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
