LAMMPS (30 Aug 2013) units metal atom_style atomic variable lattice_constant equal 4.08 variable c equal 6 # minimum size variable Ly equal $c*${lattice_constant} variable Ly equal 6*${lattice_constant} variable Ly equal 6*4.0800000000000000711 variable d equal 0.005 variable V0 equal ($c*${lattice_constant})^3 variable V0 equal (6*${lattice_constant})^3 variable V0 equal (6*4.0800000000000000711)^3 # create system lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 lattice fcc 4.0800000000000000711 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 4.08 4.08 4.08 # NOTE rect box + lagrangian is necessary to fool ATC's mesh region rectbox block 0 $c 0 $c 0 3 region rectbox block 0 6 0 $c 0 3 region rectbox block 0 6 0 6 0 3 region box prism 0 $c 0 $c 0 3 0 0 0 region box prism 0 6 0 $c 0 3 0 0 0 region box prism 0 6 0 6 0 3 0 0 0 boundary p p p create_box 1 box Created triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0 0 0) 2 by 2 by 1 MPI processor grid create_atoms 1 region box Created 432 atoms mass 1 196.97 group all region box 432 atoms in group all pair_style lj/smooth/linear 5.456108274435118 pair_coeff * * 0.7242785984051078 2.598146797350056 neighbor 1.0 bin #neigh_modify delay 1000000 log cb_shear.log thermo 100 variable gamma equal 0.0 variable step equal 0 thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma pe xy xz yz timestep 1.0 fix AtC all 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 AtC mesh create $c $c 1 rectbox p p p fix_modify AtC mesh create 6 $c 1 rectbox p p p fix_modify AtC mesh create 6 6 1 rectbox p p p ATC: created uniform mesh with 98 nodes, 36 unique nodes, and 36 elements fix_modify AtC fields add mass_density internal_energy stress fix_modify AtC fields add displacement fix_modify AtC fields add cauchy_born_energy cauchy_born_stress fix_modify AtC gradients add displacement fix_modify AtC set reference_potential_energy 0. #fix_modify AtC fields add elastic_deformation_gradient fix_modify AtC output cb_shearFE 1 text binary tensor_components ATC: Warning : text output can create _LARGE_ files ATC: output custom names: min_modify line quadratic variable dgamma equal $d/${Ly} variable dgamma equal 0.0050000000000000001041/${Ly} variable dgamma equal 0.0050000000000000001041/24.480000000000000426 print "depsilon_12: ${dgamma}" depsilon_12: 0.00020424836601307190163 timestep 0.0 variable i loop 4 label loop_i print ">>> step $i" >>> step 1 minimize 1.e-20 1.e-20 1000 1000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... ATC: CB stiffness: 28.7742 Einstein freq: 7394.9 ATC: computing bond matrix ...........done Memory usage per processor = 23.608 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 0 0 8.2990138e-10 8.090598e-10 1.2401824e-09 -2.047237e-10 -1.675329e-10 -2.052466e-10 0 -1697.76 0 0 0 2 0 1.4564068e-09 1.4626573e-09 1.5311855e-09 1.91865e-11 2.9536813e-11 -6.2429255e-12 0 -1697.76 0 0 0 Loop time of 0.00183105 on 4 procs for 2 steps with 432 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1697.76 -1697.76 -1697.76 Force two-norm initial, final = 7.25089e-13 7.69958e-13 Force max component initial, final = 6.31162e-14 5.59344e-14 Final line search alpha, max atom move = 1 5.59344e-14 Iterations, force evaluations = 2 4 Pair time (%) = 0.00122535 (66.9206) Neigh time (%) = 0 (0) Comm time (%) = 0.000386775 (21.123) Outpt time (%) = 0 (0) Other time (%) = 0.000218928 (11.9564) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4212 max 4212 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 22.9213 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 2 0 1.1686684e-09 1.1704144e-09 1.1818848e-09 -7.0034742e-11 -2.0734576e-10 -2.246665e-10 0 -1697.76 0 0 0 3 0 1.3913827e-09 1.417767e-09 1.507396e-09 1.3580144e-11 