.64762479 7.3779677 350 2.0172861 2.1072653 0.63109595 7.2807114 360 2.0065768 2.0803788 0.6147802 7.2283814 370 1.9970858 2.0639903 0.59905362 7.1747592 380 1.9925189 2.056563 0.58395055 7.103506 390 1.9935388 2.0546596 0.56945318 7.010305 400 2.0020199 2.0632095 0.55532013 6.8883647 410 2.009157 2.0732883 0.54128082 6.771521 420 2.0081687 2.0785184 0.52711525 6.6868076 430 1.9990498 2.0705469 0.51283203 6.6343482 440 1.9891528 2.0586814 0.4986104 6.5888679 450 1.9829175 2.0465778 0.4846738 6.5332233 460 1.9745599 2.031067 0.4711878 6.4903915 470 1.9581101 2.006674 0.45837961 6.4836654 480 1.9367964 1.9732882 0.44656667 6.501731 490 1.9258333 1.9561395 0.43605676 6.4879447 500 1.9287 1.9571319 0.42678362 6.4296036 510 1.9274696 1.9569118 0.41856553 6.3949919 520 1.9100149 1.9392424 0.41134511 6.4307452 530 1.8827127 1.9059412 0.40536565 6.5126603 540 1.8660696 1.8912024 0.40096324 6.5610607 550 1.8701883 1.9043254 0.3982457 6.536251 560 1.8842923 1.9289528 0.39698123 6.4785367 570 1.8906147 1.9462124 0.39684504 6.4547374 580 1.8895472 1.9472747 0.39763233 6.4630103 590 1.895375 1.9551336 0.39926725 6.449517 600 1.9115711 1.9737109 0.40163655 6.3995241 610 1.92823 1.9851787 0.404506 6.3499339 620 1.9360678 1.9889572 0.40767569 6.3367514 630 1.9346853 1.9836719 0.41105958 6.3637995 640 1.9266095 1.9757908 0.41472954 6.4212842 650 1.9213863 1.9719496 0.41879537 6.4707692 660 1.922962 1.9702923 0.42332926 6.4949933 670 1.9238956 1.9707534 0.42836303 6.5212631 680 1.9212675 1.9740379 0.43388709 6.5608915 690 1.9210314 1.976311 0.43982007 6.5904702 700 1.928081 1.9868449 0.44610463 6.5915021 710 1.9428895 2.0044235 0.45257857 6.5616141 720 1.9554783 2.0176139 0.45898384 6.5367529 730 1.969838 2.0327907 0.46505662 6.5017635 740 1.9840204 2.0467126 0.47058703 6.4649226 750 1.9946633 2.0526929 0.47535832 6.4399342 760 2.0018048 2.0535606 0.47924291 6.4280737 770 1.9991703 2.0483426 0.48222842 6.4537535 780 1.9850797 2.0312444 0.48443072 6.5234271 790 1.9691589 2.0154006 0.4861158 6.5995894 800 1.9612641 2.0031407 0.48754831 6.6430968 810 1.9637155 2.0074142 0.48891261 6.6444644 820 1.9691691 2.0110229 0.49018604 6.6304512 830 1.9763962 2.0190998 0.49130448 6.6060594 840 1.9908278 2.0352615 0.49213189 6.5510683 850 2.0105715 2.0558403 0.49238435 6.4743276 860 2.0227982 2.0645732 0.49173076 6.4260863 870 2.015555 2.064081 0.48998228 6.4528588 880 1.9889672 2.0320831 0.48722022 6.5532269 890 1.9632172 2.0025881 0.48392295 6.6494723 900 1.9527429 1.9887196 0.48054642 6.6846937 910 1.9567815 1.9953408 0.47726539 6.6606541 920 1.9666996 2.0084955 0.47397593 6.6100666 930 1.9702885 2.014774 0.47048741 6.5805871 940 1.9661802 2.0116846 0.46671831 6.579539 950 1.9576953 1.9960728 0.46273983 6.5967841 960 1.9428073 1.9802284 0.45879028 