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ATC version 2.0, date: Aug7 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10558 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones 2013-08-07 21:29:05 +00:00
parent 0e4d1e6b22
commit 666de878ad
216 changed files with 28362 additions and 3375 deletions
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7
examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat Normal file
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material Ar real
stress cauchy-born
pair_style lj/cut 13.5 #pair_style lj/cut r_cut
pair_coeff 0.238 3.405 #pair_coeff epsilon sigma
# temperature 0
# linear
end

7
examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat Normal file
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material Ar real
stress cauchy-born
pair_style lj/cut 13.5 #pair_style lj/cut r_cut
pair_coeff 0.238 3.405 #pair_coeff epsilon sigma
# temperature 0
linear
end

6
examples/USER/atc/cauchy_born/Au_CauchyBorn.mat Normal file
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material Au real
stress cauchy-born
pair_style lj/smooth/linear 5.456108274435118 #pair_style lj/smooth/linear r_cut
pair_coeff 0.7242785984051078 2.598146797350056 #pair_coeff epsilon sigma
#linear
end

6
examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat Normal file
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material Au real
stress cauchy-born
pair_style lj/smooth/linear 5.456108274435118 #pair_style lj/smooth/linear r_cut
pair_coeff 0.7242785984051078 2.598146797350056 #pair_coeff epsilon sigma
linear
end

5
examples/USER/atc/cauchy_born/Au_eam.mat Normal file
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material Au metal
stress cauchy-born
pair_style eam
end
end

6
examples/USER/atc/cauchy_born/Au_eam_linear.mat Normal file
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material Au metal
stress cauchy-born
pair_style eam
linear
end
end

5
examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat Normal file
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material Cu real
stress cauchy-born
pair_style eam
#linear
end

400
examples/USER/atc/cauchy_born/cb_biaxial.screen Normal file
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LAMMPS (14 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: 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 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 0.280059 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 (%) = 0.0039708 (1.41784)
Neigh time (%) = 0 (0)
Comm time (%) = 0.117534 (41.9677)
Outpt time (%) = 0 (0)
Other time (%) = 0.158554 (56.6145)
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 0.235875 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00137603 (0.583373)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000292778 (0.124124)
Outpt time (%) = 0.0005005 (0.212189)
Other time (%) = 0.233706 (99.0803)
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 0.275171 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 (%) = 0.00895029 (3.25263)
Neigh time (%) = 0 (0)
Comm time (%) = 0.157368 (57.1892)
Outpt time (%) = 0 (0)
Other time (%) = 0.108853 (39.5582)
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 0.249931 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00142711 (0.571004)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000403583 (0.161478)
Outpt time (%) = 0.00990075 (3.9614)
Other time (%) = 0.238199 (95.3061)
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 0.510101 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 (%) = 0.0191914 (3.76227)
Neigh time (%) = 0 (0)
Comm time (%) = 0.23774 (46.6064)
Outpt time (%) = 0 (0)
Other time (%) = 0.25317 (49.6313)
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 0.494811 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00385392 (0.778867)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0360543 (7.28647)
Outpt time (%) = 0.0442775 (8.94838)
Other time (%) = 0.410625 (82.9863)
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 0.165426 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 (%) = 0.00856608 (5.17818)
Neigh time (%) = 0 (0)
Comm time (%) = 0.116189 (70.2361)
Outpt time (%) = 0 (0)
Other time (%) = 0.0406712 (24.5857)
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 0.687404 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00261223 (0.380014)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0127067 (1.8485)
Outpt time (%) = 0.0149975 (2.18176)
Other time (%) = 0.657088 (95.5897)
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

384
examples/USER/atc/cauchy_born/cb_shear.screen Normal file
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LAMMPS (14 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: 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 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 0.00191295 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 (%) = 0.00124657 (65.1648)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000366986 (19.1843)
Outpt time (%) = 0 (0)
Other time (%) = 0.000299394 (15.6509)
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 0.0460081 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.00277305 (6.0273)
Neigh time (%) = 0 (0)
Comm time (%) = 0.012373 (26.893)
Outpt time (%) = 0.000219166 (0.476364)
Other time (%) = 0.0306429 (66.6033)
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 0.00391698 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 (%) = 0.00264663 (67.568)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000849068 (21.6766)
Outpt time (%) = 0 (0)
Other time (%) = 0.000421286 (10.7554)
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 0.02672 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000268936 (1.0065)
Neigh time (%) = 0 (0)
Comm time (%) = 9.2268e-05 (0.345314)
Outpt time (%) = 0.00226957 (8.49387)
Other time (%) = 0.0240893 (90.1543)
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 0.00320572 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 (%) = 0.00217921 (67.9787)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000676513 (21.1033)
Outpt time (%) = 0 (0)
Other time (%) = 0.000349998 (10.9179)
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 0.0443209 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000267744 (0.604103)
Neigh time (%) = 0 (0)
Comm time (%) = 9.21488e-05 (0.207913)
Outpt time (%) = 0.00152749 (3.44643)
Other time (%) = 0.0424336 (95.7416)
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 0.083416 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 (%) = 0.00221682 (2.65754)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0704444 (84.4495)
Outpt time (%) = 0 (0)
Other time (%) = 0.0107548 (12.8929)
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 0.178347 on 4 procs for 1 steps with 432 atoms
Pair time (%) = 0.000270486 (0.151663)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0174391 (9.77818)
Outpt time (%) = 0.0102363 (5.73956)
Other time (%) = 0.150401 (84.3306)
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

123
examples/USER/atc/cauchy_born/cb_unistrain.screen Normal file
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@ -0,0 +1,123 @@
LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
lattice fcc 5.256227487 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
Created orthogonal box = (-42.0498 -10.5125 -10.5125) to (42.0498 10.5125 10.5125)
4 by 1 by 1 MPI processor grid
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
Created 896 atoms
mass 1 39.95
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
768 atoms in group internal
# specify inter-atomic potential
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix AtC internal atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
fix_modify AtC mesh create 8 1 1 BOX f p p
terminate called after throwing an instance of 'terminate called after throwing an instance of 'ATC::ATC_Error'
terminate called after throwing an instance of 'ATC::ATC_Error'
ATC: P1, ERROR: elastic_deformation_gradient is not a valid field
ATC: P3, ERROR: elastic_deformation_gradient is not a valid field
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 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 fields add elastic_deformation_gradient
ATC: P0, ERROR: elastic_deformation_gradient is not a valid field
[pharsalus:35580] *** Process received signal ***
[pharsalus:35580] Signal: Aborted (6)
[pharsalus:35580] Signal code: (-6)
[pharsalus:35582] *** Process received signal ***
[pharsalus:35582] Signal: Aborted (6)
[pharsalus:35582] Signal code: (-6)
ATC::ATC_Error'
[pharsalus:35579] *** Process received signal ***
[pharsalus:35579] Signal: Aborted (6)
[pharsalus:35579] Signal code: (-6)
ATC: P2, ERROR: elastic_deformation_gradient is not a valid field
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:35581] *** Process received signal ***
[pharsalus:35581] Signal: Aborted (6)
[pharsalus:35581] Signal code: (-6)
[pharsalus:35582] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35582] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35582] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35582] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35582] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35582] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35582] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35579] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35579] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35579] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35579] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35579] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35579] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35579] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35579] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35579] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35579] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35579] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35579] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35579] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35579] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35579] *** End of error message ***
[pharsalus:35582] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35582] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35582] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35582] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35582] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35582] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35582] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35582] *** End of error message ***
[pharsalus:35581] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35581] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35581] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35581] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35581] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35581] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35581] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35581] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35581] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35581] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35581] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35581] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35581] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35581] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35581] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 35581 on node pharsalus exited on signal 6 (Aborted).
--------------------------------------------------------------------------
[pharsalus:35580] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35580] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35580] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35580] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35580] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35580] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35580] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35580] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35580] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35580] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35580] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35580] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35580] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35580] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35580] *** End of error message ***

145
examples/USER/atc/cauchy_born/cb_unistrain_eam.screen Normal file
View File

@ -0,0 +1,145 @@
LAMMPS (14 Aug 2013)
units metal
atom_style atomic
# create domain
#lattice fcc 3.615 origin 0.25 0.25 0.25
lattice fcc 3.615 origin 0.01 0.01 0.01
Lattice spacing in x,y,z = 3.615 3.615 3.615
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
Created orthogonal box = (-28.92 -7.23 -7.23) to (28.92 7.23 7.23)
4 by 1 by 1 MPI processor grid
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
Created 896 atoms
mass 1 63.55
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
768 atoms in group internal
# specify inter-atomic potential
pair_style eam
pair_coeff * * ../../../../potentials/Cu_u3.eam
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix AtC internal atc field Cu_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Cu_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
fix_modify AtC mesh create 8 1 1 BOX f p p
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
#fix_modify AtC kernel quartic_cylinder 10.0
fix_modify AtC fields none
fix_modify AtC fields add displacement
fix_modify AtC fields add internal_energy stress
fix_modify AtC fields add cauchy_born_energy
fix_modify AtC fields add cauchy_born_stress
fix_modify AtC gradients add displacement
#fix_modify AtC fields add elastic_deformation_gradient
timestep 0.0
fix_modify AtC output cb_unistrain_eamFE 1 text tensor_components binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
log cb_unistrain_eam.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
Setting up run ...
ATC: CB stiffness: 12.0537 Einstein freq: 2718.63
ATC: computing bond matrix ...........done
Memory usage per processor = 22.7644 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
0 0 -3138.143 0 -4765.0913 57.84 14.46 14.46
1 0 -3138.143 0 -4765.0913 57.84 14.46 14.46
Loop time of 0.0273568 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000983477 (3.595)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000149012 (0.544697)
Outpt time (%) = 0.000116587 (0.426171)
Other time (%) = 0.0261077 (95.4341)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 684.75 ave 843 max 484 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 0+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 22.7644 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
1 1 -3138.1235 0 -5936.0512 57.84 14.46 14.46
2 1 -3138.1235 0 -5936.0512 57.84 14.46 14.46
Loop time of 0.0527597 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000959635 (1.81888)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00559711 (10.6087)
Outpt time (%) = 0.00891805 (16.9031)
Other time (%) = 0.0372849 (70.6693)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 684.75 ave 843 max 484 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 1+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 22.7644 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
2 2 -3138.0934 0 -7103.7691 57.84 14.46 14.46
3 2 -3138.0934 0 -7103.7691 57.84 14.46 14.46
Loop time of 0.317459 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.0405899 (12.7859)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0319443 (10.0625)
Outpt time (%) = 0.0423202 (13.3309)
Other time (%) = 0.202604 (63.8207)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 684.75 ave 843 max 484 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0

