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lammps/examples/USER/atc/cauchy_born/cb_biaxial.screen
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LAMMPS (24 Aug 2013)
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal $c*${lattice_constant}
variable L equal 6*${lattice_constant}
variable L equal 6*5.2562274870000003091
variable d equal 0.005
variable s equal 1.005
variable is equal 1.0/$s
variable is equal 1.0/1.0049999999999998934
variable V0 equal $L*$L*3*${lattice_constant}
variable V0 equal 31.537364922000001854*$L*3*${lattice_constant}
variable V0 equal 31.537364922000001854*31.537364922000001854*3*${lattice_constant}
variable V0 equal 31.537364922000001854*31.537364922000001854*3*5.2562274870000003091
# create system
lattice fcc ${lattice_constant} origin 0.25 0.25 0.25
lattice fcc 5.2562274870000003091 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
region box block 0 $c 0 $c 0 3
region box block 0 6 0 $c 0 3
region box block 0 6 0 6 0 3
boundary p p p
create_box 1 box
Created orthogonal box = (0 0 0) to (31.5374 31.5374 15.7687)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 432 atoms
mass 1 39.95
group all region box
432 atoms in group all
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# ID group atc PhysicsType ParameterFile
fix AtC all atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
fix_modify AtC mesh create $c $c 1 box p p p
fix_modify AtC mesh create 6 $c 1 box p p p
fix_modify AtC mesh create 6 6 1 box p p p
ATC: created uniform mesh with 98 nodes, 36 unique nodes, and 36 elements
fix_modify AtC fields none
fix_modify AtC fields add displacement
fix_modify AtC fields add internal_energy stress 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_biaxialFE 1 full_text tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
log cb_biaxial.log
thermo 100
variable gamma1 equal 0.0
variable gamma2 equal 0.0
variable dv equal 1.0
variable step equal 0
thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma1 pe v_dv
timestep 0.0
min_modify line quadratic
timestep 0.0
variable i loop 4
label loop_i
print ">>> step $i ${gamma1} ${gamma2}"
>>> step 1 0 0
minimize 1.e-20 1.e-20 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: CB stiffness: 7.56717 Einstein freq: 0.355649
ATC: computing bond matrix ...........done
Memory usage per processor = 23.7277 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
0 0 -4.8909909e-07 -4.8909886e-07 -4.8910238e-07 3.8880943e-13 -1.7762988e-12 -1.6027127e-12 0 -871.99483 1
1 0 -4.8909976e-07 -4.8909976e-07 -4.8910453e-07 5.2088849e-13 -1.9469417e-12 -1.714206e-12 0 -871.99483 1
Loop time of 0.00493699 on 4 procs for 1 steps with 432 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-871.994833749 -871.994833749 -871.994833749
Force two-norm initial, final = 3.34475e-13 2.07006e-13
Force max component initial, final = 1.93109e-14 1.59178e-14
Final line search alpha, max atom move = 1 1.59178e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.00400245 (81.0706)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00063026 (12.7661)
Outpt time (%) = 0 (0)
Other time (%) = 0.000304282 (6.1633)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23112 max 23112 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 23.0409 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
1 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1
2 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1
Loop time of 0.109179 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00135243 (1.23872)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000175953 (0.161159)
Outpt time (%) = 0.000232399 (0.212859)
Other time (%) = 0.107419 (98.3873)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23425 max 22860 min
Histogram: 1 0 1 0 0 1 0 0 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 0+1
change_box all x scale $s y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
Changing box ...
orthogonal box = (-0.0788434 0 0) to (31.6162 31.5374 15.7687)
orthogonal box = (-0.0788434 0.0784512 0) to (31.6162 31.4589 15.7687)
variable gamma1 equal lx/$L-1.0
variable gamma1 equal lx/31.537364922000001854-1.0
variable gamma2 equal ly/$L-1.0
variable gamma2 equal ly/31.537364922000001854-1.0
variable dv equal vol/${V0}
variable dv equal vol/15683.616509356999813
next i
jump in.cb_biaxial loop_i
print ">>> step $i ${gamma1} ${gamma2}"
>>> step 2 0.0049999999999998934186 -0.0049751243781092080454
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 = 23.7277 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
2 1 -91.357902 91.748981 5.9495117 4.4461448e-13 -1.151199e-12 -1.6213907e-12 0.005 -871.8904 1
4 1 -91.357902 91.748981 5.9495117 1.1843442e-13 -1.1753736e-12 2.0631862e-13 0.005 -871.8904 1
Loop time of 0.00749826 on 4 procs for 2 steps with 432 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-871.890401015 -871.890401015 -871.890401015
Force two-norm initial, final = 5.08157e-13 2.70169e-13
Force max component initial, final = 5.63517e-14 1.97412e-14
Final line search alpha, max atom move = 1 1.97412e-14
Iterations, force evaluations = 2 4
Pair time (%) = 0.00628054 (83.7599)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000852108 (11.3641)
Outpt time (%) = 0 (0)
Other time (%) = 0.000365615 (4.87599)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23425 max 22860 min
Histogram: 1 0 1 0 0 1 0 0 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 23.0409 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
4 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1
5 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1
Loop time of 0.112613 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00136155 (1.20905)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000247359 (0.219654)
Outpt time (%) = 0.00382805 (3.39929)
Other time (%) = 0.107176 (95.172)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23233 max 22979 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 1+1
change_box all x scale $s y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
Changing box ...
