LAMMPS (30 Aug 2013) units metal atom_style atomic atom_modify map hash boundary p p p variable l equal 3 variable l2 equal 0.5*$l variable l2 equal 0.5*3 variable L equal 10 variable L2 equal 0.5*$L variable L2 equal 0.5*10 variable h equal $L variable h equal 10 lattice fcc 4.08 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 4.08 4.08 4.08 region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2} region BOX block -1.5 ${l2} -${L2} ${L2} -${l2} ${l2} region BOX block -1.5 1.5 -${L2} ${L2} -${l2} ${l2} region BOX block -1.5 1.5 -5 ${L2} -${l2} ${l2} region BOX block -1.5 1.5 -5 5 -${l2} ${l2} region BOX block -1.5 1.5 -5 5 -1.5 ${l2} region BOX block -1.5 1.5 -5 5 -1.5 1.5 create_box 1 BOX Created orthogonal box = (-6.12 -20.4 -6.12) to (6.12 20.4 6.12) 1 by 4 by 1 MPI processor grid create_atoms 1 region BOX Created 360 atoms pair_style eam pair_coeff * * Au_u3.eam mass * 196.97 ### NOTE change to CB -linear fix PP all atc field Au_elastic.mat ATC: constructing shape function field estimate with parameter file Au_elastic.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 fix_modify PP mesh create 1 $h 1 BOX p f p fix_modify PP mesh create 1 10 1 BOX p f p ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy fix_modify PP gradients add displacement fix_modify PP set reference_potential_energy fix_modify PP output counter step fix_modify PP output eam_energyPP 1 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix ATC all atc elastic Au_elastic.mat ATC: constructing elastic coupling with parameter file Au_elastic.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: computed mass density : 11.6006 ATC: computed mass density : 11.6006 ATC: 2 materials defined from Au_elastic.mat fix_modify ATC mesh create 1 $h 1 BOX p f p fix_modify ATC mesh create 1 10 1 BOX p f p ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements fix_modify ATC internal_quadrature off fix_modify ATC control momentum none #fix_modify ATC consistent_fe_initialization on fix_modify ATC output counter step fix_modify ATC output eam_energyFE 1 text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify ATC material all Au_cubic dump CONFIG all custom 1 eam_energy.dmp id type x y z thermo 1 timestep 0 # 1.e-20 # 0 variable e0 equal pe variable L0 equal ly run 0 Setting up run ... ATC: CB stiffness: 11.5362 Einstein freq: 4682.34 ATC: CB stiffness: 11.5362 Einstein freq: 4682.34 ATC: WARNING: all initial conditions for displacement have not been defined and the undefined are assumed zero ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero Memory usage per processor = 41.8034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1414.8 0 -1414.8 0.022463201 Loop time of 1.0252e-05 on 4 procs for 0 steps with 360 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0 (0) Outpt time (%) = 0 (0) Other time (%) = 1.0252e-05 (100) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 variable pe equal pe-${e0} variable pe equal pe--1414.8000000636002369 variable dL equal ly-${L0} variable dL equal ly-40.799999999999997158 variable strain equal v_dL/${L0} variable strain equal v_dL/40.799999999999997158 variable x equal y[1] variable x2 equal y[2] variable v equal vy[1] thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain thermo_modify format 2 %15.8g ############################################################################### log eam_energy.log run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 0 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0 1 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0 Loop time of 0.00549316 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000414193 (7.54015) Neigh time (%) = 0 (0) Comm time (%) = 6.98566e-05 (1.2717) Outpt time (%) = 0.0019924 (36.2706) Other time (%) = 0.00301671 (54.9175) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 velocity all set 0 0.1 0 units box fix_modify ATC fix velocity y all 0.1 run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 1 -1414.7633 0 0.036746101 0 0 -19.38 0.1 -19.38 40.8 0 0 2 -1414.7633 0 0.036746101 0.036746101 0 -19.38 0.1 -19.38 40.8 0 0 Loop time of 0.00695777 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000445962 (6.40955) Neigh time (%) = 0 (0) Comm time (%) = 0.000112355 (1.61481) Outpt time (%) = 0.00171965 (24.7156) Other time (%) = 0.0046798 (67.26) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 velocity all set 0 0.2 0 units box fix_modify ATC fix velocity y all 0.2 run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 2 -1414.653 0 0.1469844 0.036746101 0 -19.38 0.2 -19.38 40.8 0 0 3 -1414.653 0 0.1469844 0.1469844 0 -19.38 0.2 -19.38 40.8 0 0 Loop time of 0.00692767 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000420749 (6.07346) Neigh time (%) = 0 (0) Comm time (%) = 0.000110626 (1.59688) Outpt time (%) = 0.00177026 (25.5534) Other time (%) = 0.00462604 (66.7762) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 velocity all set 0 0.3 0 units box fix_modify ATC fix velocity y all 0.3 run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 3 -1414.4693 0 0.33071491 0.1469844 0 -19.38 0.3 -19.38 40.8 0 0 4 -1414.4693 0 0.33071491 0.33071491 0 -19.38 0.3 -19.38 40.8 0 0 Loop time of 0.0068838 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000432014 (6.27581) Neigh time (%) = 0 (0) Comm time (%) = 0.000115931 (1.68411) Outpt time (%) = 0.00171983 (24.9838) Other time (%) = 0.00461602 (67.0563) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 change_box all y scale 1.01 remap Changing box ... orthogonal box = (-6.12 -20.604 -6.12) to (6.12 20.604 6.12) fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0 ATC: created function : 0 + 0(x-0)+0.01(y-0)+0(z-0) run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 4 -1414.1262 0.34311553 0.33071491 0.33071491 0 -19.5738 0.3 -19.5738 41.208 0.408 0.01 5 -1414.1262 0.34311553 0.33071491 0.33071491 0.34908704 -19.5738 0.3 -19.5738 41.208 0.408 0.01 Loop time of 0.00684071 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000422955 (6.18291) Neigh time (%) = 0 (0) Comm time (%) = 8.39233e-05 (1.22682) Outpt time (%) = 0.00172395 (25.2013) Other time (%) = 0.00460988 (67.389) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 change_box all y scale 1.01 remap Changing box ... orthogonal box = (-6.12 -20.81 -6.12) to (6.12 20.81 6.12) fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0 ATC: created function : 0 + 0(x-0)+0.0201(y-0)+0(z-0) run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 5 -1413.1082 1.3610604 0.33071491 0.33071491 0 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201 6 -1413.1082 1.3610604 0.33071491 0.33071491 1.0612595 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201 Loop time of 0.00686866 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000416577 (6.06489) Neigh time (%) = 0 (0) Comm time (%) = 0.000141203 (2.05576) Outpt time (%) = 0.00175518 (25.5534) Other time (%) = 0.0045557 (66.3259) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0 change_box all y scale 1.01 remap Changing box ... orthogonal box = (-6.12 -21.0181 -6.12) to (6.12 21.0181 6.12) fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0 ATC: created function : 0 + 0(x-0)+0.030301(y-0)+0(z-0) run 1 Setting up run ... Memory usage per processor = 41.8034 Mbytes Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain 6 -1411.4328 3.0364818 0.33071491 0.33071491 0 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301 7 -1411.4328 3.0364818 0.33071491 0.33071491 1.7947982 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301 Loop time of 0.00686812 on 4 procs for 1 steps with 360 atoms Pair time (%) = 0.000451982 (6.58087) Neigh time (%) = 0 (0) Comm time (%) = 6.69956e-05 (0.975457) Outpt time (%) = 0.00174725 (25.44) Other time (%) = 0.0046019 (67.0037) Nlocal: 90 ave 90 max 90 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1184 ave 1184 max 1184 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 3870 ave 3870 max 3870 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 7740 ave 7740 max 7740 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30960 Ave neighs/atom = 86 Neighbor list builds = 0 Dangerous builds = 0