158
examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen Normal file
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@ -0,0 +1,158 @@
LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
lattice fcc 4.08 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 4.08 4.08 4.08
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
Created orthogonal box = (-32.64 -8.16 -8.16) to (32.64 8.16 8.16)
4 by 1 by 1 MPI processor grid
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
Created 896 atoms
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
768 atoms in group internal
# specify inter-atomic potential
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix PP1 internal atc field Au_eam_linear.mat
ATC: constructing shape function field estimate with parameter file Au_eam_linear.mat
ATC: peratom PE compute created with ID: 3
fix_modify PP1 mesh create 8 1 1 BOX f p p
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
fix_modify PP1 fields add displacement
fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify PP1 gradients add displacement
fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe
# ID group atc PhysicsType ParameterFile
fix PP2 internal atc field Au_eam.mat
ATC: constructing shape function field estimate with parameter file Au_eam.mat
ATC: peratom PE compute created with ID: 3
fix_modify PP2 mesh create 8 1 1 BOX f p p
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy
fix_modify PP2 set reference_potential_energy
timestep 0.0
fix_modify PP1 output cb_unistrain_eam_linearFE 1 text tensor_components binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify PP2 output cb_unistrain_eam_refFE 1 text tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
log cb_unistrain_eam_linear.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
Setting up run ...
ATC: created cubic stress function:
lammps ATC units
c11=1.14323 0.000478328
c12=0.990885 0.000414586
c44=0.279154 0.000116798
ATC: CB stiffness: 11.5362 Einstein freq: 0.975052
ATC: computing bond matrix ...........done
ATC: CB stiffness: 11.5362 Einstein freq: 0.975052
Memory usage per processor = 43.4446 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
0 0 -3488.8211 0 -387.61198 65.28 16.32 16.32
1 0 -3488.8211 0 -387.61198 65.28 16.32 16.32
Loop time of 0.0171664 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000946522 (5.51381)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000137866 (0.803114)
Outpt time (%) = 8.52942e-05 (0.496868)
Other time (%) = 0.0159967 (93.1862)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 0+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 43.4446 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
1 1 -3488.7472 0 -447.10849 65.28 16.32 16.32
2 1 -3488.7472 0 -447.10849 65.28 16.32 16.32
Loop time of 0.0233803 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000981331 (4.19726)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000181496 (0.776279)
Outpt time (%) = 0.000347793 (1.48755)
Other time (%) = 0.0218697 (93.5389)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 1+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 43.4446 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
2 2 -3488.6569 0 -506.40727 65.28 16.32 16.32
3 2 -3488.6569 0 -506.40727 65.28 16.32 16.32
Loop time of 0.0714502 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.0255377 (35.742)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0149598 (20.9374)
Outpt time (%) = 0.000393927 (0.551331)
Other time (%) = 0.0305588 (42.7693)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5808 ave 6912 max 4672 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 11616 ave 13824 max 9408 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 46464
Ave neighs/atom = 51.8571
Neighbor list builds = 0
Dangerous builds = 0

161
examples/USER/atc/cauchy_born/cb_unistrain_linear.screen Normal file
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@ -0,0 +1,161 @@
LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
lattice fcc 4.08 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 4.08 4.08 4.08
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
Created orthogonal box = (-32.64 -8.16 -8.16) to (32.64 8.16 8.16)
4 by 1 by 1 MPI processor grid
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
Created 896 atoms
#pair_style eam
#pair_coeff * * Au_u3.eam
#pair_style lj/cut/smooth 5.456108274435118
pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
mass * 196.97
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
768 atoms in group internal
# specify inter-atomic potential
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix PP1 internal atc field Au_CauchyBorn_linear.mat
ATC: constructing shape function field estimate with parameter file Au_CauchyBorn_linear.mat
ATC: peratom PE compute created with ID: 3
fix_modify PP1 mesh create 8 1 1 BOX f p p
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
fix_modify PP1 fields add displacement
fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify PP1 gradients add displacement
fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe
# ID group atc PhysicsType ParameterFile
fix PP2 internal atc field Au_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Au_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
fix_modify PP2 mesh create 8 1 1 BOX f p p
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy
fix_modify PP2 set reference_potential_energy
timestep 0.0
fix_modify PP1 output cb_unistrain_linearFE 1 text tensor_components binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify PP2 output cb_unistrain_refFE 1 text tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
log cb_unistrain_linear.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
Setting up run ...
ATC: created cubic stress function:
lammps ATC units
c11=3.10501 0.00129914
c12=1.75749 0.000735332
c44=1.75749 0.000735332
ATC: CB stiffness: 28.7742 Einstein freq: 1.53992
ATC: computing bond matrix ...........done
ATC: CB stiffness: 28.7742 Einstein freq: 1.53992
Memory usage per processor = 43.292 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
0 0 -3435.8868 0 50.003991 65.28 16.32 16.32
1 0 -3435.8868 0 50.003991 65.28 16.32 16.32
Loop time of 0.0132832 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000411749 (3.09977)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000149429 (1.12495)
Outpt time (%) = 8.07047e-05 (0.60757)
Other time (%) = 0.0126413 (95.1677)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4528 ave 5376 max 3648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 9056 ave 10752 max 7360 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 36224
Ave neighs/atom = 40.4286
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 0+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 43.292 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
1 1 -3435.904 0 -77.521908 65.28 16.32 16.32
2 1 -3435.904 0 -77.521908 65.28 16.32 16.32
Loop time of 0.0176127 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.000424206 (2.40853)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000124991 (0.709664)
Outpt time (%) = 0.000433266 (2.45997)
Other time (%) = 0.0166302 (94.4218)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4528 ave 5376 max 3648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 9056 ave 10752 max 7360 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 36224
Ave neighs/atom = 40.4286
Neighbor list builds = 0
Dangerous builds = 0
variable step equal ${step}+1
variable step equal 1+1
displace_atoms all ramp x -0.1 0.1 x -100 100
Displacing atoms ...
run 1
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 43.292 Mbytes
Step step PotEng KinEng Press Lx Ly Lz
2 2 -3435.8757 0 -203.99195 65.28 16.32 16.32
3 2 -3435.8757 0 -203.99195 65.28 16.32 16.32
Loop time of 0.0175297 on 4 procs for 1 steps with 896 atoms
Pair time (%) = 0.00041151 (2.3475)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000131011 (0.747365)
Outpt time (%) = 0.000337481 (1.9252)
Other time (%) = 0.0166497 (94.9799)
Nlocal: 224 ave 256 max 192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 903 ave 1116 max 690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4528 ave 5376 max 3648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 9056 ave 10752 max 7360 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 36224
Ave neighs/atom = 40.4286
Neighbor list builds = 0
Dangerous builds = 0

389
examples/USER/atc/cauchy_born/cb_volumetric.screen Normal file
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@ -0,0 +1,389 @@
LAMMPS (14 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: 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 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 0.152578 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 (%) = 0.00802612 (5.26033)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0638427 (41.8426)
Outpt time (%) = 0 (0)
Other time (%) = 0.0807094 (52.8971)
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 1.74483 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00266743 (0.152876)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0846363 (4.85068)
Outpt time (%) = 0.0165098 (0.946209)
Other time (%) = 1.64102 (94.0502)
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 1.44839 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 (%) = 0.0205068 (1.41584)
Neigh time (%) = 0 (0)
Comm time (%) = 1.02466 (70.7452)
Outpt time (%) = 0 (0)
Other time (%) = 0.403216 (27.8389)
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 2.702 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00525749 (0.194578)
Neigh time (%) = 0 (0)
Comm time (%) = 0.154782 (5.72844)
Outpt time (%) = 0.149323 (5.52637)
Other time (%) = 2.39264 (88.5506)
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 0.637543 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 (%) = 0.00699323 (1.0969)
Neigh time (%) = 0 (0)
Comm time (%) = 0.473002 (74.1913)
Outpt time (%) = 0 (0)
Other time (%) = 0.157548 (24.7118)
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 2.39483 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00456077 (0.190443)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0782377 (3.26694)
Outpt time (%) = 0.0521472 (2.17749)
Other time (%) = 2.25988 (94.3651)
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 0.00824732 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 (%) = 0.00639701 (77.5647)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00148129 (17.9609)
Outpt time (%) = 0 (0)
Other time (%) = 0.000369012 (4.47433)
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 1.98395 on 4 procs for 1 steps with 864 atoms
Pair time (%) = 0.00230694 (0.11628)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00056833 (0.0286464)
Outpt time (%) = 0.050661 (2.55354)
Other time (%) = 1.93041 (97.3015)
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

