LAMMPS (30 Aug 2013) units real atom_style atomic # create domain #lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) lattice fcc 5.2582305 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.25823 5.25823 5.25823 # create atoms region simRegion block -12 12 -3 3 -3 3 region atomRegion block -9 9 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3 boundary f p p create_box 1 simRegion Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747) 4 by 1 by 1 MPI processor grid create_atoms 1 region mdRegion Created 2304 atoms mass 1 39.95 # specify interal/ghost atoms region mdInternal block -6 6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3 group internal region mdInternal 1728 atoms in group internal group Lghost region leftghost 288 atoms in group Lghost group Rghost region rightghost 288 atoms in group Rghost group ghosts union Lghost Rghost 576 atoms in group ghosts # velocities have Vcm = 0 #velocity internal create 40. 87287 mom yes loop geom pair_style lj/cut 13. #pair_coeff 1 1 0.010323166 3.405 13. pair_coeff 1 1 .2381 3.405 13. neighbor 5. bin neigh_modify every 10 delay 0 check no # define layer # ID group atc PhysicsType ParameterFile fix AtC internal atc elastic Ar_elastic.mat ATC: constructing elastic coupling with parameter file Ar_elastic.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: computed mass density : 1.09915 ATC: computed mass density : 1.09915 ATC: computed mass density : 1.09915 ATC: 3 materials defined from Ar_elastic.mat #fix_modify AtC boundary Lghost #fix_modify AtC boundary Rghost fix_modify AtC boundary ghosts # ID part keywords nx ny nz region fix_modify AtC mesh create 12 1 1 simRegion f p p ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward ATC: created faceset obndy with 2 faces # initial conditions fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement y all 0.0 fix_modify AtC initial displacement z all 0.0 fix_modify AtC initial velocity x all 0.0 fix_modify AtC initial velocity y all 0.0 fix_modify AtC initial velocity z all 0.0 # set node sets and bcs # ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF ATC: created nodeset lbc with 1 nodes fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF ATC: created nodeset rbc with 1 nodes fix_modify AtC fix velocity x rbc 0.00000004 #fix_modify AtC fix velocity x rbc 0. #fix_modify AtC fix displacement x rbc 0. fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix velocity x lbc 0. #fix_modify AtC output follow_ex.fe 50 fix_modify AtC internal_quadrature off #fix_modify AtC control lumped_lambda_solve on #fix_modify AtC momentum control glc_velocity #fix_modify AtC momentum control flux faceset obndy fix_modify AtC control momentum flux interpolate #fix_modify AtC filter scale 1000.0 # run to extension compute myTemp internal temp compute atomStress internal stress/atom compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) thermo_style custom step c_myTemp v_myPres pe fix_modify AtC output bar1d_fluxFE 10 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: timestep 5 thermo 100 run 1000 Setting up run ... Memory usage per processor = 65.6268 Mbytes Step myTemp myPres PotEng 0 0 -0.00072339042 -4509.8851 100 