LAMMPS (30 Aug 2013) units real atom_style atomic # create domain lattice fcc 4.08 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 4.08 4.08 4.08 region BOX block -8 8 -2 2 -2 2 boundary f p p create_box 1 BOX Created orthogonal box = (-32.64 -8.16 -8.16) to (32.64 8.16 8.16) 4 by 1 by 1 MPI processor grid # create atoms region MD block -7 7 -2 2 -2 2 create_atoms 1 region MD Created 896 atoms #pair_style eam #pair_coeff * * Au_u3.eam #pair_style lj/cut/smooth 5.456108274435118 pair_style lj/smooth/linear 5.456108274435118 pair_coeff * * 0.7242785984051078 2.598146797350056 mass * 196.97 # specify interal/ghost atoms region FREE block -6 6 -2 2 -2 2 group internal region FREE 768 atoms in group internal # specify inter-atomic potential # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz # ID group atc PhysicsType ParameterFile fix PP1 internal atc field Au_CauchyBorn_linear.mat ATC: constructing shape function field estimate with parameter file Au_CauchyBorn_linear.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 fix_modify PP1 mesh create 8 1 1 BOX f p p ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements fix_modify PP1 fields add displacement fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress fix_modify PP1 gradients add displacement fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe # ID group atc PhysicsType ParameterFile fix PP2 internal atc field Au_CauchyBorn.mat ATC: constructing shape function field estimate with parameter file Au_CauchyBorn.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 fix_modify PP2 mesh create 8 1 1 BOX f p p ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy fix_modify PP2 set reference_potential_energy timestep 0.0 fix_modify PP1 output cb_unistrain_linearFE 1 text tensor_components binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify PP2 output cb_unistrain_refFE 1 text tensor_components ATC: Warning : text output can create _LARGE_ files ATC: output custom names: log cb_unistrain_linear.log variable step equal 0 thermo_style custom step v_step pe ke press lx ly lz run 1 Setting up run ... ATC: created cubic stress function: lammps ATC units c11=3.10501 0.00129914 c12=1.75749 0.000735332 c44=1.75749 0.000735332 ATC: CB stiffness: 28.7742 Einstein freq: 1.53992 ATC: computing bond matrix ...........done ATC: CB stiffness: 28.7742 Einstein freq: 1.53992 Memory usage per processor = 43.9024 Mbytes Step step PotEng KinEng Press Lx Ly Lz 0 0 -3435.8868 0 50.003991 65.28 16.32 16.32 1 0 -3435.8868 0 50.003991 65.28 16.32 16.32 Loop time of 0.00921357 on 4 procs for 1 steps with 896 atoms Pair time (%) = 0.000425279 (4.61579) Neigh time (%) = 0 (0) Comm time (%) = 0.000171542 (1.86184) Outpt time (%) = 0.000129223 (1.40253) Other time (%) = 0.00848752 (92.1198) Nlocal: 224 ave 256 max 192 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 903 ave 1116 max 690 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 4528 ave 5376 max 3648 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 9056 ave 10752 max 7360 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 36224 Ave neighs/atom = 40.4286 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 0+1 displace_atoms all ramp x -0.1 0.1 x -100 100 Displacing atoms ... run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 43.9024 Mbytes Step step PotEng KinEng Press Lx Ly Lz 1 1 -3435.904 0 -77.521908 65.28 16.32 16.32 2 1 -3435.904 0 -77.521908 65.28 16.32 16.32 Loop time of 0.0131642 on 4 procs for 1 steps with 896 atoms Pair time (%) = 0.000412822 (3.13595) Neigh time (%) = 0 (0) Comm time (%) = 0.000241101 (1.83149) Outpt time (%) = 0.000350773 (2.66461) Other time (%) = 0.0121595 (92.3679) Nlocal: 224 ave 256 max 192 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 903 ave 1116 max 690 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 4528 ave 5376 max 3648 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 9056 ave 10752 max 7360 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 36224 Ave neighs/atom = 40.4286 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 1+1 displace_atoms all ramp x -0.1 0.1 x -100 100 Displacing atoms ... run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 43.9024 Mbytes Step step PotEng KinEng Press Lx Ly Lz 2 2 -3435.8757 0 -203.99195 65.28 16.32 16.32 3 2 -3435.8757 0 -203.99195 65.28 16.32 16.32 Loop time of 0.0132811 on 4 procs for 1 steps with 896 atoms Pair time (%) = 0.000422537 (3.18149) Neigh time (%) = 0 (0) Comm time (%) = 0.000141799 (1.06768) Outpt time (%) = 0.000341833 (2.57383) Other time (%) = 0.0123749 (93.177) Nlocal: 224 ave 256 max 192 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 903 ave 1116 max 690 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 4528 ave 5376 max 3648 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 9056 ave 10752 max 7360 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 36224 Ave neighs/atom = 40.4286 Neighbor list builds = 0 Dangerous builds = 0