6.6395002 970 1.9256011 1.9584581 0.45515059 6.6916425 980 1.913512 1.9478848 0.45214528 6.7233279 990 1.9174938 1.9449699 0.44994026 6.6943867 1000 1.9365527 1.9663901 0.44852349 6.6101761 Loop time of 0.324261 on 1 procs for 1000 steps with 2775 atoms Performance: 266452.077 tau/day, 3083.936 timesteps/s, 8.558 Matom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19361 | 0.19361 | 0.19361 | 0.0 | 59.71 Neigh | 0.025544 | 0.025544 | 0.025544 | 0.0 | 7.88 Comm | 0.0023292 | 0.0023292 | 0.0023292 | 0.0 | 0.72 Output | 0.0046269 | 0.0046269 | 0.0046269 | 0.0 | 1.43 Modify | 0.092779 | 0.092779 | 0.092779 | 0.0 | 28.61 Other | | 0.005374 | | | 1.66 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 = 8.7682883 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 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Gaussian dynamics package: doi:10.1021/acs.jpcb.6b09387 @Article{strong_water_2017, title = {The Dynamics of Water in Porous Two-Dimensional Crystals}, volume = {121}, number = {1}, url = {https://doi.org/10.1021/acs.jpcb.6b09387}, doi = {10.1021/acs.jpcb.6b09387}, urldate = {2016-12-07}, journal = {J.~Phys.\ Chem.~B}, author = {Strong, Steven E. and Eaves, Joel D.}, year = {2017}, pages = {189--207} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes Step c_myT c_myTp TotEng Press 1000 1.9477212 1.9663901 0.45928547 6.6176422 1010 1.9617328 1.9828061 0.45840963 6.555968 1020 1.9570976 1.9825696 0.45782895 6.5690613 1030 1.9356292 1.9690101 0.45753984 6.6493822 1040 1.9174914 1.9448868 0.4577768 6.7171474 1050 1.9202482 1.9432766 0.4588733 6.7039634 1060 1.9419998 1.9718217 0.46086407 6.617366 1070 1.9666048 1.996346 0.46339522 6.5207175 1080 1.9775489 2.0078489 0.46608862 6.4794239 1090 1.9725172 2.0005028 0.46876174 6.5044299 1100 1.9659582 1.9931537 0.47147394 6.5409107 1110 1.9670607 1.9965504 0.47432892 6.5527414 1120 1.9716302 1.9984924 0.47732198 6.5530022 1130 1.9752703 2.0057031 0.48043914 6.5579379 1140 1.976368 2.0061152 0.48358744 6.5719123 1150 1.9748014 2.0056689 0.48673155 6.5957896 1160 1.9729115 2.0036854 0.48986563 6.6200102 1170 1.9702742 2.0016461 0.49302426 6.6455948 1180 1.9680418 1.9978705 0.49625385 6.6697165 1190 1.9640159 1.9937501 0.49962311 6.7004634 1200 1.9616719 1.9932085 0.50320747 6.7253219 1210 1.9658831 1.9985624 0.50702861 6.7242078 1220 1.9790884 2.0132679 0.51100573 6.688483 1230 1.9946749 2.0324782 0.51491484 6.6422423 1240 2.0039182 2.0484588 0.5184382 6.6190292 1250 2.0033685 2.0545791 0.52130299 6.6322608 1260 1.9991533 2.0533011 0.52339221 6.6590872 1270 1.9969511 2.0571182 0.5246505 6.6789676 1280 1.9911353 2.0488281 0.52501304 6.7125634 1290 1.9712819 2.0209437 0.52460315 6.7967237 1300 1.9486195 1.9967749 0.5238106 6.886265 1310 1.951612 2.0051749 0.52294383 