orthogonal box = (-0.158081 0.0784512 0) to (31.6954 31.4589 15.7687)
orthogonal box = (-0.158081 0.156512 0) to (31.6954 31.3809 15.7687)
variable gamma1 equal lx/$L-1.0
variable gamma1 equal lx/31.537364922000001854-1.0
variable gamma2 equal ly/$L-1.0
variable gamma2 equal ly/31.537364922000001854-1.0
variable dv equal vol/${V0}
variable dv equal vol/15683.616509356999813
next i
jump in.cb_biaxial loop_i
print ">>> step $i ${gamma1} ${gamma2}"
>>> step 3 0.010024999999999728573 -0.009925496893640972651
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 = 23.7277 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
5 2 -171.87971 184.21354 24.007425 2.4269349e-13 3.1283039e-12 2.293625e-12 0.010025 -871.15868 1
7 2 -171.87971 184.21354 24.007425 -1.0629975e-12 1.690591e-12 2.2967994e-12 0.010025 -871.15868 1
Loop time of 0.00739127 on 4 procs for 2 steps with 432 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-871.158684158 -871.158684158 -871.158684158
Force two-norm initial, final = 5.1376e-13 2.56079e-13
Force max component initial, final = 5.97855e-14 2.52853e-14
Final line search alpha, max atom move = 1 2.52853e-14
Iterations, force evaluations = 2 4
Pair time (%) = 0.00619501 (83.8152)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000802398 (10.856)
Outpt time (%) = 0 (0)
Other time (%) = 0.000393867 (5.32882)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23234 max 22979 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 23.0409 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
7 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1
8 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1
Loop time of 0.112138 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00134319 (1.1978)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000202775 (0.180826)
Outpt time (%) = 0.0036608 (3.26454)
Other time (%) = 0.106932 (95.3568)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23314 max 22858 min
Histogram: 1 0 0 0 0 1 0 1 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 2+1
change_box all x scale $s y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
Changing box ...
orthogonal box = (-0.237715 0.156512 0) to (31.7751 31.3809 15.7687)
orthogonal box = (-0.237715 0.234184 0) to (31.7751 31.3032 15.7687)
variable gamma1 equal lx/$L-1.0
variable gamma1 equal lx/31.537364922000001854-1.0
variable gamma2 equal ly/$L-1.0
variable gamma2 equal ly/31.537364922000001854-1.0
variable dv equal vol/${V0}
variable dv equal vol/15683.616509356999813
next i
jump in.cb_biaxial loop_i
print ">>> step $i ${gamma1} ${gamma2}"
>>> step 4 0.015075124999999633957 -0.014851240690189837501
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 = 23.7277 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
8 3 -256.21626 277.50951 57.50796 -1.4695091e-13 4.1657011e-13 7.7445306e-13 0.015075125 -870.22745 1
11 3 -256.21626 277.50951 57.50796 -7.7055184e-13 3.5561707e-14 -1.2297109e-12 0.015075125 -870.22745 1
Loop time of 0.0100762 on 4 procs for 3 steps with 432 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-870.227446396 -870.227446396 -870.227446396
Force two-norm initial, final = 4.73029e-13 2.08011e-13
Force max component initial, final = 4.59355e-14 2.3731e-14
Final line search alpha, max atom move = 1 2.3731e-14
Iterations, force evaluations = 3 6
Pair time (%) = 0.00842237 (83.5866)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00119847 (11.894)
Outpt time (%) = 0 (0)
Other time (%) = 0.000455379 (4.51935)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23314 max 22862 min
Histogram: 1 0 0 0 0 1 1 0 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 23.0409 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
11 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1
12 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1
Loop time of 0.163245 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00132376 (0.810903)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000195086 (0.119505)
Outpt time (%) = 0.0115035 (7.04678)
Other time (%) = 0.150223 (92.0228)
Nlocal: 108 ave 108 max 108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2808 ave 2808 max 2808 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 23112 ave 23264 max 23042 min
Histogram: 2 0 1 0 0 0 0 0 0 1
FullNghs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184896
Ave neighs/atom = 428
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 3+1
change_box all x scale $s y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale ${is} remap
change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
Changing box ...
orthogonal box = (-0.317747 0.234184 0) to (31.8551 31.3032 15.7687)
orthogonal box = (-0.317747 0.311471 0) to (31.8551 31.2259 15.7687)
variable gamma1 equal lx/$L-1.0
variable gamma1 equal lx/31.537364922000001854-1.0
variable gamma2 equal ly/$L-1.0
variable gamma2 equal ly/31.537364922000001854-1.0
variable dv equal vol/${V0}
variable dv equal vol/15683.616509356999813
next i
jump in.cb_biaxial loop_i
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