568
examples/USER/atc/cauchy_born/flying_cube.screen Normal file
View File

@ -0,0 +1,568 @@
LAMMPS (14 Aug 2013)
log log.flying_cube
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal (${lattice_constant}*$c)
variable L equal (5.2562274870000003091*$c)
variable L equal (5.2562274870000003091*6)
variable V equal $L*$L*$L
variable V equal 31.537364922000001854*$L*$L
variable V equal 31.537364922000001854*31.537364922000001854*$L
variable V equal 31.537364922000001854*31.537364922000001854*31.537364922000001854
print "Volume : $V"
Volume : 31367.233018713999627
variable s equal 10
variable dt equal 0.1
variable v equal 0.1
variable m equal 39.95
# create system
lattice fcc ${lattice_constant} origin 0.01 0.01 0.01
lattice fcc 5.2562274870000003091 origin 0.01 0.01 0.01
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
# boundary p s s
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 region box
Created 864 atoms
mass 1 $m
mass 1 39.950000000000002842
group all region box
864 atoms in group all
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 0 every 200 check no
# neigh_modify delay 0 every $n
reset_timestep 0
thermo $s
thermo 10
compute_modify thermo_temp extra 0
thermo_style custom step temp pxx pyy pzz etotal lx ly lz
timestep ${dt}
timestep 0.10000000000000000555
min_modify line quadratic
minimize 0. 0. 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
Memory usage per processor = 2.90511 Mbytes
Step Temp Pxx Pyy Pzz TotEng Lx Ly Lz
0 0 -4.8909602e-07 -4.8909602e-07 -4.8909727e-07 -1743.9897 31.537365 31.537365 31.537365
10 0 -4.8910206e-07 -4.8910173e-07 -4.891027e-07 -1743.9897 31.537365 31.537365 31.537365
20 0 -4.8910163e-07 -4.8910171e-07 -4.8910289e-07 -1743.9897 31.537365 31.537365 31.537365
30 0 -4.8910045e-07 -4.8910034e-07 -4.8910129e-07 -1743.9897 31.537365 31.537365 31.537365
40 0 -4.8910136e-07 -4.891012e-07 -4.8910284e-07 -1743.9897 31.537365 31.537365 31.537365
50 0 -4.8910093e-07 -4.8910075e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365
60 0 -4.8910118e-07 -4.8910068e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365
70 0 -4.8910152e-07 -4.891015e-07 -4.8910292e-07 -1743.9897 31.537365 31.537365 31.537365
80 0 -4.8910039e-07 -4.891003e-07 -4.8910152e-07 -1743.9897 31.537365 31.537365 31.537365
90 0 -4.8910067e-07 -4.8910044e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365
100 0 -4.8910167e-07 -4.8910159e-07 -4.8910289e-07 -1743.9897 31.537365 31.537365 31.537365
110 0 -4.8910086e-07 -4.8910059e-07 -4.8910202e-07 -1743.9897 31.537365 31.537365 31.537365
120 0 -4.8910062e-07 -4.8910061e-07 -4.8910155e-07 -1743.9897 31.537365 31.537365 31.537365
130 0 -4.8910107e-07 -4.8910086e-07 -4.8910219e-07 -1743.9897 31.537365 31.537365 31.537365
140 0 -4.8910086e-07 -4.8910076e-07 -4.8910157e-07 -1743.9897 31.537365 31.537365 31.537365
150 0 -4.8910119e-07 -4.8910116e-07 -4.8910235e-07 -1743.9897 31.537365 31.537365 31.537365
160 0 -4.8910081e-07 -4.8910037e-07 -4.8910204e-07 -1743.9897 31.537365 31.537365 31.537365
170 0 -4.8910074e-07 -4.8910056e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365
180 0 -4.8910116e-07 -4.8910096e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365
190 0 -4.8910145e-07 -4.8910125e-07 -4.8910243e-07 -1743.9897 31.537365 31.537365 31.537365
200 0 -4.891014e-07 -4.8910125e-07 -4.8910228e-07 -1743.9897 31.537365 31.537365 31.537365
210 0 -4.8910087e-07 -4.8910055e-07 -4.8910194e-07 -1743.9897 31.537365 31.537365 31.537365
220 0 -4.8910114e-07 -4.8910114e-07 -4.8910217e-07 -1743.9897 31.537365 31.537365 31.537365
230 0 -4.8910091e-07 -4.8910061e-07 -4.8910186e-07 -1743.9897 31.537365 31.537365 31.537365
240 0 -4.8909998e-07 -4.8909969e-07 -4.8910083e-07 -1743.9897 31.537365 31.537365 31.537365
250 0 -4.8910075e-07 -4.8910067e-07 -4.8910187e-07 -1743.9897 31.537365 31.537365 31.537365
260 0 -4.8910094e-07 -4.8910053e-07 -4.8910199e-07 -1743.9897 31.537365 31.537365 31.537365
270 0 -4.8910052e-07 -4.8910007e-07 -4.8910129e-07 -1743.9897 31.537365 31.537365 31.537365
280 0 -4.8910008e-07 -4.8910018e-07 -4.8910121e-07 -1743.9897 31.537365 31.537365 31.537365
290 0 -4.8910141e-07 -4.8910101e-07 -4.8910247e-07 -1743.9897 31.537365 31.537365 31.537365
300 0 -4.8910129e-07 -4.8910131e-07 -4.8910231e-07 -1743.9897 31.537365 31.537365 31.537365
310 0 -4.8910076e-07 -4.8910049e-07 -4.8910202e-07 -1743.9897 31.537365 31.537365 31.537365
320 0 -4.8910069e-07 -4.8910069e-07 -4.8910182e-07 -1743.9897 31.537365 31.537365 31.537365
330 0 -4.8910161e-07 -4.891015e-07 -4.8910243e-07 -1743.9897 31.537365 31.537365 31.537365
340 0 -4.8910108e-07 -4.8910082e-07 -4.8910234e-07 -1743.9897 31.537365 31.537365 31.537365
350 0 -4.8910041e-07 -4.891003e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365
360 0 -4.8910112e-07 -4.8910093e-07 -4.8910167e-07 -1743.9897 31.537365 31.537365 31.537365
370 0 -4.8910094e-07 -4.8910056e-07 -4.8910189e-07 -1743.9897 31.537365 31.537365 31.537365
380 0 -4.8910084e-07 -4.8910062e-07 -4.8910171e-07 -1743.9897 31.537365 31.537365 31.537365
390 0 -4.8910136e-07 -4.8910096e-07 -4.8910228e-07 -1743.9897 31.537365 31.537365 31.537365
400 0 -4.8910095e-07 -4.8910088e-07 -4.8910169e-07 -1743.9897 31.537365 31.537365 31.537365
410 0 -4.8910022e-07 -4.8910021e-07 -4.891012e-07 -1743.9897 31.537365 31.537365 31.537365
420 0 -4.8910064e-07 -4.8910021e-07 -4.8910148e-07 -1743.9897 31.537365 31.537365 31.537365
430 0 -4.8910133e-07 -4.8910124e-07 -4.8910259e-07 -1743.9897 31.537365 31.537365 31.537365
440 0 -4.8910157e-07 -4.8910149e-07 -4.8910257e-07 -1743.9897 31.537365 31.537365 31.537365
450 0 -4.8910088e-07 -4.8910081e-07 -4.8910183e-07 -1743.9897 31.537365 31.537365 31.537365
460 0 -4.8910078e-07 -4.8910056e-07 -4.8910168e-07 -1743.9897 31.537365 31.537365 31.537365
470 0 -4.8910048e-07 -4.8910015e-07 -4.8910164e-07 -1743.9897 31.537365 31.537365 31.537365
480 0 -4.8910054e-07 -4.8910048e-07 -4.8910165e-07 -1743.9897 31.537365 31.537365 31.537365
490 0 -4.8910103e-07 -4.8910094e-07 -4.8910185e-07 -1743.9897 31.537365 31.537365 31.537365
500 0 -4.8910081e-07 -4.8910044e-07 -4.891017e-07 -1743.9897 31.537365 31.537365 31.537365
Loop time of 4.18888 on 4 procs for 500 steps with 864 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-1743.9896675 -1743.9896675 -1743.9896675
Force two-norm initial, final = 4.69398e-13 3.47977e-13
Force max component initial, final = 2.08236e-14 1.74791e-14
Final line search alpha, max atom move = 1 1.74791e-14
Iterations, force evaluations = 500 1000
Pair time (%) = 2.3942 (57.1561)
Neigh time (%) = 0 (0)
Comm time (%) = 1.44252 (34.4369)
Outpt time (%) = 0.00359005 (0.0857043)
Other time (%) = 0.348568 (8.32127)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3107 ave 3107 max 3107 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 39744 ave 39744 max 39744 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158976
Ave neighs/atom = 184
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
variable xLO equal xlo
variable xHI equal xhi
variable yLO equal ylo
variable yHI equal yhi
variable zLO equal zlo
variable zHI equal zhi
# region BOX block ${xLO} ${xHI} ${yLO} ${yHI} ${zLO} ${zHI} units box
region BOX block ${xLO} ${xHI} -0.5 31.7 -0.5 31.7 units box
region BOX block 0 ${xHI} -0.5 31.7 -0.5 31.7 units box
region BOX block 0 31.537364922000001854 -0.5 31.7 -0.5 31.7 units box
fix ATC all atc field
ATC: constructing shape function field estimate
ATC: peratom PE compute created with ID: 3
fix_modify ATC mesh create 1 1 1 box p p p
ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements
fix_modify ATC fields add stress velocity displacement
fix_modify ATC fields add temperature kinetic_temperature
fix_modify ATC fields add internal_energy energy
fix_modify ATC output flying_cubeFE $s text binary tensor_components
fix_modify ATC output flying_cubeFE 10 text binary tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# fix_modify ATC atomic_output flying_cubeMD $m text binary tensor_components
dump dumpfc all atom $s flying_cube.dmp
dump dumpfc all atom 10 flying_cube.dmp
velocity all set $v 0.0 0.0 units box
velocity all set 0.10000000000000000555 0.0 0.0 units box
fix NVE all nve
run 3500
Setting up run ...
ATC: computing bond matrix ...........done
Memory usage per processor = 23.3621 Mbytes
Step Temp Pxx Pyy Pzz TotEng Lx Ly Lz
0 160162.49 1803377.9 -4.8910028e-07 -4.8910148e-07 410741.67 31.537365 31.537365 31.537365
10 160162.49 1803377.9 -4.891001e-07 -4.8910151e-07 410741.67 31.537365 31.537365 31.537365
20 160162.49 1803377.9 -4.8910035e-07 -4.8910193e-07 410741.67 31.537365 31.537365 31.537365
30 160162.49 1803377.9 -4.8909978e-07 -4.8910135e-07 410741.67 31.537365 31.537365 31.537365
40 160162.49 1803377.9 -4.8910011e-07 -4.8910149e-07 410741.67 31.537365 31.537365 31.537365
50 160162.49 1803377.9 -4.8910063e-07 -4.8910222e-07 410741.67 31.537365 31.537365 31.537365
60 160162.49 1803377.9 -4.8910116e-07 -4.8910273e-07 410741.67 31.537365 31.537365 31.537365
70 160162.49 1803377.9 -4.8909952e-07 -4.8910063e-07 410741.67 31.537365 31.537365 31.537365
80 160162.49 1803377.9 -4.8909944e-07 -4.8910079e-07 410741.67 31.537365 31.537365 31.537365
90 160162.49 1803377.9 -4.8909983e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365
100 160162.49 1803377.9 -4.8910034e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365
110 160162.49 1803377.9 -4.89101e-07 -4.8910251e-07 410741.67 31.537365 31.537365 31.537365
120 160162.49 1803377.9 -4.8910056e-07 -4.8910197e-07 410741.67 31.537365 31.537365 31.537365
130 160162.49 1803377.9 -4.8909949e-07 -4.8910097e-07 410741.67 31.537365 31.537365 31.537365
140 160162.49 1803377.9 -4.8909962e-07 -4.891013e-07 410741.67 31.537365 31.537365 31.537365
150 160162.49 1803377.9 -4.8910071e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365
160 160162.49 1803377.9 -4.8910088e-07 -4.8910202e-07 410741.67 31.537365 31.537365 31.537365
170 160162.49 1803377.9 -4.8910129e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365
180 160162.49 1803377.9 -4.890993e-07 -4.8910071e-07 410741.67 31.537365 31.537365 31.537365
190 160162.49 1803377.9 -4.8909971e-07 -4.8910093e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
200 160162.49 1803377.9 -4.891008e-07 -4.8910283e-07 410741.67 31.537365 31.537365 31.537365
210 160162.49 1803377.9 -4.890997e-07 -4.8910144e-07 410741.67 31.537365 31.537365 31.537365
220 160162.49 1803377.9 -4.8910119e-07 -4.8910291e-07 410741.67 31.537365 31.537365 31.537365
230 160162.49 1803377.9 -4.8909943e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365
240 160162.49 1803377.9 -4.8910063e-07 -4.8910215e-07 410741.67 31.537365 31.537365 31.537365
250 160162.49 1803377.9 -4.8909965e-07 -4.8910022e-07 410741.67 31.537365 31.537365 31.537365
260 160162.49 1803377.9 -4.891006e-07 -4.891015e-07 410741.67 31.537365 31.537365 31.537365
270 160162.49 1803377.9 -4.8909947e-07 -4.8910024e-07 410741.67 31.537365 31.537365 31.537365
280 160162.49 1803377.9 -4.8910084e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365
290 160162.49 1803377.9 -4.8909975e-07 -4.8910054e-07 410741.67 31.537365 31.537365 31.537365
300 160162.49 1803377.9 -4.8910072e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365
310 160162.49 1803377.9 -4.8909944e-07 -4.8910007e-07 410741.67 31.537365 31.537365 31.537365
320 160162.49 1803377.9 -4.8910063e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365
330 160162.49 1803377.9 -4.8909953e-07 -4.8910017e-07 410741.67 31.537365 31.537365 31.537365
340 160162.49 1803377.9 -4.891006e-07 -4.8910125e-07 410741.67 31.537365 31.537365 31.537365
350 160162.49 1803377.9 -4.8909961e-07 -4.8910025e-07 410741.67 31.537365 31.537365 31.537365
360 160162.49 1803377.9 -4.8910103e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365
370 160162.49 1803377.9 -4.8909975e-07 -4.8910072e-07 410741.67 31.537365 31.537365 31.537365
380 160162.49 1803377.9 -4.8910078e-07 -4.8910186e-07 410741.67 31.537365 31.537365 31.537365
390 160162.49 1803377.9 -4.8909978e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
400 160162.49 1803377.9 -4.8910055e-07 -4.891012e-07 410741.67 31.537365 31.537365 31.537365
410 160162.49 1803377.9 -4.8910124e-07 -4.8910227e-07 410741.67 31.537365 31.537365 31.537365
420 160162.49 1803377.9 -4.8910154e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365
430 160162.49 1803377.9 -4.8909931e-07 -4.8910036e-07 410741.67 31.537365 31.537365 31.537365
440 160162.49 1803377.9 -4.8909944e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365
450 160162.49 1803377.9 -4.8910046e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365
460 160162.49 1803377.9 -4.8910099e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365
470 160162.49 1803377.9 -4.890996e-07 -4.8910061e-07 410741.67 31.537365 31.537365 31.537365
480 160162.49 1803377.9 -4.8910115e-07 -4.8910244e-07 410741.67 31.537365 31.537365 31.537365
490 160162.49 1803377.9 -4.890994e-07 -4.8910022e-07 410741.67 31.537365 31.537365 31.537365
500 160162.49 1803377.9 -4.8910113e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365
510 160162.49 1803377.9 -4.8909993e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365
520 160162.49 1803377.9 -4.8910114e-07 -4.891021e-07 410741.67 31.537365 31.537365 31.537365
530 160162.49 1803377.9 -4.8909951e-07 -4.8910036e-07 410741.67 31.537365 31.537365 31.537365
540 160162.49 1803377.9 -4.8910118e-07 -4.891021e-07 410741.67 31.537365 31.537365 31.537365
550 160162.49 1803377.9 -4.8909977e-07 -4.8910067e-07 410741.67 31.537365 31.537365 31.537365
560 160162.49 1803377.9 -4.891014e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365
570 160162.49 1803377.9 -4.8910006e-07 -4.8910084e-07 410741.67 31.537365 31.537365 31.537365
580 160162.49 1803377.9 -4.8910121e-07 -4.8910187e-07 410741.67 31.537365 31.537365 31.537365
590 160162.49 1803377.9 -4.8910007e-07 -4.8910063e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
600 160162.49 1803377.9 -4.8910068e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365
610 160162.49 1803377.9 -4.8910136e-07 -4.891022e-07 410741.67 31.537365 31.537365 31.537365
620 160162.49 1803377.9 -4.891021e-07 -4.8910323e-07 410741.67 31.537365 31.537365 31.537365