6.8723332 1320 1.9800953 2.0397207 0.52186525 6.7537937 1330 2.0084961 2.0723584 0.52001894 6.6279995 1340 2.021654 2.085105 0.51675149 6.554461 1350 2.0193685 2.0672662 0.5117514 6.5349176 1360 2.0084017 2.0471065 0.50518646 6.5453141 1370 1.994978 2.030683 0.49737164 6.5627932 1380 1.9781978 2.0044236 0.48871071 6.5903683 1390 1.9572368 1.9833426 0.47978207 6.6326472 1400 1.9400481 1.956474 0.47117436 6.6600696 1410 1.9380218 1.9552501 0.46336325 6.6314231 1420 1.9494747 1.9681145 0.45642218 6.5527615 1430 1.9610978 1.9824506 0.4501938 6.4763851 1440 1.9639503 1.9890985 0.44452289 6.4375535 1450 1.9560428 1.9821594 0.43936988 6.4453654 1460 1.9399344 1.9627639 0.43486138 6.488055 1470 1.9247229 1.9440629 0.43123378 6.5292381 1480 1.9213375 1.9369273 0.42866841 6.5271097 1490 1.9265729 1.9383637 0.42719968 6.4940959 1500 1.930987 1.9416689 0.4267225 6.4673585 1510 1.9303444 1.9418498 0.42714462 6.4648027 1520 1.9258423 1.940384 0.42844066 6.4834098 1530 1.9131202 1.9296653 0.4306338 6.5390881 1540 1.8990016 1.9101025 0.43386405 6.6052091 1550 1.9012878 1.9120047 0.43834036 6.6147792 1560 1.9153287 1.9388751 0.44404054 6.5851781 1570 1.9266928 1.9596147 0.45057056 6.5705776 1580 1.9358289 1.9745564 0.45744022 6.5674622 1590 1.9415248 1.9818707 0.46425451 6.5778534 1600 1.9466876 1.98498 0.47075833 6.5878483 1610 1.9557175 1.9930268 0.47674103 6.5777205 1620 1.9712902 2.0112337 0.48200984 6.5367922 1630 1.9900646 2.0303946 0.48631888 6.4790095 1640 1.9960901 2.039173 0.48947508 6.4661574 1650 1.9879046 2.0329046 0.49151173 6.504063 1660 1.9832967 2.0325843 0.49266284 6.5255647 1670 1.9875656 2.034783 0.49313513 6.5093662 1680 1.9967654 2.0492931 0.49299896 6.4699787 1690 2.0025957 2.0532539 0.49216931 6.4389613 1700 2.0022202 2.0424508 0.49070612 6.4276702 1710 2.0083188 2.0437945 0.48879489 6.3909243 1720 2.0178792 2.0439212 0.48646135 6.3411063 1730 2.0210944 2.0444299 0.48367905 6.3141106 1740 2.0170566 2.0337564 0.48044951 6.3158785 1750 2.0099049 2.0231598 0.47693196 6.3313851 1760 1.9990395 2.0132651 0.47329842 6.3631889 1770 1.9823237 1.9969291 0.46970233 6.4208124 1780 1.9640169 1.9798655 0.4663519 6.4879798 1790 1.9457657 1.9626633 0.46348315 6.557165 1800 1.9253222 1.9443136 0.46134123 6.6365286 1810 1.9123385 1.9339816 0.46011796 6.6879846 1820 1.9098744 1.9287702 0.45993599 6.7001355 1830 1.9096278 1.9220243 0.460898 6.7020982 1840 1.9223081 1.9378963 0.46303724 6.6558132 1850 1.9481113 1.9718786 0.46616351 6.5618175 1860 1.9704143 1.9931969 0.46987208 6.484088 1870 1.9864974 2.017655 0.47377416 6.4360445 1880 1.993165 2.0276398 0.47750238 6.4296162 1890 1.9852177 2.0249022 0.48088382 6.4843765 1900 1.9692398 2.0101062 0.4839255 6.5735477 1910 1.9516968 1.9893586 0.48689095 6.6692995 1920 1.9380452 1.9750949 