6.6948897e-11 3.137377e-13 0 -1697.76 0 0 0 Loop time of 0.0191327 on 4 procs for 1 steps with 432 atoms Pair time (%) = 0.000261724 (1.36794) Neigh time (%) = 0 (0) Comm time (%) = 0.000138581 (0.724315) Outpt time (%) = 0.000174522 (0.912169) Other time (%) = 0.0185578 (96.9956) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4380 max 4051 min Histogram: 1 0 0 1 0 1 0 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 0+1 change_box all xy delta $d remap change_box all xy delta 0.0050000000000000001041 remap Changing box ... triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0204 0 0) variable gamma equal $i*${dgamma} variable gamma equal 1*${dgamma} variable gamma equal 1*0.00020424836601307190163 next i jump in.cb_shear loop_i print ">>> step $i" >>> step 2 minimize 1.e-20 1.e-20 1000 1000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... ATC: computing bond matrix ...........done Memory usage per processor = 23.608 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 3 1 6.886337 10.047566 -1.1516625 -2346.5185 -2.2571381e-10 -2.3527902e-10 0.00020424837 -1697.7555 0.0204 0 0 8 1 6.886337 10.047566 -1.1516625 -2346.5185 -2.9823269e-11 1.6162796e-11 0.00020424837 -1697.7555 0.0204 0 0 Loop time of 0.00383186 on 4 procs for 5 steps with 432 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1697.75552385 -1697.75552385 -1697.75552385 Force two-norm initial, final = 1.45516e-12 6.75826e-13 Force max component initial, final = 2.43972e-13 6.33382e-14 Final line search alpha, max atom move = 1 6.33382e-14 Iterations, force evaluations = 5 10 Pair time (%) = 0.00254309 (66.367) Neigh time (%) = 0 (0) Comm time (%) = 0.00077039 (20.1048) Outpt time (%) = 0 (0) Other time (%) = 0.000518382 (13.5282) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4380 max 4051 min Histogram: 1 0 0 1 0 1 0 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 22.9213 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 8 1 6.886337 10.047566 -1.1516625 -2346.5185 -1.3329305e-10 -1.817966e-10 0.00020424837 -1697.7555 0.0204 0 0 9 1 6.886337 10.047566 -1.1516625 -2346.5185 -1.153706e-11 6.5233191e-11 0.00020424837 -1697.7555 0.0204 0 0 Loop time of 0.0221808 on 4 procs for 1 steps with 432 atoms Pair time (%) = 0.000268757 (1.21167) Neigh time (%) = 0 (0) Comm time (%) = 0.000102341 (0.461395) Outpt time (%) = 0.00232071 (10.4627) Other time (%) = 0.019489 (87.8643) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4312 max 4085 min Histogram: 1 0 0 0 0 1 1 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 1+1 change_box all xy delta $d remap change_box all xy delta 0.0050000000000000001041 remap Changing box ... triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0408 0 0) variable gamma equal $i*${dgamma} variable gamma equal 2*${dgamma} variable gamma equal 2*0.00020424836601307190163 next i jump in.cb_shear loop_i print ">>> step $i" >>> step 3 minimize 1.e-20 1.e-20 1000 1000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... ATC: computing bond matrix ...........done Memory usage per processor = 23.608 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 9 2 27.545381 40.190743 -4.6066242 -4693.1379 -1.3165313e-10 -1.7366821e-10 0.00040849673 -1697.7421 0.0408 0 0 13 2 27.545381 40.190743 -4.6066242 -4693.1379 -2.0177729e-11 5.6927478e-11 0.00040849673 -1697.7421 0.0408 0 0 Loop time of 0.00312275 on 4 procs for 4 steps with 432 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1697.74209519 -1697.74209519 -1697.74209519 Force two-norm initial, final = 1.45582e-12 6.63859e-13 Force max component initial, final = 2.16244e-13 6.87297e-14 Final line search alpha, max atom move = 1 6.87297e-14 Iterations, force evaluations = 4 8 Pair time (%) = 0.00211573 (67.7521) Neigh time (%) = 0 (0) Comm time (%) = 0.000591516 (18.9422) Outpt time (%) = 0 (0) Other time (%) = 0.000415504 (13.3057) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4312 max 4085 min Histogram: 1 0 0 0 0 1 1 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 22.9213 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 13 2 27.545381 40.190743 -4.6066242 -4693.1379 -1.1765618e-10 -1.586376e-10 0.00040849673 -1697.7421 0.0408 0 0 14 2 27.545381 40.190743 -4.6066242 -4693.1379 -3.767429e-11 6.1228867e-11 0.00040849673 -1697.7421 0.0408 0 0 Loop time of 0.0225732 on 4 procs for 1 steps with 432 atoms Pair time (%) = 0.000268519 (1.18955) Neigh time (%) = 0 (0) Comm time (%) = 8.98838e-05 (0.398188) Outpt time (%) = 0.00227594 (10.0825) Other time (%) = 0.0199389 (88.3298) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4347 max 4038 min Histogram: 1 0 0 0 0 0 2 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 2+1 change_box all xy delta $d remap change_box all xy delta 0.0050000000000000001041 remap Changing box ... triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0612 0 0) variable gamma equal $i*${dgamma} variable gamma equal 3*${dgamma} variable gamma equal 3*0.00020424836601307190163 next i jump in.cb_shear loop_i print ">>> step $i" >>> step 4 minimize 1.e-20 1.e-20 1000 1000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... ATC: computing bond matrix ...........done Memory usage per processor = 23.608 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 14 3 61.977233 90.430962 -10.364808 -7039.9591 -1.4718693e-10 -1.6595966e-10 0.0006127451 -1697.7197 0.0612 0 0 18 3 61.977233 90.430962 -10.364808 -7039.9591 -9.9031986e-12 6.1389525e-11 0.0006127451 -1697.7197 0.0612 0 0 Loop time of 0.0029906 on 4 procs for 4 steps with 432 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1697.71971345 -1697.71971345 -1697.71971345 Force two-norm initial, final = 1.6934e-12 6.96493e-13 Force max component initial, final = 2.55476e-13 6.86812e-14 Final line search alpha, max atom move = 1 6.86812e-14 Iterations, force evaluations = 4 8 Pair time (%) = 0.00209922 (70.1937) Neigh time (%) = 0 (0) Comm time (%) = 0.000570774 (19.0856) Outpt time (%) = 0 (0) Other time (%) = 0.000320613 (10.7207) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4347 max 4038 min Histogram: 1 0 0 0 0 0 2 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 run 1 Setting up run ... ATC: computing bond matrix ...........done Memory usage per processor = 22.9213 Mbytes Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz 18 3 61.977233 90.430962 -10.364808 -7039.9591 -5.2551822e-11 -1.5970613e-10 0.0006127451 -1697.7197 0.0612 0 0 19 3 61.977233 90.430962 -10.364808 -7039.9591 -1.697518e-12 6.6900396e-11 0.0006127451 -1697.7197 0.0612 0 0 Loop time of 0.0220599 on 4 procs for 1 steps with 432 atoms Pair time (%) = 0.000261307 (1.18453) Neigh time (%) = 0 (0) Comm time (%) = 9.43542e-05 (0.427718) Outpt time (%) = 0.00232553 (10.5419) Other time (%) = 0.0193787 (87.8458) Nlocal: 108 ave 108 max 108 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 756 ave 756 max 756 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 4212 ave 4379 max 4068 min Histogram: 1 0 0 1 0 1 0 0 0 1 FullNghs: 8424 ave 8424 max 8424 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 78 Neighbor list builds = 0 Dangerous builds = 0 variable step equal ${step}+1 variable step equal 3+1 change_box all xy delta $d remap change_box all xy delta 0.0050000000000000001041 remap Changing box ... triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0816 0 0) variable gamma equal $i*${dgamma} variable gamma equal 4*${dgamma} variable gamma equal 4*0.00020424836601307190163 next i jump in.cb_shear loop_i