630 160162.49 1803377.9 -4.8910001e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365
640 160162.49 1803377.9 -4.8910029e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365
650 160162.49 1803377.9 -4.8910081e-07 -4.8910162e-07 410741.67 31.537365 31.537365 31.537365
660 160162.49 1803377.9 -4.8910154e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365
670 160162.49 1803377.9 -4.8910161e-07 -4.8910291e-07 410741.67 31.537365 31.537365 31.537365
680 160162.49 1803377.9 -4.8910203e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365
690 160162.49 1803377.9 -4.8910016e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365
700 160162.49 1803377.9 -4.8910066e-07 -4.8910144e-07 410741.67 31.537365 31.537365 31.537365
710 160162.49 1803377.9 -4.891009e-07 -4.8910203e-07 410741.67 31.537365 31.537365 31.537365
720 160162.49 1803377.9 -4.8910149e-07 -4.8910252e-07 410741.67 31.537365 31.537365 31.537365
730 160162.49 1803377.9 -4.8910048e-07 -4.8910151e-07 410741.67 31.537365 31.537365 31.537365
740 160162.49 1803377.9 -4.8910177e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365
750 160162.49 1803377.9 -4.891001e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365
760 160162.49 1803377.9 -4.8910154e-07 -4.8910271e-07 410741.67 31.537365 31.537365 31.537365
770 160162.49 1803377.9 -4.8910033e-07 -4.8910152e-07 410741.67 31.537365 31.537365 31.537365
780 160162.49 1803377.9 -4.8910155e-07 -4.8910272e-07 410741.67 31.537365 31.537365 31.537365
790 160162.49 1803377.9 -4.8910029e-07 -4.89101e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
800 160162.49 1803377.9 -4.8910078e-07 -4.8910154e-07 410741.67 31.537365 31.537365 31.537365
810 160162.49 1803377.9 -4.891018e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365
820 160162.49 1803377.9 -4.891006e-07 -4.8910146e-07 410741.67 31.537365 31.537365 31.537365
830 160162.49 1803377.9 -4.8910022e-07 -4.891007e-07 410741.67 31.537365 31.537365 31.537365
840 160162.49 1803377.9 -4.8910043e-07 -4.891009e-07 410741.67 31.537365 31.537365 31.537365
850 160162.49 1803377.9 -4.8910087e-07 -4.8910142e-07 410741.67 31.537365 31.537365 31.537365
860 160162.49 1803377.9 -4.8910141e-07 -4.8910245e-07 410741.67 31.537365 31.537365 31.537365
870 160162.49 1803377.9 -4.8910209e-07 -4.8910276e-07 410741.67 31.537365 31.537365 31.537365
880 160162.49 1803377.9 -4.891025e-07 -4.8910339e-07 410741.67 31.537365 31.537365 31.537365
890 160162.49 1803377.9 -4.8910017e-07 -4.8910105e-07 410741.67 31.537365 31.537365 31.537365
900 160162.49 1803377.9 -4.8910109e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365
910 160162.49 1803377.9 -4.891016e-07 -4.8910262e-07 410741.67 31.537365 31.537365 31.537365
920 160162.49 1803377.9 -4.8910171e-07 -4.891025e-07 410741.67 31.537365 31.537365 31.537365
930 160162.49 1803377.9 -4.8910262e-07 -4.8910309e-07 410741.67 31.537365 31.537365 31.537365
940 160162.49 1803377.9 -4.8910059e-07 -4.891009e-07 410741.67 31.537365 31.537365 31.537365
950 160162.49 1803377.9 -4.8910111e-07 -4.8910188e-07 410741.67 31.537365 31.537365 31.537365
960 160162.49 1803377.9 -4.8910107e-07 -4.8910157e-07 410741.67 31.537365 31.537365 31.537365
970 160162.49 1803377.9 -4.891018e-07 -4.8910219e-07 410741.67 31.537365 31.537365 31.537365
980 160162.49 1803377.9 -4.8910204e-07 -4.8910243e-07 410741.67 31.537365 31.537365 31.537365
990 160162.49 1803377.9 -4.8910035e-07 -4.8910071e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
1000 160162.49 1803377.9 -4.8910205e-07 -4.8910244e-07 410741.67 31.537365 31.537365 31.537365
1010 160162.49 1803377.9 -4.8910037e-07 -4.8910126e-07 410741.67 31.537365 31.537365 31.537365
1020 160162.49 1803377.9 -4.8910181e-07 -4.8910224e-07 410741.67 31.537365 31.537365 31.537365
1030 160162.49 1803377.9 -4.891006e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365
1040 160162.49 1803377.9 -4.8910185e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365
1050 160162.49 1803377.9 -4.8910046e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365
1060 160162.49 1803377.9 -4.8910166e-07 -4.8910217e-07 410741.67 31.537365 31.537365 31.537365
1070 160162.49 1803377.9 -4.8910042e-07 -4.8910091e-07 410741.67 31.537365 31.537365 31.537365
1080 160162.49 1803377.9 -4.8910181e-07 -4.8910253e-07 410741.67 31.537365 31.537365 31.537365
1090 160162.49 1803377.9 -4.8910038e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365
1100 160162.49 1803377.9 -4.8910188e-07 -4.8910256e-07 410741.67 31.537365 31.537365 31.537365
1110 160162.49 1803377.9 -4.891003e-07 -4.8910088e-07 410741.67 31.537365 31.537365 31.537365
1120 160162.49 1803377.9 -4.8910208e-07 -4.8910255e-07 410741.67 31.537365 31.537365 31.537365
1130 160162.49 1803377.9 -4.8910067e-07 -4.8910136e-07 410741.67 31.537365 31.537365 31.537365
1140 160162.49 1803377.9 -4.8910201e-07 -4.8910268e-07 410741.67 31.537365 31.537365 31.537365
1150 160162.49 1803377.9 -4.8910075e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365
1160 160162.49 1803377.9 -4.8910156e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365
1170 160162.49 1803377.9 -4.8910063e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365
1180 160162.49 1803377.9 -4.8910186e-07 -4.8910287e-07 410741.67 31.537365 31.537365 31.537365
1190 160162.49 1803377.9 -4.8910059e-07 -4.8910133e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
1200 160162.49 1803377.9 -4.8910131e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365
1210 160162.49 1803377.9 -4.8910182e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365
1220 160162.49 1803377.9 -4.8910251e-07 -4.891035e-07 410741.67 31.537365 31.537365 31.537365
1230 160162.49 1803377.9 -4.8910028e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365
1240 160162.49 1803377.9 -4.8910048e-07 -4.8910147e-07 410741.67 31.537365 31.537365 31.537365
1250 160162.49 1803377.9 -4.8910121e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365
1260 160162.49 1803377.9 -4.8909966e-07 -4.8910047e-07 410741.67 31.537365 31.537365 31.537365
1270 160162.49 1803377.9 -4.8910146e-07 -4.8910223e-07 410741.67 31.537365 31.537365 31.537365
1280 160162.49 1803377.9 -4.8909992e-07 -4.8910094e-07 410741.67 31.537365 31.537365 31.537365
1290 160162.49 1803377.9 -4.8910138e-07 -4.891019e-07 410741.67 31.537365 31.537365 31.537365
1300 160162.49 1803377.9 -4.891001e-07 -4.8910051e-07 410741.67 31.537365 31.537365 31.537365
1310 160162.49 1803377.9 -4.8910147e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365
1320 160162.49 1803377.9 -4.8909992e-07 -4.8910037e-07 410741.67 31.537365 31.537365 31.537365
1330 160162.49 1803377.9 -4.891013e-07 -4.8910207e-07 410741.67 31.537365 31.537365 31.537365
1340 160162.49 1803377.9 -4.8910014e-07 -4.8910084e-07 410741.67 31.537365 31.537365 31.537365
1350 160162.49 1803377.9 -4.8910161e-07 -4.891024e-07 410741.67 31.537365 31.537365 31.537365
1360 160162.49 1803377.9 -4.8909974e-07 -4.8910055e-07 410741.67 31.537365 31.537365 31.537365
1370 160162.49 1803377.9 -4.8910123e-07 -4.8910198e-07 410741.67 31.537365 31.537365 31.537365
1380 160162.49 1803377.9 -4.891002e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365
1390 160162.49 1803377.9 -4.8910142e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
1400 160162.49 1803377.9 -4.8910123e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365
1410 160162.49 1803377.9 -4.8910199e-07 -4.8910214e-07 410741.67 31.537365 31.537365 31.537365
1420 160162.49 1803377.9 -4.8910181e-07 -4.8910242e-07 410741.67 31.537365 31.537365 31.537365
1430 160162.49 1803377.9 -4.8909979e-07 -4.8910018e-07 410741.67 31.537365 31.537365 31.537365
1440 160162.49 1803377.9 -4.8910055e-07 -4.8910117e-07 410741.67 31.537365 31.537365 31.537365
1450 160162.49 1803377.9 -4.8910125e-07 -4.8910179e-07 410741.67 31.537365 31.537365 31.537365
1460 160162.49 1803377.9 -4.8910148e-07 -4.8910232e-07 410741.67 31.537365 31.537365 31.537365
1470 160162.49 1803377.9 -4.8910211e-07 -4.8910265e-07 410741.67 31.537365 31.537365 31.537365
1480 160162.49 1803377.9 -4.8910259e-07 -4.8910328e-07 410741.67 31.537365 31.537365 31.537365
1490 160162.49 1803377.9 -4.8910061e-07 -4.8910073e-07 410741.67 31.537365 31.537365 31.537365
1500 160162.49 1803377.9 -4.8910132e-07 -4.8910159e-07 410741.67 31.537365 31.537365 31.537365
1510 160162.49 1803377.9 -4.8910164e-07 -4.8910222e-07 410741.67 31.537365 31.537365 31.537365
1520 160162.49 1803377.9 -4.8910047e-07 -4.8910077e-07 410741.67 31.537365 31.537365 31.537365
1530 160162.49 1803377.9 -4.8910171e-07 -4.891024e-07 410741.67 31.537365 31.537365 31.537365
1540 160162.49 1803377.9 -4.8910063e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365
1550 160162.49 1803377.9 -4.8910194e-07 -4.8910254e-07 410741.67 31.537365 31.537365 31.537365
1560 160162.49 1803377.9 -4.8910033e-07 -4.891013e-07 410741.67 31.537365 31.537365 31.537365
1570 160162.49 1803377.9 -4.8910162e-07 -4.8910241e-07 410741.67 31.537365 31.537365 31.537365
1580 160162.49 1803377.9 -4.8910061e-07 -4.8910107e-07 410741.67 31.537365 31.537365 31.537365
1590 160162.49 1803377.9 -4.891018e-07 -4.8910259e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
1600 160162.49 1803377.9 -4.8910144e-07 -4.8910146e-07 410741.67 31.537365 31.537365 31.537365
1610 160162.49 1803377.9 -4.8910161e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365
1620 160162.49 1803377.9 -4.8910094e-07 -4.8910177e-07 410741.67 31.537365 31.537365 31.537365
1630 160162.49 1803377.9 -4.8910123e-07 -4.8910162e-07 410741.67 31.537365 31.537365 31.537365
1640 160162.49 1803377.9 -4.8910206e-07 -4.8910241e-07 410741.67 31.537365 31.537365 31.537365
1650 160162.49 1803377.9 -4.8910246e-07 -4.8910282e-07 410741.67 31.537365 31.537365 31.537365
1660 160162.49 1803377.9 -4.891003e-07 -4.8910094e-07 410741.67 31.537365 31.537365 31.537365
1670 160162.49 1803377.9 -4.8910089e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365
1680 160162.49 1803377.9 -4.8910108e-07 -4.8910139e-07 410741.67 31.537365 31.537365 31.537365
1690 160162.49 1803377.9 -4.8910193e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365
1700 160162.49 1803377.9 -4.8910253e-07 -4.89103e-07 410741.67 31.537365 31.537365 31.537365
1710 160162.49 1803377.9 -4.8910023e-07 -4.8910072e-07 410741.67 31.537365 31.537365 31.537365
1720 160162.49 1803377.9 -4.8910078e-07 -4.8910154e-07 410741.67 31.537365 31.537365 31.537365
1730 160162.49 1803377.9 -4.8910159e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365
1740 160162.49 1803377.9 -4.8910166e-07 -4.8910204e-07 410741.67 31.537365 31.537365 31.537365
1750 160162.49 1803377.9 -4.8910241e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365
1760 160162.49 1803377.9 -4.8910319e-07 -4.8910314e-07 410741.67 31.537365 31.537365 31.537365
1770 160162.49 1803377.9 -4.8910061e-07 -4.8910065e-07 410741.67 31.537365 31.537365 31.537365
1780 160162.49 1803377.9 -4.8910212e-07 -4.8910225e-07 410741.67 31.537365 31.537365 31.537365
1790 160162.49 1803377.9 -4.8910003e-07 -4.8910077e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
1800 160162.49 1803377.9 -4.8910129e-07 -4.8910219e-07 410741.67 31.537365 31.537365 31.537365
1810 160162.49 1803377.9 -4.8910037e-07 -4.8910129e-07 410741.67 31.537365 31.537365 31.537365
1820 160162.49 1803377.9 -4.8910138e-07 -4.8910184e-07 410741.67 31.537365 31.537365 31.537365
1830 160162.49 1803377.9 -4.8910012e-07 -4.8910085e-07 410741.67 31.537365 31.537365 31.537365
1840 160162.49 1803377.9 -4.8910138e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365
1850 160162.49 1803377.9 -4.8910015e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365
1860 160162.49 1803377.9 -4.8910204e-07 -4.8910242e-07 410741.67 31.537365 31.537365 31.537365
1870 160162.49 1803377.9 -4.8910022e-07 -4.8910074e-07 410741.67 31.537365 31.537365 31.537365
1880 160162.49 1803377.9 -4.8910147e-07 -4.8910194e-07 410741.67 31.537365 31.537365 31.537365
1890 160162.49 1803377.9 -4.8910029e-07 -4.8910108e-07 410741.67 31.537365 31.537365 31.537365
1900 160162.49 1803377.9 -4.8910167e-07 -4.8910199e-07 410741.67 31.537365 31.537365 31.537365
1910 160162.49 1803377.9 -4.891003e-07 -4.8910093e-07 410741.67 31.537365 31.537365 31.537365
1920 160162.49 1803377.9 -4.8910133e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365
1930 160162.49 1803377.9 -4.8910033e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365
1940 160162.49 1803377.9 -4.8910152e-07 -4.8910179e-07 410741.67 31.537365 31.537365 31.537365
1950 160162.49 1803377.9 -4.8910025e-07 -4.8910087e-07 410741.67 31.537365 31.537365 31.537365
1960 160162.49 1803377.9 -4.8910156e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365
1970 160162.49 1803377.9 -4.8910009e-07 -4.8910059e-07 410741.67 31.537365 31.537365 31.537365
1980 160162.49 1803377.9 -4.8910173e-07 -4.8910251e-07 410741.67 31.537365 31.537365 31.537365
1990 160162.49 1803377.9 -4.8910036e-07 -4.8910106e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
2000 160162.49 1803377.9 -4.891014e-07 -4.8910256e-07 410741.67 31.537365 31.537365 31.537365
2010 160162.49 1803377.9 -4.8910159e-07 -4.8910279e-07 410741.67 31.537365 31.537365 31.537365
2020 160162.49 1803377.9 -4.8910238e-07 -4.8910344e-07 410741.67 31.537365 31.537365 31.537365
2030 160162.49 1803377.9 -4.891e-07 -4.8910112e-07 410741.67 31.537365 31.537365 31.537365
2040 160162.49 1803377.9 -4.8910103e-07 -4.89102e-07 410741.67 31.537365 31.537365 31.537365
2050 160162.49 1803377.9 -4.8910276e-07 -4.8910344e-07 410741.67 31.537365 31.537365 31.537365
2060 160162.49 1803377.9 -4.8910112e-07 -4.8910212e-07 410741.67 31.537365 31.537365 31.537365
2070 160162.49 1803377.9 -4.8910247e-07 -4.8910356e-07 410741.67 31.537365 31.537365 31.537365
2080 160162.49 1803377.9 -4.89101e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365
2090 160162.49 1803377.9 -4.8910249e-07 -4.891037e-07 410741.67 31.537365 31.537365 31.537365
2100 160162.49 1803377.9 -4.8910084e-07 -4.8910161e-07 410741.67 31.537365 31.537365 31.537365
2110 160162.49 1803377.9 -4.8910238e-07 -4.8910322e-07 410741.67 31.537365 31.537365 31.537365
2120 160162.49 1803377.9 -4.8910078e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365