0.49014596 6.7488323 1930 1.9323223 1.9719977 0.49399992 6.7947629 1940 1.9402144 1.9786701 0.49859677 6.7846787 1950 1.9589972 1.9956447 0.50392573 6.7291499 1960 1.979631 2.0201087 0.50984934 6.6648708 1970 2.0002749 2.0392081 0.51605302 6.6026647 1980 2.0143746 2.0524405 0.52221277 6.5687042 1990 2.0166553 2.0466885 0.5281276 6.5835144 2000 2.0130617 2.0424179 0.53381506 6.6234083 Loop time of 0.33442 on 1 procs for 1000 steps with 2775 atoms Performance: 258357.633 tau/day, 2990.250 timesteps/s, 8.298 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19616 | 0.19616 | 0.19616 | 0.0 | 58.66 Neigh | 0.023799 | 0.023799 | 0.023799 | 0.0 | 7.12 Comm | 0.0022819 | 0.0022819 | 0.0022819 | 0.0 | 0.68 Output | 0.0046967 | 0.0046967 | 0.0046967 | 0.0 | 1.40 Modify | 0.10212 | 0.10212 | 0.10212 | 0.0 | 30.54 Other | | 0.005366 | | | 1.60 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: 24370 ave 24370 max 24370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24370 Ave neighs/atom = 8.781982 Neighbor list builds = 35 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 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 5.175 | 5.175 | 5.175 Mbytes Step c_myT c_myTp TotEng Press 2000 2.0130617 2.0424179 0.53381506 6.6234083 2010 2.011712 2.0399428 0.53937165 6.6546944 2020 2.0177252 2.0516588 0.54483848 6.6575988 2030 2.0192267 2.054258 0.55012466 6.6761208 2040 2.0155308 2.0513866 0.55518707 6.7132509 2050 2.016831 2.0539288 0.56007247 6.7306192 2060 2.0213378 2.0690043 0.56479732 6.7330132 2070 2.0292987 2.0799825 0.56913353 6.7186216 2080 2.0342188 2.0900923 0.57283821 6.7098434 2090 2.0376411 2.096351 0.57566175 6.6998818 2100 2.053128 2.1238481 0.57727694 6.637431 2110 2.0783941 2.1609599 0.5768993 6.5304031 2120 2.0887269 2.1760645 0.57341638 6.4706853 2130 2.06944 2.1522354 0.5659988 6.5099284 2140 2.0380605 2.115767 0.55466476 6.5802578 2150 2.0195872 2.0868424 0.54025148 6.5885111 2160 2.0061251 2.069266 0.52417244 6.5682875 2170 1.992682 2.0526743 0.50812177 6.5470052 2180 1.9816004 2.0352692 0.49354583 6.5244099 2190 1.9688265 2.0226679 0.4811848 6.5185172 2200 1.9574266 2.000155 0.47107703 6.5176047 2210 1.9502736 1.9925522 0.46298224 6.5078398 2220 1.9475332 1.9936032 0.45641728 6.4850252 2230 1.9545128 2.0045053 0.45087489 6.4291405 2240 1.9627871 2.0112148 0.44588526 6.3715676 2250 1.9617694 2.0073769 0.44121477 6.3541518 2260 1.9579423 2.0079137 0.43675541 6.3542735 2270 1.9475845 1.998983 0.43243494 6.3854071 2280 1.9253275 1.9715083 0.42839782 6.464845 2290 1.8996763 1.9456257 0.42496367 6.5591177 2300 1.8823546 1.9240543 0.42247729 6.6211062 2310 1.8844318 1.9216768 0.42116372 6.6085376 2320 1.8965287 1.933936 0.42103218 6.5584198 2330 1.902103 1.9433708 0.421956 6.5350698 2340 1.9061826 1.950462 