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lammps/examples/USER/atc/cauchy_born/cb_shear.screen
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LAMMPS (24 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 0.0331877 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 (%) = 0.00367767 (11.0814)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0172022 (51.8331)
Outpt time (%) = 0 (0)
Other time (%) = 0.0123078 (37.0855)
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 0.0194613 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000263691 (1.35495)
Neigh time (%) = 0 (0)
Comm time (%) = 8.98838e-05 (0.461858)
Outpt time (%) = 0.000126779 (0.651441)
Other time (%) = 0.018981 (97.5318)
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 0.00386053 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 (%) = 0.00253791 (65.7398)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000785768 (20.3539)
Outpt time (%) = 0 (0)
Other time (%) = 0.000536859 (13.9063)
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 0.0218393 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000262439 (1.20168)
Neigh time (%) = 0 (0)
Comm time (%) = 8.62479e-05 (0.39492)
Outpt time (%) = 0.00235128 (10.7663)
Other time (%) = 0.0191393 (87.6371)
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 0.00320125 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 (%) = 0.00207806 (64.914)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000690341 (21.5648)
Outpt time (%) = 0 (0)
Other time (%) = 0.000432849 (13.5213)
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 0.240252 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00276661 (1.15155)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0216646 (9.01744)
Outpt time (%) = 0.05042 (20.9863)
Other time (%) = 0.165401 (68.8447)
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 0.0030961 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 (%) = 0.00208038 (67.1935)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000579238 (18.7086)
Outpt time (%) = 0 (0)
Other time (%) = 0.000436485 (14.0979)
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 0.0218921 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000263453 (1.20342)
Neigh time (%) = 0 (0)
Comm time (%) = 8.04663e-05 (0.367559)
Outpt time (%) = 0.00220877 (10.0894)
Other time (%) = 0.0193394 (88.3397)
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
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