2130 160162.49 1803377.9 -4.8910225e-07 -4.8910277e-07 410741.67 31.537365 31.537365 31.537365
2140 160162.49 1803377.9 -4.8910056e-07 -4.891012e-07 410741.67 31.537365 31.537365 31.537365
2150 160162.49 1803377.9 -4.8910213e-07 -4.8910283e-07 410741.67 31.537365 31.537365 31.537365
2160 160162.49 1803377.9 -4.8910045e-07 -4.8910105e-07 410741.67 31.537365 31.537365 31.537365
2170 160162.49 1803377.9 -4.8910228e-07 -4.8910236e-07 410741.67 31.537365 31.537365 31.537365
2180 160162.49 1803377.9 -4.8910033e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365
2190 160162.49 1803377.9 -4.8910193e-07 -4.8910273e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
2200 160162.49 1803377.9 -4.8910067e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365
2210 160162.49 1803377.9 -4.8910082e-07 -4.8910183e-07 410741.67 31.537365 31.537365 31.537365
2220 160162.49 1803377.9 -4.8910178e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365
2230 160162.49 1803377.9 -4.890995e-07 -4.8909947e-07 410741.67 31.537365 31.537365 31.537365
2240 160162.49 1803377.9 -4.8909972e-07 -4.8910015e-07 410741.67 31.537365 31.537365 31.537365
2250 160162.49 1803377.9 -4.8910077e-07 -4.8910141e-07 410741.67 31.537365 31.537365 31.537365
2260 160162.49 1803377.9 -4.8910119e-07 -4.8910189e-07 410741.67 31.537365 31.537365 31.537365
2270 160162.49 1803377.9 -4.8910159e-07 -4.8910229e-07 410741.67 31.537365 31.537365 31.537365
2280 160162.49 1803377.9 -4.8910186e-07 -4.8910267e-07 410741.67 31.537365 31.537365 31.537365
2290 160162.49 1803377.9 -4.8910025e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365
2300 160162.49 1803377.9 -4.8910045e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365
2310 160162.49 1803377.9 -4.8910175e-07 -4.8910306e-07 410741.67 31.537365 31.537365 31.537365
2320 160162.49 1803377.9 -4.8910062e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365
2330 160162.49 1803377.9 -4.8910162e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365
2340 160162.49 1803377.9 -4.891007e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365
2350 160162.49 1803377.9 -4.8910169e-07 -4.8910269e-07 410741.67 31.537365 31.537365 31.537365
2360 160162.49 1803377.9 -4.8910031e-07 -4.8910156e-07 410741.67 31.537365 31.537365 31.537365
2370 160162.49 1803377.9 -4.8910172e-07 -4.8910282e-07 410741.67 31.537365 31.537365 31.537365
2380 160162.49 1803377.9 -4.8910065e-07 -4.8910159e-07 410741.67 31.537365 31.537365 31.537365
2390 160162.49 1803377.9 -4.891016e-07 -4.8910331e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
2400 160162.49 1803377.9 -4.8910081e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365
2410 160162.49 1803377.9 -4.8910149e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365
2420 160162.49 1803377.9 -4.8910171e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365
2430 160162.49 1803377.9 -4.8909949e-07 -4.8910035e-07 410741.67 31.537365 31.537365 31.537365
2440 160162.49 1803377.9 -4.8910033e-07 -4.8910099e-07 410741.67 31.537365 31.537365 31.537365
2450 160162.49 1803377.9 -4.891006e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365
2460 160162.49 1803377.9 -4.8910117e-07 -4.8910191e-07 410741.67 31.537365 31.537365 31.537365
2470 160162.49 1803377.9 -4.8910153e-07 -4.8910231e-07 410741.67 31.537365 31.537365 31.537365
2480 160162.49 1803377.9 -4.8910223e-07 -4.8910317e-07 410741.67 31.537365 31.537365 31.537365
2490 160162.49 1803377.9 -4.8909994e-07 -4.8910083e-07 410741.67 31.537365 31.537365 31.537365
2500 160162.49 1803377.9 -4.8910056e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365
2510 160162.49 1803377.9 -4.8910114e-07 -4.8910212e-07 410741.67 31.537365 31.537365 31.537365
2520 160162.49 1803377.9 -4.8910159e-07 -4.8910264e-07 410741.67 31.537365 31.537365 31.537365
2530 160162.49 1803377.9 -4.89102e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365
2540 160162.49 1803377.9 -4.8910012e-07 -4.8910058e-07 410741.67 31.537365 31.537365 31.537365
2550 160162.49 1803377.9 -4.8910014e-07 -4.8910104e-07 410741.67 31.537365 31.537365 31.537365
2560 160162.49 1803377.9 -4.8910087e-07 -4.8910118e-07 410741.67 31.537365 31.537365 31.537365
2570 160162.49 1803377.9 -4.8909951e-07 -4.8909979e-07 410741.67 31.537365 31.537365 31.537365
2580 160162.49 1803377.9 -4.8910101e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365
2590 160162.49 1803377.9 -4.8910231e-07 -4.8910311e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
2600 160162.49 1803377.9 -4.8910045e-07 -4.891011e-07 410741.67 31.537365 31.537365 31.537365
2610 160162.49 1803377.9 -4.8909927e-07 -4.8910014e-07 410741.67 31.537365 31.537365 31.537365
2620 160162.49 1803377.9 -4.8910087e-07 -4.8910142e-07 410741.67 31.537365 31.537365 31.537365
2630 160162.49 1803377.9 -4.8910236e-07 -4.8910302e-07 410741.67 31.537365 31.537365 31.537365
2640 160162.49 1803377.9 -4.8910086e-07 -4.8910143e-07 410741.67 31.537365 31.537365 31.537365
2650 160162.49 1803377.9 -4.8909943e-07 -4.8909999e-07 410741.67 31.537365 31.537365 31.537365
2660 160162.49 1803377.9 -4.8910109e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365
2670 160162.49 1803377.9 -4.8910245e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365
2680 160162.49 1803377.9 -4.8910079e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365
2690 160162.49 1803377.9 -4.8909909e-07 -4.8909976e-07 410741.67 31.537365 31.537365 31.537365
2700 160162.49 1803377.9 -4.8910075e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365
2710 160162.49 1803377.9 -4.8910231e-07 -4.8910315e-07 410741.67 31.537365 31.537365 31.537365
2720 160162.49 1803377.9 -4.8910065e-07 -4.8910118e-07 410741.67 31.537365 31.537365 31.537365
2730 160162.49 1803377.9 -4.890993e-07 -4.8910017e-07 410741.67 31.537365 31.537365 31.537365
2740 160162.49 1803377.9 -4.8910051e-07 -4.8910166e-07 410741.67 31.537365 31.537365 31.537365
2750 160162.49 1803377.9 -4.8910219e-07 -4.8910304e-07 410741.67 31.537365 31.537365 31.537365
2760 160162.49 1803377.9 -4.8910068e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365
2770 160162.49 1803377.9 -4.8909954e-07 -4.8910049e-07 410741.67 31.537365 31.537365 31.537365
2780 160162.49 1803377.9 -4.8910117e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365
2790 160162.49 1803377.9 -4.891023e-07 -4.8910319e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
2800 160162.49 1803377.9 -4.8910068e-07 -4.8910187e-07 410741.67 31.537365 31.537365 31.537365
2810 160162.49 1803377.9 -4.891017e-07 -4.891029e-07 410741.67 31.537365 31.537365 31.537365
2820 160162.49 1803377.9 -4.8910195e-07 -4.8910323e-07 410741.67 31.537365 31.537365 31.537365
2830 160162.49 1803377.9 -4.8909982e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365
2840 160162.49 1803377.9 -4.8910224e-07 -4.8910355e-07 410741.67 31.537365 31.537365 31.537365
2850 160162.49 1803377.9 -4.8910081e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365
2860 160162.49 1803377.9 -4.8910183e-07 -4.8910321e-07 410741.67 31.537365 31.537365 31.537365
2870 160162.49 1803377.9 -4.8910058e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365
2880 160162.49 1803377.9 -4.8910233e-07 -4.8910328e-07 410741.67 31.537365 31.537365 31.537365
2890 160162.49 1803377.9 -4.891007e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365
2900 160162.49 1803377.9 -4.8910183e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365
2910 160162.49 1803377.9 -4.8910014e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365
2920 160162.49 1803377.9 -4.8910169e-07 -4.8910278e-07 410741.67 31.537365 31.537365 31.537365
2930 160162.49 1803377.9 -4.8910007e-07 -4.8910125e-07 410741.67 31.537365 31.537365 31.537365
2940 160162.49 1803377.9 -4.8910148e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365
2950 160162.49 1803377.9 -4.8910016e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365
2960 160162.49 1803377.9 -4.8910147e-07 -4.8910314e-07 410741.67 31.537365 31.537365 31.537365
2970 160162.49 1803377.9 -4.8910006e-07 -4.8910153e-07 410741.67 31.537365 31.537365 31.537365
2980 160162.49 1803377.9 -4.8910123e-07 -4.8910287e-07 410741.67 31.537365 31.537365 31.537365
2990 160162.49 1803377.9 -4.8909973e-07 -4.8910132e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
3000 160162.49 1803377.9 -4.8910075e-07 -4.8910221e-07 410741.67 31.537365 31.537365 31.537365
3010 160162.49 1803377.9 -4.8910144e-07 -4.8910237e-07 410741.67 31.537365 31.537365 31.537365
3020 160162.49 1803377.9 -4.8910171e-07 -4.8910255e-07 410741.67 31.537365 31.537365 31.537365
3030 160162.49 1803377.9 -4.8909877e-07 -4.8910042e-07 410741.67 31.537365 31.537365 31.537365
3040 160162.49 1803377.9 -4.8909954e-07 -4.8910108e-07 410741.67 31.537365 31.537365 31.537365
3050 160162.49 1803377.9 -4.8910053e-07 -4.8910155e-07 410741.67 31.537365 31.537365 31.537365
3060 160162.49 1803377.9 -4.8910092e-07 -4.8910213e-07 410741.67 31.537365 31.537365 31.537365
3070 160162.49 1803377.9 -4.8910167e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365
3080 160162.49 1803377.9 -4.8909919e-07 -4.8910041e-07 410741.67 31.537365 31.537365 31.537365
3090 160162.49 1803377.9 -4.8909999e-07 -4.8910152e-07 410741.67 31.537365 31.537365 31.537365
3100 160162.49 1803377.9 -4.8910143e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365
3110 160162.49 1803377.9 -4.8910001e-07 -4.8910126e-07 410741.67 31.537365 31.537365 31.537365
3120 160162.49 1803377.9 -4.8910185e-07 -4.8910299e-07 410741.67 31.537365 31.537365 31.537365
3130 160162.49 1803377.9 -4.8909979e-07 -4.8910147e-07 410741.67 31.537365 31.537365 31.537365
3140 160162.49 1803377.9 -4.8910143e-07 -4.8910276e-07 410741.67 31.537365 31.537365 31.537365
3150 160162.49 1803377.9 -4.8910037e-07 -4.8910137e-07 410741.67 31.537365 31.537365 31.537365
3160 160162.49 1803377.9 -4.8910153e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365
3170 160162.49 1803377.9 -4.8909966e-07 -4.8910099e-07 410741.67 31.537365 31.537365 31.537365
3180 160162.49 1803377.9 -4.8910152e-07 -4.891028e-07 410741.67 31.537365 31.537365 31.537365
3190 160162.49 1803377.9 -4.8909987e-07 -4.8910153e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
3200 160162.49 1803377.9 -4.8910041e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365
3210 160162.49 1803377.9 -4.8910076e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365
3220 160162.49 1803377.9 -4.8910132e-07 -4.89103e-07 410741.67 31.537365 31.537365 31.537365
3230 160162.49 1803377.9 -4.8909954e-07 -4.8910119e-07 410741.67 31.537365 31.537365 31.537365
3240 160162.49 1803377.9 -4.8909979e-07 -4.8910156e-07 410741.67 31.537365 31.537365 31.537365
3250 160162.49 1803377.9 -4.8910039e-07 -4.8910223e-07 410741.67 31.537365 31.537365 31.537365
3260 160162.49 1803377.9 -4.8910064e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365
3270 160162.49 1803377.9 -4.8910155e-07 -4.8910333e-07 410741.67 31.537365 31.537365 31.537365
3280 160162.49 1803377.9 -4.8910184e-07 -4.8910355e-07 410741.67 31.537365 31.537365 31.537365
3290 160162.49 1803377.9 -4.8910006e-07 -4.8910145e-07 410741.67 31.537365 31.537365 31.537365
3300 160162.49 1803377.9 -4.8910003e-07 -4.891019e-07 410741.67 31.537365 31.537365 31.537365
3310 160162.49 1803377.9 -4.8910065e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365
3320 160162.49 1803377.9 -4.8910106e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365
3330 160162.49 1803377.9 -4.8910174e-07 -4.8910364e-07 410741.67 31.537365 31.537365 31.537365
3340 160162.49 1803377.9 -4.8909972e-07 -4.8910113e-07 410741.67 31.537365 31.537365 31.537365
3350 160162.49 1803377.9 -4.8910047e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365
3360 160162.49 1803377.9 -4.891017e-07 -4.8910326e-07 410741.67 31.537365 31.537365 31.537365
3370 160162.49 1803377.9 -4.8910039e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365
3380 160162.49 1803377.9 -4.8910152e-07 -4.8910252e-07 410741.67 31.537365 31.537365 31.537365
3390 160162.49 1803377.9 -4.8910045e-07 -4.8910129e-07 410741.67 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
3400 160162.49 1803377.9 -4.89102e-07 -4.8910296e-07 410741.67 31.537365 31.537365 31.537365
3410 160162.49 1803377.9 -4.8910045e-07 -4.8910141e-07 410741.67 31.537365 31.537365 31.537365
3420 160162.49 1803377.9 -4.8910145e-07 -4.8910301e-07 410741.67 31.537365 31.537365 31.537365
3430 160162.49 1803377.9 -4.8910057e-07 -4.8910173e-07 410741.67 31.537365 31.537365 31.537365
3440 160162.49 1803377.9 -4.8910176e-07 -4.8910303e-07 410741.67 31.537365 31.537365 31.537365
3450 160162.49 1803377.9 -4.8910044e-07 -4.8910165e-07 410741.67 31.537365 31.537365 31.537365
3460 160162.49 1803377.9 -4.8910172e-07 -4.8910311e-07 410741.67 31.537365 31.537365 31.537365
3470 160162.49 1803377.9 -4.8910048e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365
3480 160162.49 1803377.9 -4.8910193e-07 -4.8910309e-07 410741.67 31.537365 31.537365 31.537365
3490 160162.49 1803377.9 -4.8910055e-07 -4.8910166e-07 410741.67 31.537365 31.537365 31.537365
3500 160162.49 1803377.9 -4.8910204e-07 -4.8910346e-07 410741.67 31.537365 31.537365 31.537365
Loop time of 260.545 on 4 procs for 3500 steps with 864 atoms
Pair time (%) = 7.82867 (3.00473)
Neigh time (%) = 0.516552 (0.198258)
Comm time (%) = 67.7833 (26.016)
Outpt time (%) = 11.4734 (4.40363)
Other time (%) = 172.943 (66.3774)
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3108 ave 3108 max 3108 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 39744 ave 39850 max 39638 min
Histogram: 1 0 0 0 1 1 0 0 0 1
FullNghs: 79488 ave 79488 max 79488 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 317952
Ave neighs/atom = 368
Neighbor list builds = 17
Dangerous builds = 0
variable c equal 48.88821291*48.88821291/(3.*0.0019872067)
variable T equal $m*$v*$v*$c
variable T equal 39.950000000000002842*$v*$v*$c
variable T equal 39.950000000000002842*0.10000000000000000555*$v*$c
variable T equal 39.950000000000002842*0.10000000000000000555*0.10000000000000000555*$c
variable T equal 39.950000000000002842*0.10000000000000000555*0.10000000000000000555*400907.35763815121027
print "kinetic temperature: $T"
kinetic temperature: 160162.48937644143007