0.42378825 6.5228738 2350 1.9180306 1.961141 0.42644522 6.489172 2360 1.9296124 1.9748542 0.42981448 6.4628168 2370 1.9328566 1.9718181 0.43373762 6.4721746 2380 1.9360042 1.9769998 0.43819906 6.4840942 2390 1.9387073 1.9778749 0.44317927 6.49778 2400 1.9445619 1.9882647 0.4486142 6.4971899 2410 1.9553344 1.9997412 0.45435544 6.4749774 2420 1.9710783 2.0211926 0.46019236 6.4320181 2430 1.9903873 2.046553 0.46575694 6.3751343 2440 2.0041158 2.0721071 0.47060398 6.3415121 2450 2.0020392 2.0728953 0.47431806 6.3708096 2460 1.9839851 2.0568906 0.47681718 6.465129 2470 1.9566365 2.0258852 0.47838596 6.5966256 2480 1.929674 2.0032606 0.47952215 6.7260074 2490 1.9153613 1.990031 0.48061628 6.8035919 2500 1.9188373 1.9920514 0.4819225 6.8075788 2510 1.9371656 2.0138698 0.48343533 6.7492701 2520 1.9566481 2.0340995 0.48485699 6.6821181 2530 1.9636141 2.0389496 0.48583392 6.6581326 2540 1.9585172 2.0207113 0.48622314 6.6762792 2550 1.9516934 2.0024186 0.48621721 6.6980104 2560 1.9509543 1.9960852 0.48612286 6.6946311 2570 1.9601672 2.0072552 0.48602872 6.6528934 2580 1.973804 2.0230879 0.48576601 6.5942862 2590 1.9788378 2.034436 0.48505027 6.5689819 2600 1.9716493 2.0208578 0.48368043 6.5897554 2610 1.9618006 2.007098 0.48174365 6.6188626 2620 1.9631458 2.0075461 0.4793429 6.6026194 2630 1.9706918 2.0174955 0.47638698 6.5591053 2640 1.9759585 2.0213828 0.47264742 6.5198595 2650 1.9761708 2.0225139 0.46794373 6.4977306 2660 1.9611574 2.0083871 0.46221598 6.5299021 2670 1.9342882 1.9720247 0.45576624 6.6034695 2680 1.9142009 1.9520382 0.44913109 6.6474082 2690 1.9052096 1.9428107 0.4426988 6.645123 2700 1.902446 1.9459937 0.43672046 6.6152926 2710 1.9099036 1.9594727 0.43120889 6.5473804 2720 1.9180788 1.9767479 0.42599739 6.4792536 2730 1.9142892 1.9798275 0.42092791 6.4604982 2740 1.9019844 1.9674244 0.41601841 6.4795855 2750 1.8895632 1.958412 0.41144638 6.5037424 2760 1.8824401 1.9494985 0.40739848 6.5113925 2770 1.8852759 1.9525073 0.40398809 6.484535 2780 1.8998168 1.9664907 0.40114076 6.4159782 2790 1.9153937 1.9810349 0.39863439 6.346934 2800 1.9162707 1.9824285 0.39627973 6.3364828 2810 1.9087999 1.9666258 0.39408314 6.360755 2820 1.9073152 1.956153 0.39226387 6.3655719 2830 1.9091743 1.9493705 0.39098546 6.3595054 2840 1.9042021 1.9424118 0.39036698 6.381752 2850 1.8901401 1.9353495 0.39057524 6.4417859 2860 1.872943 1.915215 0.39190057 6.5158585 2870 1.8732626 1.9181551 0.39474702 6.5269257 2880 1.8931021 1.9396049 0.39938934 6.467715 2890 1.9217069 1.9733171 0.40581935 6.3811936 2900 1.9452213 1.9949806 0.41374968 6.3217226 2910 1.9591065 2.0105363 0.42280483 6.3087055 2920 1.9649158 2.0234068 0.43256139 6.3353204 2930 1.9647653 2.0265233 0.4425691 6.3902862 2940 1.9623876 2.0281154 0.45237409 6.4560778 2950 1.9591057 