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 region simRegion block -12 12 -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, NOTE next for lines commented out for restart 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 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 fix_modify AtC internal_quadrature off fix_modify AtC internal_atom_integrate off fix iNVE internal nve # initial conditions fix_modify AtC initial displacement x all 0.0 fix_modify AtC fix displacement y all 0.0 fix_modify AtC fix displacement z all 0.0 fix_modify AtC initial velocity x all 0.0 fix_modify AtC fix velocity y all 0.0 fix_modify AtC fix 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. #fix_modify AtC fix displacement x rbc 0. fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix velocity x lbc 0. # turn on multiscale fix_modify AtC control momentum ghost_flux # new boundary conditions fix_modify AtC fix velocity x rbc 0.00000004 #fix_modify AtC output follow_ex.fe 50 #fix_modify AtC localized_lambda on #fix_modify AtC momentum control glc_velocity #fix_modify AtC momentum control flux faceset obndy #fix_modify AtC control momentum flux #fix_modify AtC control momentum ghost_flux #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_ghost_fluxFE 500 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: #dump D1 all atom 100 bar1d_ghost_flux.dmp 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 7.1225566e-14 -0.00069609188 -4509.8851 200 3.7853133e-13 -0.00065829543 -4509.8851 300 1.6363911e-11 -0.00093014878 -4509.8851 400 2.6679578e-10 -0.0022162027 -4509.8852 500 1.616056e-09 -0.0053039586 -4509.8852 600 5.0333459e-09 -0.010270696 -4509.8852 700 9.7370581e-09 -0.016093983 -4509.8852 800 1.3809125e-08 -0.021486202 -4509.8852 900 1.6783957e-08 -0.026147268 -4509.8852 1000 1.9615527e-08 -0.030744945 -4509.8852 Loop time of 18.3775 on 4 procs for 1000 steps with 2304 atoms Pair time (%) = 5.94283 (32.3375) Neigh time (%) = 2.46573 (13.4171) Comm time (%) = 6.00265 (32.663) Outpt time (%) = 0.00820392 (0.044641) Other time (%) = 3.95812 (21.5378) 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 288581 max 68542 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 unfix velocity x rbc #fix_modify AtC fix displacement x rbc 0.0002 #fix_modify AtC output bar1d_fluxFE 500 text binary # run to equilibrium timestep 5 thermo 100 run 3000 Setting up run ... Memory usage per processor = 66.0846 Mbytes Step myTemp myPres PotEng 1000 1.9615527e-08 -0.030744945 -4509.8852 1100 2.3080841e-08 -0.035570103 -4509.8852 1200 2.6803382e-08 -0.039749355 -4509.8852 1300 2.8836885e-08 -0.041881649 -4509.8852 1400 2.7038886e-08 -0.04118176 -4509.8852 1500 2.247439e-08 -0.037776265 -4509.8852 1600 1.8021787e-08 -0.032491325 -4509.8852 1700 1.4774855e-08 -0.026754505 -4509.8852 1800 1.2061023e-08 -0.022034601 -4509.8852 1900 8.5768539e-09 -0.018709001 -4509.8852 2000 3.6373058e-09 -0.016114748 -4509.8852 2100 5.3669536e-10 -0.014163462 -4509.8853 2200 3.2454928e-09 -0.014205399 -4509.8853 2300 1.030702e-08 -0.017492992 -4509.8853 2400 1.6038797e-08 -0.023210717 -4509.8852 2500 1.7061988e-08 -0.029013462 -4509.8851 2600 1.9296258e-08 -0.03339452 -4509.8852 2700 2.2816944e-08 -0.036626152 -4509.8852 2800 2.6944075e-08 -0.039307649 -4509.8852 2900 2.8170813e-08 -0.040972921 -4509.8852 3000 2.7256286e-08 -0.040327211 -4509.8852 3100 2.445985e-08 -0.036617618 -4509.8852 3200 1.8787648e-08 -0.03049195 -4509.8852 3300 1.4750104e-08 -0.023629006 -4509.8852 3400 1.3515772e-08 -0.017473229 -4509.8852 3500 1.157919e-08 -0.012114855 -4509.8851 3600 9.6213234e-09 -0.0064144434 -4509.8851 3700 9.1781574e-09 0.00062376196 -4509.8851 3800 9.0938842e-09 0.0087100206 -4509.885 3900 7.7454581e-09 0.016669158 -4509.885 4000 9.3314606e-09 0.023405906 -4509.885 Loop time of 54.728 on 4 procs for 3000 steps with 2304 atoms Pair time (%) = 17.812 (32.5465) Neigh time (%) = 7.39237 (13.5075) Comm time (%) = 17.7536 (32.4397) Outpt time (%) = 0.0253569 (0.0463326) Other time (%) = 11.7446 (21.46) 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 288933 max 68141 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 = 300 Dangerous builds = 0