300
examples/USER/atc/cauchy_born/ftcb_constV.screen Normal file
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LAMMPS (14 Aug 2013)
log ftcb_constV.log
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal (${lattice_constant}*$c)
variable L equal (5.2562274870000003091*$c)
variable L equal (5.2562274870000003091*6)
variable V equal $L*$L*$L
variable V equal 31.537364922000001854*$L*$L
variable V equal 31.537364922000001854*31.537364922000001854*$L
variable V equal 31.537364922000001854*31.537364922000001854*31.537364922000001854
print "Volume : $V"
Volume : 31367.233018713999627
variable Ti equal 0.0001
variable dT equal 0.2
variable n equal 10000
variable m equal 200
variable dt equal 0.1
# create system
lattice fcc ${lattice_constant}
lattice fcc 5.2562274870000003091
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
pair_style lj/cut 13.5
read_data ftcb_constV_setup.data
Reading data file ...
orthogonal box = (0 0 0) to (31.5374 31.5374 31.5374)
1 by 2 by 2 MPI processor grid
864 atoms
864 velocities
mass 1 39.95
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 0 every 2000 check no
reset_timestep 0
thermo $m
thermo 200
compute_modify thermo_temp extra 0
variable nrepeat equal $n/$m
variable nrepeat equal 10000/$m
variable nrepeat equal 10000/200
variable sxx equal -pxx
variable intenergy equal etotal
fix TDAVE all ave/time $m ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
fix TDAVE all ave/time 200 ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
fix TDAVE all ave/time 200 50 $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
fix TDAVE all ave/time 200 50 10000 c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
thermo_style custom step temp press etotal lx ly lz
timestep ${dt}
timestep 0.10000000000000000555
# filtered
fix ATCFILT all atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
#fix_modify ATCFILT reset_atomic_reference_positions ftcb_constV_setup.data
fix_modify ATCFILT mesh create 1 1 1 box p p p
ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements
fix_modify ATCFILT fields none
fix_modify ATCFILT fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify ATCFILT fields add temperature displacement
fix_modify ATCFILT gradients add displacement
fix_modify ATCFILT output ftcb_constV_filteredFE $n text binary tensor_components
fix_modify ATCFILT output ftcb_constV_filteredFE 10000 text binary tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify ATCFILT sample_frequency $m
fix_modify ATCFILT sample_frequency 200
variable scale equal $n*${dt}
variable scale equal 10000*${dt}
variable scale equal 10000*0.10000000000000000555
fix_modify ATCFILT filter scale ${scale}
fix_modify ATCFILT filter scale 1000
fix_modify ATCFILT filter on
fix_modify ATCFILT filter type step
# not filtered
fix ATC all atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
#fix_modify ATC reset_atomic_reference_positions ftcb_constV_setup.data
fix_modify ATC mesh create 1 1 1 box p p p
ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements
fix_modify ATC fields none
fix_modify ATC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify ATC fields add temperature displacement
fix_modify ATC gradients add displacement
fix_modify ATC output ftcb_constVFE $m text binary tensor_components
fix_modify ATC output ftcb_constVFE 200 text binary tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
velocity all create ${Ti} 102486 mom yes rot yes dist gaussian
velocity all create 0.00010000000000000000479 102486 mom yes rot yes dist gaussian
# step iu T,V space
variable i loop 1
label loop_i
print ">>> step $i, T: ${Ti}, V: $V"
>>> step 1, T: 0.00010000000000000000479, V: 31367.233018713999627
variable Tf equal ${Ti}+${dT}
variable Tf equal 0.00010000000000000000479+${dT}
variable Tf equal 0.00010000000000000000479+0.2000000000000000111
fix NVT all nvt temp ${Ti} ${Tf} 20 drag 0.5 tchain 1
fix NVT all nvt temp 0.00010000000000000000479 ${Tf} 20 drag 0.5 tchain 1
fix NVT all nvt temp 0.00010000000000000000479 0.20010000000000000009 20 drag 0.5 tchain 1
run $n
run 10000
Setting up run ...
ATC: CB stiffness: 7.56717 Einstein freq: 0.355649
ATC: computing bond matrix ...........done
ATC: CB stiffness: 7.56717 Einstein freq: 0.355649
ATC: computing bond matrix ...........done
Memory usage per processor = 43.8852 Mbytes
Step Temp Press TotEng Lx Ly Lz
0 9.9884259e-05 0.00037439907 -1743.9894 31.537365 31.537365 31.537365
200 0.00018395916 0.0008038753 -1743.9892 31.537365 31.537365 31.537365
400 0.00072207452 0.0035412421 -1743.9877 31.537365 31.537365 31.537365
600 0.0035009087 0.01765789 -1743.9803 31.537365 31.537365 31.537365
800 0.013509969 0.072367846 -1743.953 31.537365 31.537365 31.537365
1000 0.024404761 0.16748542 -1743.9203 31.537365 31.537365 31.537365
1200 0.02269474 0.25683396 -1743.9165 31.537365 31.537365 31.537365
1400 0.020977736 0.37083837 -1743.9105 31.537365 31.537365 31.537365
1600 0.023822771 0.52655981 -1743.8907 31.537365 31.537365 31.537365
1800 0.029504552 0.724909 -1743.8607 31.537365 31.537365 31.537365
ATC: computing bond matrix ..........done
ATC: computing bond matrix ..........done
2000 0.034895124 0.95292512 -1743.8286 31.537365 31.537365 31.537365
2200 0.038474547 1.1919487 -1743.7994 31.537365 31.537365 31.537365
2400 0.041549289 1.4317242 -1743.7711 31.537365 31.537365 31.537365
2600 0.045486492 1.6680358 -1743.741 31.537365 31.537365 31.537365
2800 0.050155213 1.8970903 -1743.7096 31.537365 31.537365 31.537365
3000 0.054672553 2.1168131 -1743.6792 31.537365 31.537365 31.537365
3200 0.058605281 2.3306834 -1743.6507 31.537365 31.537365 31.537365
3400 0.062199376 2.5471875 -1743.6227 31.537365 31.537365 31.537365
3600 0.065809649 2.7748986 -1743.594 31.537365 31.537365 31.537365
3800 0.069568751 3.0179585 -1743.564 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
4000 0.073508373 3.2739196 -1743.5326 31.537365 31.537365 31.537365
4200 0.077717909 3.5333376 -1743.5006 31.537365 31.537365 31.537365
4400 0.082309308 3.7807471 -1743.469 31.537365 31.537365 31.537365
4600 0.087284711 3.9974133 -1743.4392 31.537365 31.537365 31.537365
4800 0.092475466 4.166069 -1743.413 31.537365 31.537365 31.537365
5000 0.097607659 4.2765824 -1743.3918 31.537365 31.537365 31.537365
5200 0.10242915 4.3301667 -1743.3761 31.537365 31.537365 31.537365
5400 0.10679915 4.3398975 -1743.3649 31.537365 31.537365 31.537365
5600 0.11070065 4.3272641 -1743.3567 31.537365 31.537365 31.537365
5800 0.11420842 4.3165087 -1743.3493 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
6000 0.11745522 4.3289911 -1743.3405 31.537365 31.537365 31.537365
6200 0.12060841 4.3789965 -1743.3288 31.537365 31.537365 31.537365
6400 0.1238495 4.4714313 -1743.3135 31.537365 31.537365 31.537365
6600 0.12734883 4.6013368 -1743.2946 31.537365 31.537365 31.537365
6800 0.13123277 4.7550795 -1743.2728 31.537365 31.537365 31.537365
7000 0.1355461 4.9131529 -1743.2497 31.537365 31.537365 31.537365
7200 0.14022279 5.0544601 -1743.2271 31.537365 31.537365 31.537365
7400 0.14508669 5.161526 -1743.2068 31.537365 31.537365 31.537365
7600 0.14989701 5.2254132 -1743.19 31.537365 31.537365 31.537365
7800 0.15442502 5.2486878 -1743.1772 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
8000 0.1585231 5.245194 -1743.1674 31.537365 31.537365 31.537365
8200 0.16215368 5.2366567 -1743.159 31.537365 31.537365 31.537365
8400 0.16537863 5.2473985 -1743.1498 31.537365 31.537365 31.537365
8600 0.16833152 5.2988909 -1743.1379 31.537365 31.537365 31.537365
8800 0.17119053 5.4054221 -1743.1217 31.537365 31.537365 31.537365
9000 0.17415442 5.5714574 -1743.1004 31.537365 31.537365 31.537365
9200 0.17741609 5.7907947 -1743.074 31.537365 31.537365 31.537365
9400 0.18112875 6.0474639 -1743.0437 31.537365 31.537365 31.537365
9600 0.18536621 6.3183401 -1743.011 31.537365 31.537365 31.537365
9800 0.19008819 6.5773705 -1742.9782 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
10000 0.19513095 6.800965 -1742.9477 31.537365 31.537365 31.537365
Loop time of 217.59 on 4 procs for 10000 steps with 864 atoms
Pair time (%) = 22.0583 (10.1375)
Neigh time (%) = 0.106731 (0.0490514)
Comm time (%) = 92.9321 (42.7096)
Outpt time (%) = 0.514863 (0.23662)
Other time (%) = 101.978 (46.8672)
Nlocal: 216 ave 223 max 212 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 3107 ave 3111 max 3100 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 39744 ave 41133 max 38895 min
Histogram: 1 1 0 0 1 0 0 0 0 1
FullNghs: 79488 ave 82064 max 78016 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 317952
Ave neighs/atom = 368
Neighbor list builds = 5
Dangerous builds = 0
unfix NVT
fix NVT all nvt temp ${Tf} ${Tf} 20 drag 0.5 tchain 1
fix NVT all nvt temp 0.20010000000000000009 ${Tf} 20 drag 0.5 tchain 1
fix NVT all nvt temp 0.20010000000000000009 0.20010000000000000009 20 drag 0.5 tchain 1
run $n
run 10000
Setting up run ...
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
Memory usage per processor = 44.3449 Mbytes
Step Temp Press TotEng Lx Ly Lz
10000 0.19513095 6.800965 -1742.9477 31.537365 31.537365 31.537365
10200 0.1942722 6.9478502 -1742.937 31.537365 31.537365 31.537365
10400 0.19883577 7.0539144 -1742.9173 31.537365 31.537365 31.537365
10600 0.20139901 7.1014941 -1742.907 31.537365 31.537365 31.537365
10800 0.20081668 7.1047619 -1742.9075 31.537365 31.537365 31.537365
11000 0.19970238 7.094286 -1742.9103 31.537365 31.537365 31.537365
11200 0.1992728 7.0940423 -1742.9108 31.537365 31.537365 31.537365
11400 0.19903616 7.1168902 -1742.9091 31.537365 31.537365 31.537365
11600 0.1985796 7.1677194 -1742.9056 31.537365 31.537365 31.537365
11800 0.1981405 7.2439973 -1742.9 31.537365 31.537365 31.537365
ATC: computing bond matrix ..........done
ATC: computing bond matrix ..........done
12000 0.19807517 7.3351555 -1742.8924 31.537365 31.537365 31.537365
12200 0.19846191 7.4244524 -1742.884 31.537365 31.537365 31.537365
12400 0.19916212 7.4934365 -1742.8766 31.537365 31.537365 31.537365
12600 0.19999074 7.5270309 -1742.8719 31.537365 31.537365 31.537365
12800 0.20077516 7.5175279 -1742.8707 31.537365 31.537365 31.537365
13000 0.20135496 7.4665953 -1742.8734 31.537365 31.537365 31.537365
13200 0.20160734 7.38492 -1742.8792 31.537365 31.537365 31.537365
13400 0.20148742 7.2895976 -1742.887 31.537365 31.537365 31.537365
13600 0.2010393 7.2000327 -1742.895 31.537365 31.537365 31.537365
13800 0.20037365 7.1335653 -1742.9015 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
14000 0.19963599 7.1019254 -1742.9054 31.537365 31.537365 31.537365
14200 0.1989806 7.1091181 -1742.9058 31.537365 31.537365 31.537365
14400 0.19854825 7.1508728 -1742.9031 31.537365 31.537365 31.537365
14600 0.1984433 7.2155437 -1742.8978 31.537365 31.537365 31.537365
14800 0.19871156 7.2862513 -1742.8914 31.537365 31.537365 31.537365
15000 0.19932573 7.3439691 -1742.8855 31.537365 31.537365 31.537365
15200 0.20018644 7.371098 -1742.8818 31.537365 31.537365 31.537365
15400 0.20114408 7.3548507 -1742.8818 31.537365 31.537365 31.537365
15600 0.202037 7.2896442 -1742.8862 31.537365 31.537365 31.537365
15800 0.2027327 7.1778389 -1742.8951 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
16000 0.20315567 7.0286376 -1742.9079 31.537365 31.537365 31.537365
16200 0.20329394 6.8555641 -1742.9235 31.537365 31.537365 31.537365
16400 0.20318777 6.673354 -1742.9405 31.537365 31.537365 31.537365
16600 0.20290989 6.4951258 -1742.9576 31.537365 31.537365 31.537365
16800 0.20254493 6.3304266 -1742.9738 31.537365 31.537365 31.537365
17000 0.20217197 6.1843778 -1742.9884 31.537365 31.537365 31.537365
17200 0.20185124 6.0578536 -1743.0013 31.537365 31.537365 31.537365
17400 0.20161576 5.94845 -1743.0124 31.537365 31.537365 31.537365
17600 0.20146835 5.8519278 -1743.0222 31.537365 31.537365 31.537365
17800 0.20138485 5.7637939 -1743.0311 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
18000 0.20132247 5.6807023 -1743.0393 31.537365 31.537365 31.537365
18200 0.20123183 5.6014137 -1743.047 31.537365 31.537365 31.537365
18400 0.20106914 5.5271637 -1743.0542 31.537365 31.537365 31.537365
18600 0.20080571 5.4614233 -1743.0607 31.537365 31.537365 31.537365
18800 0.20043268 5.4091822 -1743.0661 31.537365 31.537365 31.537365
19000 0.19996085 5.3759725 -1743.0697 31.537365 31.537365 31.537365
19200 0.1994168 5.3668762 -1743.0712 31.537365 31.537365 31.537365
19400 0.198837 5.3857152 -1743.0701 31.537365 31.537365 31.537365
19600 0.19826151 5.434538 -1743.0662 31.537365 31.537365 31.537365
19800 0.19772836 5.5134332 -1743.0595 31.537365 31.537365 31.537365
ATC: computing bond matrix ...........done
ATC: computing bond matrix ...........done
20000 0.19726939 5.6206257 -1743.0501 31.537365 31.537365 31.537365
Loop time of 100.792 on 4 procs for 10000 steps with 864 atoms
Pair time (%) = 15.7625 (15.6386)
Neigh time (%) = 0.0767966 (0.0761931)
Comm time (%) = 22.8833 (22.7034)
Outpt time (%) = 0.135321 (0.134258)
Other time (%) = 61.9342 (61.4475)
Nlocal: 216 ave 231 max 208 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 3107 ave 3115 max 3092 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 39744 ave 42595 max 38315 min
Histogram: 1 2 0 0 0 0 0 0 0 1
FullNghs: 79488 ave 85008 max 76544 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 317952
Ave neighs/atom = 368
Neighbor list builds = 5
Dangerous builds = 0
unfix NVT
variable Ti equal ${Tf}
variable Ti equal 0.20010000000000000009
next i
jump in.ftcb_constV loop_i