1.7485737e-12 -0.00065677838 -4509.8851 200 2.1209236e-12 -0.00058835409 -4509.8851 300 3.1757662e-11 -0.00088336321 -4509.8851 400 4.4437682e-10 -0.0022808215 -4509.8852 500 2.1276171e-09 -0.0055205162 -4509.8852 600 5.3746766e-09 -0.010513144 -4509.8852 700 9.3752238e-09 -0.016165157 -4509.8852 800 1.3218953e-08 -0.02139071 -4509.8852 900 1.6753544e-08 -0.026203391 -4509.8852 1000 2.0559423e-08 -0.031228823 -4509.8852 Loop time of 20.2117 on 4 procs for 1000 steps with 2304 atoms Pair time (%) = 5.83883 (28.8884) Neigh time (%) = 2.45972 (12.1698) Comm time (%) = 5.73308 (28.3652) Outpt time (%) = 0.0113837 (0.0563225) Other time (%) = 6.16865 (30.5203) Nlocal: 576 ave 864 max 288 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 5170 ave 6910 max 3430 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 178632 ave 288102 max 69229 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 357264 ave 577008 max 137520 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 1429056 Ave neighs/atom = 620.25 Neighbor list builds = 100 Dangerous builds = 0 # change nodes to fixed fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix displacement x rbc 0.0002 fix_modify AtC output bar1d_fluxFE 500 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: # run to equilibrium timestep 5 thermo 100 run 10000 Setting up run ... Memory usage per processor = 66.0846 Mbytes Step myTemp myPres PotEng 1000 2.0559423e-08 -0.031228823 -4509.8852 1100 2.4448613e-08 -0.036521719 -4509.8852 1200 2.7029986e-08 -0.040978057 -4509.8852 1300 2.7245337e-08 -0.042998684 -4509.8852 1400 2.5759549e-08 -0.041645718 -4509.8852 1500 2.2667557e-08 -0.037303114 -4509.8852 1600 1.8985753e-08 -0.031463351 -4509.8852 1700 1.6073802e-08 -0.025662764 -4509.8852 1800 1.2763714e-08 -0.020737937 -4509.8852 1900 7.2995795e-09 -0.01675253 -4509.8852 2000 2.1755431e-09 -0.013533314 -4509.8853 2100 1.1934319e-09 -0.011450448 -4509.8853 2200 5.1850465e-09 -0.011687818 -4509.8853 2300 1.1883622e-08 -0.015251299 -4509.8852 2400 1.6266667e-08 -0.021397871 -4509.8852 2500 1.9099042e-08 -0.02792249 -4509.8851 2600 2.184558e-08 -0.033185039 -4509.8852 2700 2.4595817e-08 -0.037175923 -4509.8852 2800 2.6643068e-08 -0.040355693 -4509.8852 2900 2.6394943e-08 -0.042183343 -4509.8852 3000 2.3989422e-08 -0.041411974 -4509.8852 3100 2.0979363e-08 -0.037465063 -4509.8851 3200 1.7427127e-08 -0.031310189 -4509.8852 3300 1.3963242e-08 -0.024887233 -4509.8852 3400 1.0069796e-08 -0.019686777 -4509.8852 3500 4.9395633e-09 -0.01603797 -4509.8853 3600 1.5407167e-09 -0.013620537 -4509.8853 3700 2.5284685e-09 -0.012392513 -4509.8853 3800 7.790979e-09 -0.012777012 -4509.8852 3900 1.3465317e-08 -0.015407232 -4509.8852 4000 1.7796468e-08 -0.02062936 -4509.8852 4100 2.137127e-08 -0.027628973 -4509.8852 4200 2.3606809e-08 -0.034315098 -4509.8852 4300 2.5221837e-08 -0.038703928 -4509.8852 4400 2.6247664e-08 -0.040548555 -4509.8852 4500 2.5017987e-08 -0.040839998 -4509.8852 4600 2.1628404e-08 -0.040012148 -4509.8852 4700 1.7878834e-08 -0.037370745 -4509.8851 4800 1.5934582e-08 -0.032277925 -4509.8851 4900 1.2990149e-08 -0.025549108 -4509.8852 5000 7.8316754e-09 -0.01918358 -4509.8853 5100 3.3266953e-09 -0.014887033 -4509.8853 5200 1.805252e-09 -0.01286358 -4509.8853 5300 4.2912871e-09 -0.012392579 -4509.8852 5400 9.9026848e-09 -0.013257092 -4509.8852 5500 1.6165255e-08 -0.015976619 -4509.8852 5600 2.1206295e-08 -0.020907339 -4509.8852 5700 2.4000025e-08 -0.027469529 -4509.8852 5800 2.5521345e-08 -0.034321126 -4509.8852 5900 2.5894586e-08 -0.039670766 -4509.8852 6000 2.5086791e-08 -0.042046228 -4509.8852 6100 2.360407e-08 -0.041352366 -4509.8852 6200 1.9586346e-08 -0.038824048 -4509.8852 6300 1.6684228e-08 -0.035608606 -4509.8852 6400 1.4893508e-08 -0.031584998 -4509.8852 6500 1.1127507e-08 -0.026164353 -4509.8852 6600 5.9884577e-09 -0.019764802 -4509.8853 6700 2.2391294e-09 -0.014210542 -4509.8853 6800 2.7797654e-09 -0.011431487 -4509.8853 6900 6.7664929e-09 -0.011810438 -4509.8852 7000 1.1980057e-08 -0.014206493 -4509.8852 7100 1.7989445e-08 -0.017536849 -4509.8852 7200 2.3218176e-08 -0.02190877 -4509.8852 7300 2.5628573e-08 -0.027653206 -4509.8852 7400 2.610839e-08 -0.034000347 -4509.8852 7500 2.4944322e-08 -0.039281243 -4509.8852 7600 2.2693765e-08 -0.042058723 -4509.8852 7700 1.9767428e-08 -0.041825858 -4509.8851 7800 1.6504232e-08 -0.039030684 -4509.8851 7900 1.4309561e-08 -0.03485307 -4509.8852 8000 1.3055145e-08 -0.030357952 -4509.8852 8100 9.5625542e-09 -0.025706075 -4509.8852 8200 4.6410355e-09 -0.02054295 -4509.8853 8300 3.2795872e-09 -0.015185677 -4509.8853 8400 5.509246e-09 -0.011181309 -4509.8853 8500 9.2654236e-09 -0.010336847 -4509.8852 8600 1.5169111e-08 -0.013152226 -4509.8852 8700 2.1124719e-08 -0.018237266 -4509.8852 8800 2.5607376e-08 -0.023635507 -4509.8852 8900 2.7829768e-08 -0.028664368 -4509.8853 9000 2.7490864e-08 -0.033752079 -4509.8853 9100 2.4629425e-08 -0.038717883 -4509.8852 9200 1.9856317e-08 -0.042074213 -4509.8851 9300 1.5754223e-08 -0.042397751 -4509.8851 9400 1.4158011e-08 -0.039645985 -4509.8851 9500 1.293562e-08 -0.034905375 -4509.8852 9600 1.0925115e-08 -0.029498287 -4509.8852 9700 8.2117111e-09 -0.024274276 -4509.8853 9800 4.2073503e-09 -0.019498803 -4509.8853 9900 3.6200071e-09 -0.015198764 -4509.8853 10000 7.3205984e-09 -0.011878546 -4509.8852 10100 1.2327605e-08 -0.010695702 -4509.8852 10200 1.7930358e-08 -0.012691556 -4509.8852 10300 2.4534101e-08 -0.017839785 -4509.8852 10400 2.8574489e-08 -0.024561434 -4509.8852 10500 2.944535e-08 -0.030655475 -4509.8852 10600 2.7962098e-08 -0.034958095 -4509.8852 10700 2.3119076e-08 -0.037998711 -4509.8852 10800 1.684499e-08 -0.040493081 -4509.8852 10900 1.2305474e-08 -0.041691151 -4509.8851 11000 1.1330272e-08 -0.040137729 -4509.8851 Loop time of 198.827 on 4 procs for 10000 steps with 2304 atoms Pair time (%) = 58.1282 (29.2355) Neigh time (%) = 24.4055 (12.2747) Comm time (%) = 55.6289 (27.9785) Outpt time (%) = 0.0868983 (0.0437054) Other time (%) = 60.5779 (30.4676) Nlocal: 576 ave 864 max 288 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 5170 ave 6910 max 3430 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 178632 ave 288705 max 68731 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 357264 ave 577008 max 137520 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 1429056 Ave neighs/atom = 620.25 Neighbor list builds = 1000 Dangerous builds = 0