2.0276078 0.46164197 6.5239614 2960 1.9556907 2.0254377 0.47016674 6.5883236 2970 1.9524475 2.0203546 0.47782337 6.6457078 2980 1.9556442 2.0212175 0.48459527 6.6731473 2990 1.9663638 2.0285202 0.49047217 6.667322 3000 1.976263 2.0326354 0.49540098 6.6601492 3010 1.9734917 2.0251301 0.49938916 6.6970878 3020 1.955368 1.9974693 0.50265656 6.7865104 3030 1.9476644 1.9780945 0.50564273 6.8327176 3040 1.9584769 1.9887952 0.50867872 6.8046262 3050 1.9705616 2.0030557 0.51168699 6.7669575 3060 1.9766986 2.0112576 0.51444822 6.74919 3070 1.9766671 2.0076853 0.51685838 6.7523339 3080 1.9763383 2.0045916 0.51896849 6.7532253 3090 1.9855877 2.0260371 0.52081442 6.7160131 3100 2.0011042 2.042205 0.52215192 6.653598 3110 2.0039819 2.0511266 0.52275172 6.6355885 3120 1.9958773 2.0457899 0.52253307 6.6565817 3130 1.9933925 2.04521 0.52158082 6.6543706 3140 1.9936643 2.0477262 0.51996279 6.639564 3150 1.9921223 2.0455965 0.51768794 6.6291901 3160 1.9914788 2.0365842 0.51483187 6.6154874 3170 1.9922866 2.0422451 0.51144092 6.5976334 3180 1.9872806 2.0376593 0.50747923 6.6043774 3190 1.9708577 2.0198422 0.50308657 6.6551127 3200 1.9534272 1.9982319 0.49857904 6.7093718 3210 1.9423425 1.9876311 0.49429833 6.7370529 3220 1.941974 1.984738 0.49043179 6.7218879 3230 1.9456357 1.9916666 0.48697785 6.6917144 3240 1.9392412 1.9874858 0.48388805 6.7004046 3250 1.9312152 1.9814714 0.4812083 6.7175714 3260 1.9364393 1.9840125 0.47897357 6.6870787 3270 1.9490184 1.9871802 0.47715672 6.6308261 3280 1.9578901 1.9917218 0.47568803 6.589659 3290 1.9598612 1.9918098 0.47449561 6.5756965 3300 1.9538424 1.9845316 0.47357576 6.5931068 3310 1.944957 1.9676243 0.47302774 6.6211221 3320 1.9479975 1.9720828 0.47296613 6.6058089 3330 1.9569283 1.98719 0.47330356 6.5698601 3340 1.9558114 1.9861834 0.47383928 6.5729191 3350 1.9461606 1.9777192 0.47452365 6.6090135 3360 1.942095 1.9776297 0.47540879 6.6255417 3370 1.9482423 1.981145 0.47643851 6.6032207 3380 1.9564098 1.992645 0.47752314 6.5736007 3390 1.9607986 2.0006048 0.47852085 6.5587348 3400 1.9595637 2.0047228 0.47933656 6.5656692 3410 1.9628181 2.013785 0.47991082 6.5570579 3420 1.9698466 2.0200788 0.48018617 6.536373 3430 1.969877 2.0210764 0.48013786 6.543084 3440 1.96327 2.0103631 0.47979187 6.5761448 3450 1.9566516 1.9996494 0.47933398 6.6098616 3460 1.9511915 1.9976175 0.47891646 6.6401481 3470 1.9410601 1.9950284 0.47859124 6.6862584 3480 1.9307395 1.98193 0.47840998 6.7307929 3490 1.9206678 1.9678856 0.47853003 6.7702613 3500 1.9139405 1.955324 0.47914241 6.7934071 3510 1.9206383 1.957176 0.48041531 6.763312 3520 1.9449301 1.9816996 0.4823109 6.6651453 3530 1.9752924 2.0115126 0.48452681 6.5438659 3540 1.9951599 2.037759 0.48660439 6.463461 3550 2.00071 2.0413872 0.48813252 6.4405933 3560 1.9939017 