53
examples/USER/atc/cauchy_born/in.cb_biaxial Normal file
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to biaxial deformation equivalent to shearing.
echo both
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal $c*${lattice_constant}
variable d equal 0.005
variable s equal 1.005
variable is equal 1.0/$s
variable V0 equal $L*$L*3*${lattice_constant}
# create system
lattice fcc ${lattice_constant} origin 0.25 0.25 0.25
region box block 0 $c 0 $c 0 3
boundary p p p
create_box 1 box
create_atoms 1 box
mass 1 39.95
group all region box
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
fix_modify AtC mesh create $c $c 1 box p p p
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 fields add elastic_deformation_gradient
fix_modify AtC output cb_biaxialFE 1 full_text tensor_components
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}"
minimize 1.e-20 1.e-20 1000 1000
run 1
variable step equal ${step}+1
change_box all x scale $s y scale ${is} remap
variable gamma1 equal lx/$L-1.0
variable gamma2 equal ly/$L-1.0
variable dv equal vol/${V0}
next i
jump in.cb_biaxial loop_i

54
examples/USER/atc/cauchy_born/in.cb_shear Normal file
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to shear deformation.
#
# NOTE possible problems with large shear and handling a non-ortho box
echo both
units metal
atom_style atomic
variable lattice_constant equal 4.08
variable c equal 6 # minimum size
variable Ly equal $c*${lattice_constant}
variable d equal 0.005
variable V0 equal ($c*${lattice_constant})^3
# create system
lattice fcc ${lattice_constant} origin 0.25 0.25 0.25
# NOTE rect box + lagrangian is necessary to fool ATC's mesh
region rectbox block 0 $c 0 $c 0 3
region box prism 0 $c 0 $c 0 3 0 0 0
boundary p p p
create_box 1 box
create_atoms 1 region box
mass 1 196.97
group all region box
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
fix_modify AtC mesh create $c $c 1 rectbox p p p
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 fields add elastic_deformation_gradient
fix_modify AtC output cb_shearFE 1 text binary tensor_components
min_modify line quadratic
variable dgamma equal $d/${Ly}
print "depsilon_12: ${dgamma}"
timestep 0.0
variable i loop 4
label loop_i
print ">>> step $i"
minimize 1.e-20 1.e-20 1000 1000
run 1
variable step equal ${step}+1
change_box all xy delta $d remap
variable gamma equal $i*${dgamma}
next i
jump in.cb_shear loop_i

