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 -8 8 -3 3 -3 3 region mdRegion block -6 6 -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 atomRegion 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 pair_style lj/cut 13. #pair_coeff 1 1 0.010323166 3.405 13.5 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 # 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 # 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 fix_modify AtC time_integration fractional_step fix_modify AtC internal_atom_integrate off fix iNVE internal nve # 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 displacement x lbc 0. fix_modify AtC fix velocity x lbc 0. # specify atom types #fix_modify AtC boundary Lghost #fix_modify AtC boundary Rghost fix_modify AtC boundary ghosts fix_modify AtC internal_quadrature off fix_modify AtC control localized_lambda on fix_modify AtC control momentum flux interpolate #fix_modify AtC control momentum hoover # tested in this mode #fix_modify AtC filter type exponential #fix_modify AtC filter scale 1000.0 #fix_modify AtC filter on # run to extension #fix_modify AtC output bar1d_frac_step_initFE 50 text binary #dump D1 all atom 50 bar1d_frac_step_init.dmp timestep 5 thermo 100 run 1000 Setting up run ... Memory usage per processor = 65.169 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4509.8851 0 -4509.8851 26.948349 100 4.7374019e-13 -4509.8851 0 -4509.8851 26.94834 200 9.7683427e-13 -4509.8851 0 -4509.8851 26.94803 300 1.9565172e-11 -4509.8851 0 -4509.8851 26.946439 400 2.6411547e-10 -4509.8852 0 -4509.8852 26.942798 500 1.351766e-09 -4509.8852 0 -4509.8852 26.93773 600 3.6802148e-09 -4509.8852 0 -4509.8852 26.932648 700 6.6530697e-09 -4509.8852 0 -4509.8852 26.928033 800 9.5474556e-09 -4509.8852 0 -4509.8852 26.923147 900 1.2412323e-08 -4509.8852 0 -4509.8852 26.917542 1000 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973 Loop time of 19.6581 on 4 procs for 1000 steps with 2304 atoms Pair time (%) = 5.96992 (30.3688) Neigh time (%) = 2.49911 (12.7129) Comm time (%) = 6.03219 (30.6855) Outpt time (%) = 0.000867546 (0.00441317) Other time (%) = 5.15602 (26.2285) 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 288910 max 68513 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 # reset time fix_modify AtC reset_time 0. reset_timestep 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_frac_stepFE 500 text #binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: #fix_modify AtC output index step #undump D1 #dump D1 all atom 500 bar1d_frac_step.dmp # run to equilibrium timestep 5 thermo 100 run 5000 Setting up run ... Memory usage per processor = 65.169 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973 100 1.809994e-08 -4509.8852 0 -4509.8852 26.907429 200 1.9777109e-08 -4509.8852 0 -4509.8852 26.904241 300 2.0275205e-08 -4509.8852 0 -4509.8852 26.902912 400 1.9266773e-08 -4509.8852 0 -4509.8852 26.904281 500 1.6821974e-08 -4509.8851 0 -4509.8851 26.908126 600 1.370661e-08 -4509.8852 0 -4509.8852 26.912761 700 1.0292223e-08 -4509.8852 0 -4509.8852 26.916838 800 6.5498338e-09 -4509.8853 0 -4509.8853 26.920715 900 3.1643856e-09 -4509.8853 0 -4509.8853 26.925094 1000 1.0112513e-09 -4509.8852 0 -4509.8852 26.928958 1100 4.4564547e-10 -4509.8852 0 -4509.8852 26.930177 1200 2.264627e-09 -4509.8852 0 -4509.8852 26.92803 1300 6.3325706e-09 -4509.8853 0 -4509.8853 26.923952 1400 1.1281983e-08 -4509.8853 0 -4509.8853 26.919616 1500 1.5582979e-08 -4509.8852 0 -4509.8852 26.915411 1600 1.8378446e-08 -4509.8852 0 -4509.8852 26.911278 1700 1.9544417e-08 -4509.8852 0 -4509.8852 26.907886 1800 1.993739e-08 -4509.8851 0 -4509.8851 26.905965 1900 1.9956722e-08 -4509.8851 0 -4509.8851 26.905229 2000 1.9225238e-08 -4509.8852 0 -4509.8852 26.905144 2100 1.6580757e-08 -4509.8853 0 -4509.8853 26.906419 2200 1.2058028e-08 -4509.8853 0 -4509.8853 26.910376 2300 7.4549951e-09 -4509.8852 0 -4509.8852 26.916716 2400 4.0264612e-09 -4509.8852 0 -4509.8852 26.923054 2500 1.8321195e-09 -4509.8852 0 -4509.8852 26.92718 2600 5.8894583e-10 -4509.8852 0 -4509.8852 26.92887 2700 1.1822868e-09 -4509.8853 0 -4509.8853 26.928935 2800 4.1199827e-09 -4509.8853 0 -4509.8853 26.927485 2900 8.3401571e-09 -4509.8853 0 -4509.8853 26.924202 3000 1.2795486e-08 -4509.8852 0 -4509.8852 26.91968 3100 1.656454e-08 -4509.8852 0 -4509.8852 26.915184 3200 1.8809835e-08 -4509.8852 0 -4509.8852 26.911167 3300 1.9524689e-08 -4509.8852 0 -4509.8852 26.907277 3400 1.9239653e-08 -4509.8852 0 -4509.8852 26.904028 3500 1.8306513e-08 -4509.8852 0 -4509.8852 26.903155 3600 1.6715381e-08 -4509.8852 0 -4509.8852 26.905573 3700 1.4633381e-08 -4509.8851 0 -4509.8851 26.909896 3800 1.1933216e-08 -4509.8851 0 -4509.8851 26.913983 3900 8.1608505e-09 -4509.8852 0 -4509.8852 26.917338 4000 4.081711e-09 -4509.8853 0 -4509.8853 26.920926 4100 1.5631282e-09 -4509.8853 0 -4509.8853 26.924958 4200 1.2262219e-09 -4509.8853 0 -4509.8853 26.928167 4300 2.985009e-09 -4509.8852 0 -4509.8852 26.929352 4400 6.8933386e-09 -4509.8852 0 -4509.8852 26.928435 4500 1.1278724e-08 -4509.8852 0 -4509.8852 26.925624 4600 1.4438096e-08 -4509.8852 0 -4509.8852 26.920742 4700 1.6779441e-08 -4509.8852 0 -4509.8852 26.914294 4800 1.8690218e-08 -4509.8853 0 -4509.8853 26.908349 4900 1.9317873e-08 -4509.8852 0 -4509.8852 26.905059 5000 1.8273072e-08 -4509.8851 0 -4509.8851 26.904542 Loop time of 97.2827 on 4 procs for 5000 steps with 2304 atoms Pair time (%) = 29.7789 (30.6107) Neigh time (%) = 12.5179 (12.8676) Comm time (%) = 29.2909 (30.109) Outpt time (%) = 0.00928915 (0.00954861) Other time (%) = 25.6857 (26.4032) 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 288957 max 67836 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 = 500 Dangerous builds = 0