2.0277566 0.48901382 6.4684771 3570 1.9766844 2.0031366 0.48946452 6.5392906 3580 1.9600495 1.9790718 0.48988281 6.6106541 3590 1.9522334 1.9727673 0.49062615 6.6517495 3600 1.9522007 1.9829458 0.49183552 6.6635632 3610 1.9614098 1.9992781 0.49340617 6.6407777 3620 1.9739926 2.0159629 0.49511752 6.6062456 3630 1.9726539 2.0152219 0.49675445 6.6254361 3640 1.9613098 2.0017247 0.49829011 6.6828523 3650 1.9577727 2.0000723 0.49991877 6.7111788 3660 1.9626403 2.0037309 0.50175296 6.7072182 3670 1.9603974 1.9937256 0.50383808 6.7277464 3680 1.9532611 1.9846903 0.50638428 6.766139 3690 1.9541656 1.9798331 0.50962883 6.7752527 3700 1.9656726 1.9951191 0.51377056 6.7462001 3710 1.9834474 2.0193011 0.5187681 6.6957856 3720 2.0017372 2.0396413 0.52433682 6.6470375 3730 2.0109702 2.0469463 0.53011728 6.6363717 3740 2.0096859 2.0458572 0.53588234 6.6682277 3750 2.0066189 2.0519843 0.54153099 6.7085484 3760 2.0096126 2.0561094 0.54689937 6.7250788 3770 2.0117777 2.0668795 0.55183559 6.7400961 3780 2.0154601 2.0763941 0.55607392 6.7423369 3790 2.0313954 2.0972106 0.55930714 6.6920109 3800 2.0496133 2.1176374 0.56110467 6.6271089 3810 2.0553084 2.1205041 0.56098738 6.6034667 3820 2.0478771 2.1131255 0.5587031 6.6239895 3830 2.0342107 2.0991257 0.55418078 6.6632309 3840 2.0142205 2.0767164 0.5475632 6.7196407 3850 1.9879527 2.0516847 0.53919956 6.7932756 3860 1.9593315 2.0232738 0.52966135 6.8686984 3870 1.9362884 1.9952027 0.51970091 6.9156688 3880 1.9292997 1.988308 0.50996281 6.8957697 3890 1.9372437 1.9978667 0.50073928 6.8160964 3900 1.949918 2.0107188 0.49208883 6.7186535 3910 1.9547594 2.0160936 0.48397839 6.6537347 3920 1.9543568 2.0191268 0.47640162 6.6136066 3930 1.9582199 2.020036 0.46933873 6.5629723 3940 1.9644632 2.0304626 0.4627222 6.5077173 3950 1.9645883 2.030183 0.45644411 6.4795254 3960 1.9546999 2.0197243 0.45050582 6.4943661 3970 1.9424307 2.0063453 0.44500624 6.5237706 3980 1.9281472 1.9910524 0.44010499 6.5640156 3990 1.9168821 1.976369 0.43594016 6.592621 4000 1.9150056 1.9752502 0.43256473 6.5855641 Loop time of 0.696491 on 1 procs for 2000 steps with 2775 atoms Performance: 248100.709 tau/day, 2871.536 timesteps/s, 7.969 Matom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39664 | 0.39664 | 0.39664 | 0.0 | 56.95 Neigh | 0.051502 | 0.051502 | 0.051502 | 0.0 | 7.39 Comm | 0.0047546 | 0.0047546 | 0.0047546 | 0.0 | 0.68 Output | 0.0095092 | 0.0095092 | 0.0095092 | 0.0 | 1.37 Modify | 0.22322 | 0.22322 | 0.22322 | 0.0 | 32.05 Other | | 0.01087 | | | 1.56 Nlocal: 2775 ave 2775 max 2775 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24313 ave 24313 max 24313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24313 Ave neighs/atom = 8.7614414 Neighbor list builds = 75 Dangerous builds = 0 Total wall time: 0:00:01