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lammps/examples/USER/atc/cauchy_born/cb_volumetric.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*${lattice_constant}
variable L equal 6*5.2562274870000003091
#variable d equal 0.01
variable d equal 0.005
variable s equal 1.005
variable V0 equal ($c*${lattice_constant})^3
variable V0 equal (6*${lattice_constant})^3
variable V0 equal (6*5.2562274870000003091)^3
# 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 $c
region box block 0 6 0 $c 0 $c
region box block 0 6 0 6 0 $c
region box block 0 6 0 6 0 6
boundary p p p
create_box 1 box
Created orthogonal box = (0 0 0) to (31.5374 31.5374 31.5374)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 864 atoms
mass 1 39.95
group all region box
864 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 $c box p p p
fix_modify AtC mesh create 6 $c $c box p p p
fix_modify AtC mesh create 6 6 $c box p p p
fix_modify AtC mesh create 6 6 6 box p p p
ATC: created uniform mesh with 343 nodes, 216 unique nodes, and 216 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 output cb_volumetricFE 1 full_text tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
log cb_volumetric.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
timestep 0.0
min_modify line quadratic
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: 7.56717 Einstein freq: 0.355649
ATC: computing bond matrix ...........done
Memory usage per processor = 23.7542 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
0 0 -4.8909542e-07 -4.8909515e-07 -4.8909708e-07 3.5104429e-13 -1.4141608e-12 -8.6196267e-13 0 -1743.9897
1 0 -4.8909445e-07 -4.8909445e-07 -4.8909627e-07 2.4570879e-13 -1.3724298e-12 -8.8539776e-13 0 -1743.9897
Loop time of 0.00986111 on 4 procs for 1 steps with 864 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-1743.9896675 -1743.9896675 -1743.9896675
Force two-norm initial, final = 4.7305e-13 3.32302e-13
Force max component initial, final = 1.93665e-14 1.80689e-14
Final line search alpha, max atom move = 1 1.80689e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.00795078 (80.6277)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00155658 (15.785)
Outpt time (%) = 0 (0)
Other time (%) = 0.000353754 (3.58736)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46224 max 46224 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 = 23.0675 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
1 0 -4.8909426e-07 -4.890941e-07 -4.8909627e-07 1.0203176e-13 -1.3879622e-12 -8.8539776e-13 0 -1743.9897
2 0 -4.8909426e-07 -4.890941e-07 -4.8909627e-07 1.0203176e-13 -1.3879622e-12 -8.8539776e-13 0 -1743.9897
Loop time of 0.589029 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00269467 (0.457476)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000495553 (0.0841305)
Outpt time (%) = 0.000582933 (0.0989652)
Other time (%) = 0.585256 (99.3594)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46289 max 46159 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap
Changing box ...
orthogonal box = (-0.0788434 0 0) to (31.6162 31.5374 31.5374)
orthogonal box = (-0.0788434 -0.0788434 0) to (31.6162 31.6162 31.5374)
orthogonal box = (-0.0788434 -0.0788434 -0.0788434) to (31.6162 31.6162 31.6162)
variable gamma equal lx/$L-1.0
variable gamma equal lx/31.537364922000001854-1.0
next i
jump in.cb_volumetric 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 = 23.7542 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
2 1 -429.84615 -429.84615 -429.84615 1.6244616e-13 -2.4910642e-13 -7.3535979e-13 0.005 -1742.4738
4 1 -429.84615 -429.84615 -429.84615 -1.2399576e-13 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738
Loop time of 0.0154624 on 4 procs for 2 steps with 864 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-1742.47382006 -1742.47382006 -1742.47382006
Force two-norm initial, final = 5.8003e-13 4.02116e-13
Force max component initial, final = 2.59532e-14 1.42178e-14
Final line search alpha, max atom move = 1 1.42178e-14
Iterations, force evaluations = 2 4
Pair time (%) = 0.0126531 (81.8311)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00235188 (15.2103)
Outpt time (%) = 0 (0)
Other time (%) = 0.000457466 (2.95857)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46281 max 46167 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 = 23.0675 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
4 1 -429.84615 -429.84615 -429.84615 -9.7213572e-14 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738
5 1 -429.84615 -429.84615 -429.84615 -9.7213572e-14 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738
Loop time of 0.584488 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00271827 (0.465068)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000644147 (0.110207)
Outpt time (%) = 0.0140409 (2.40226)
Other time (%) = 0.567085 (97.0225)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46339 max 46109 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap
Changing box ...
orthogonal box = (-0.158081 -0.0788434 -0.0788434) to (31.6954 31.6162 31.6162)
orthogonal box = (-0.158081 -0.158081 -0.0788434) to (31.6954 31.6954 31.6162)
orthogonal box = (-0.158081 -0.158081 -0.158081) to (31.6954 31.6954 31.6954)
variable gamma equal lx/$L-1.0
variable gamma equal lx/31.537364922000001854-1.0
next i
jump in.cb_volumetric 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 = 23.7542 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
5 2 -778.0092 -778.0092 -778.0092 7.4220526e-13 1.122178e-12 -9.6027588e-13 0.010025 -1730.6001
6 2 -778.0092 -778.0092 -778.0092 2.027045e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001
Loop time of 0.00881428 on 4 procs for 1 steps with 864 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-1730.60014837 -1730.60014837 -1730.60014837
Force two-norm initial, final = 8.6018e-13 3.15291e-13
Force max component initial, final = 4.77673e-14 1.4759e-14
Final line search alpha, max atom move = 1 1.4759e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.00673956 (76.4618)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00156629 (17.7699)
Outpt time (%) = 0 (0)
Other time (%) = 0.000508428 (5.76823)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46339 max 46109 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 = 23.0675 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
6 2 -778.0092 -778.0092 -778.0092 2.7752314e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001
7 2 -778.0092 -778.0092 -778.0092 2.7752314e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001
Loop time of 0.608097 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00230396 (0.37888)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000505984 (0.0832078)
Outpt time (%) = 0.0128615 (2.11504)
Other time (%) = 0.592426 (97.4229)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 46224 ave 46348 max 46100 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 92448 ave 92448 max 92448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369792
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 $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap
Changing box ...
orthogonal box = (-0.237715 -0.158081 -0.158081) to (31.7751 31.6954 31.6954)
orthogonal box = (-0.237715 -0.237715 -0.158081) to (31.7751 31.7751 31.6954)
orthogonal box = (-0.237715 -0.237715 -0.237715) to (31.7751 31.7751 31.7751)
variable gamma equal lx/$L-1.0
variable gamma equal lx/31.537364922000001854-1.0
next i
jump in.cb_volumetric 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 = 23.7542 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
7 3 -1113.9681 -1113.9681 -1113.9681 -7.697124e-13 -4.3806097e-13 1.4128091e-12 0.015075125 -1723.8495
8 3 -1113.9681 -1113.9681 -1113.9681 6.6266201e-13 4.7186976e-13 2.719048e-12 0.015075125 -1723.8495
Loop time of 0.00839263 on 4 procs for 1 steps with 864 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-1723.84952404 -1723.84952404 -1723.84952404
Force two-norm initial, final = 8.94607e-13 5.41927e-13
Force max component initial, final = 4.1616e-14 2.31482e-14
Final line search alpha, max atom move = 1 2.31482e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.00648439 (77.2629)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00149041 (17.7586)
Outpt time (%) = 0 (0)
Other time (%) = 0.000417829 (4.97852)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 41040 ave 41099 max 40981 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 82080 ave 82080 max 82080 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 328320
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
run 1
Setting up run ...
ATC: computing bond matrix ..........done
Memory usage per processor = 23.0675 Mbytes
Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng
8 3 -1113.9681 -1113.9681 -1113.9681 6.4417311e-13 5.3127209e-13 2.719048e-12 0.015075125 -1723.8495
9 3 -1113.9681 -1113.9681 -1113.9681 6.4417311e-13 5.3127209e-13 2.719048e-12 0.015075125 -1723.8495
Loop time of 0.545379 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00224721 (0.412046)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000599265 (0.109881)
Outpt time (%) = 0.0199156 (3.6517)
Other time (%) = 0.522617 (95.8264)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3672 ave 3672 max 3672 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 41040 ave 41313 max 40767 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 82080 ave 82080 max 82080 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 328320
Ave neighs/atom = 380
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 $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap
change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap
Changing box ...
orthogonal box = (-0.317747 -0.237715 -0.237715) to (31.8551 31.7751 31.7751)
orthogonal box = (-0.317747 -0.317747 -0.237715) to (31.8551 31.8551 31.7751)
orthogonal box = (-0.317747 -0.317747 -0.317747) to (31.8551 31.8551 31.8551)
variable gamma equal lx/$L-1.0
variable gamma equal lx/31.537364922000001854-1.0
next i
jump in.cb_volumetric loop_i
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