46
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to uniaxial strain deformation.
echo both
units real
atom_style atomic
# create domain
lattice fcc 5.256227487 origin 0.25 0.25 0.25
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
mass 1 39.95
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
# specify inter-atomic potential
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix AtC internal atc field Ar_CauchyBorn.mat
fix_modify AtC mesh create 8 1 1 BOX f p p
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 fields add elastic_deformation_gradient
timestep 0.0
fix_modify AtC output cb_unistrainFE 1 text tensor_components binary
log cb_unistrain.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1

51
examples/USER/atc/cauchy_born/in.cb_unistrain_eam Normal file
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an EAM system subjected to uniaxial strain deformation.
# NOTE currently the convergence is distinctly exponential, the LJ version is quadratic
echo both
units metal
atom_style atomic
# create domain
#lattice fcc 3.615 origin 0.25 0.25 0.25
lattice fcc 3.615 origin 0.01 0.01 0.01
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
mass 1 63.55
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
# specify inter-atomic potential
pair_style eam
pair_coeff * * ../../../../potentials/Cu_u3.eam
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix AtC internal atc field Cu_CauchyBorn.mat
fix_modify AtC mesh create 8 1 1 BOX f p p
#fix_modify AtC kernel quartic_cylinder 10.0
fix_modify AtC fields none
fix_modify AtC fields add displacement
fix_modify AtC fields add internal_energy stress
fix_modify AtC fields add cauchy_born_energy
fix_modify AtC fields add cauchy_born_stress
fix_modify AtC gradients add displacement
#fix_modify AtC fields add elastic_deformation_gradient
timestep 0.0
fix_modify AtC output cb_unistrain_eamFE 1 text tensor_components binary
log cb_unistrain_eam.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1

51
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to uniaxial strain deformation.
echo both
units real
atom_style atomic
# create domain
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
# specify inter-atomic potential
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix PP1 internal atc field Au_eam_linear.mat
fix_modify PP1 mesh create 8 1 1 BOX f p p
fix_modify PP1 fields add displacement
fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify PP1 gradients add displacement
fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe
# ID group atc PhysicsType ParameterFile
fix PP2 internal atc field Au_eam.mat
fix_modify PP2 mesh create 8 1 1 BOX f p p
fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy
fix_modify PP2 set reference_potential_energy
timestep 0.0
fix_modify PP1 output cb_unistrain_eam_linearFE 1 text tensor_components binary
fix_modify PP2 output cb_unistrain_eam_refFE 1 text tensor_components
log cb_unistrain_eam_linear.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1

54
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to uniaxial strain deformation.
echo both
units real
atom_style atomic
# create domain
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
#pair_style eam
#pair_coeff * * Au_u3.eam
#pair_style lj/cut/smooth 5.456108274435118
pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
mass * 196.97
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
# specify inter-atomic potential
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix PP1 internal atc field Au_CauchyBorn_linear.mat
fix_modify PP1 mesh create 8 1 1 BOX f p p
fix_modify PP1 fields add displacement
fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify PP1 gradients add displacement
fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe
# ID group atc PhysicsType ParameterFile
fix PP2 internal atc field Au_CauchyBorn.mat
fix_modify PP2 mesh create 8 1 1 BOX f p p
fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy
fix_modify PP2 set reference_potential_energy
timestep 0.0
fix_modify PP1 output cb_unistrain_linearFE 1 text tensor_components binary
fix_modify PP2 output cb_unistrain_refFE 1 text tensor_components
log cb_unistrain_linear.log
variable step equal 0
thermo_style custom step v_step pe ke press lx ly lz
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1
variable step equal ${step}+1
displace_atoms all ramp x -0.1 0.1 x -100 100
run 1

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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system subjected to volumetric stretching.
echo both
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal $c*${lattice_constant}
#variable d equal 0.01
variable d equal 0.005
variable s equal 1.005
variable V0 equal ($c*${lattice_constant})^3
# create system
lattice fcc ${lattice_constant} origin 0.25 0.25 0.25
region box block 0 $c 0 $c 0 $c
boundary p p p
create_box 1 box
create_atoms 1 box
mass 1 39.95
group all region box
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
fix_modify AtC mesh create $c $c $c box p p p
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 output cb_volumetricFE 1 full_text tensor_components
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"
minimize 1.e-20 1.e-20 1000 1000
run 1
variable step equal ${step}+1
change_box all x scale $s y scale $s z scale $s remap
variable gamma equal lx/$L-1.0
next i
jump in.cb_volumetric loop_i

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# This test evaluates Hardy fields for a small block of LJ material
# that's undergoing translation in the x-direction through the
# periodic boundary.
echo both
log log.flying_cube
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal (${lattice_constant}*$c)
variable V equal $L*$L*$L
print "Volume : $V"
variable s equal 10
variable dt equal 0.1
variable v equal 0.1
variable m equal 39.95
# create system
lattice fcc ${lattice_constant} origin 0.01 0.01 0.01
region box block 0 $c 0 $c 0 $c
boundary p p p
# boundary p s s
create_box 1 box
create_atoms 1 region box
mass 1 $m
group all region box
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 0 every 200 check no
# neigh_modify delay 0 every $n
reset_timestep 0
thermo $s
compute_modify thermo_temp extra 0
thermo_style custom step temp pxx pyy pzz etotal lx ly lz
timestep ${dt}
min_modify line quadratic
minimize 0. 0. 1000 1000
reset_timestep 0
variable xLO equal xlo
variable xHI equal xhi
variable yLO equal ylo
variable yHI equal yhi
variable zLO equal zlo
variable zHI equal zhi
# region BOX block ${xLO} ${xHI} ${yLO} ${yHI} ${zLO} ${zHI} units box
region BOX block ${xLO} ${xHI} -0.5 31.7 -0.5 31.7 units box
fix ATC all atc field
fix_modify ATC mesh create 1 1 1 box p p p
fix_modify ATC fields add stress velocity displacement
fix_modify ATC fields add temperature kinetic_temperature
fix_modify ATC fields add internal_energy energy
fix_modify ATC output flying_cubeFE $s text binary tensor_components
# fix_modify ATC atomic_output flying_cubeMD $m text binary tensor_components
dump dumpfc all atom $s flying_cube.dmp
velocity all set $v 0.0 0.0 units box
fix NVE all nve
run 3500
variable c equal 48.88821291*48.88821291/(3.*0.0019872067)
variable T equal $m*$v*$v*$c
print "kinetic temperature: $T"

74
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# This test compares Hardy and Cauchy-Born metrics of energy density and stress
# for an Ar system undergoing dynamics at a finite temperature.
echo both
log ftcb_constV.log
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 6
variable L equal (${lattice_constant}*$c)
variable V equal $L*$L*$L
print "Volume : $V"
variable Ti equal 0.0001
variable dT equal 0.2
variable n equal 10000
variable m equal 200
variable dt equal 0.1
# create system
lattice fcc ${lattice_constant}
region box block 0 $c 0 $c 0 $c
boundary p p p
pair_style lj/cut 13.5
read_data ftcb_constV_setup.data
mass 1 39.95
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 0 every 2000 check no
reset_timestep 0
thermo $m
compute_modify thermo_temp extra 0
variable nrepeat equal $n/$m
variable sxx equal -pxx
variable intenergy equal etotal
fix TDAVE all ave/time $m ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
thermo_style custom step temp press etotal lx ly lz
timestep ${dt}
# filtered
fix ATCFILT all atc field Ar_CauchyBorn.mat
#fix_modify ATCFILT reset_atomic_reference_positions ftcb_constV_setup.data
fix_modify ATCFILT mesh create 1 1 1 box p p p
fix_modify ATCFILT fields none
fix_modify ATCFILT fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify ATCFILT fields add temperature displacement
fix_modify ATCFILT gradients add displacement
fix_modify ATCFILT output ftcb_constV_filteredFE $n text binary tensor_components
fix_modify ATCFILT sample_frequency $m
variable scale equal $n*${dt}
fix_modify ATCFILT filter scale ${scale}
fix_modify ATCFILT filter on
fix_modify ATCFILT filter type step
# not filtered
fix ATC all atc field Ar_CauchyBorn.mat
#fix_modify ATC reset_atomic_reference_positions ftcb_constV_setup.data
fix_modify ATC mesh create 1 1 1 box p p p
fix_modify ATC fields none
fix_modify ATC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify ATC fields add temperature displacement
fix_modify ATC gradients add displacement
fix_modify ATC output ftcb_constVFE $m text binary tensor_components
velocity all create ${Ti} 102486 mom yes rot yes dist gaussian
# step iu T,V space
variable i loop 1
label loop_i
print ">>> step $i, T: ${Ti}, V: $V"
variable Tf equal ${Ti}+${dT}
fix NVT all nvt temp ${Ti} ${Tf} 20 drag 0.5 tchain 1
run $n
unfix NVT
fix NVT all nvt temp ${Tf} ${Tf} 20 drag 0.5 tchain 1
run $n
unfix NVT
variable Ti equal ${Tf}
next i
jump in.ftcb_constV loop_i

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# This is a test for reading an atomic reference configuration
echo both
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 4
variable L equal (${lattice_constant}*$c)
# create system
lattice fcc ${lattice_constant}
region box block 0 $c 0 $c 0 $c
boundary p p p
# the stretched configuration of the atoms
read_data read_xref_1.data
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 1000000
thermo 1
thermo_style custom step vol etotal
timestep 0
fix ATC all atc field Ar_CauchyBorn.mat
# the original configuration of the atoms
fix_modify ATC reset_atomic_reference_positions read_xref_0.data
# "box" is the original box
fix_modify ATC mesh create 1 1 1 box f f f
fix_modify ATC fields none
fix_modify ATC fields add mass_density
fix_modify ATC output read_xrefFE 1 text
fix_modify ATC output index step
variable u1 atom x-f_ATC[1]
variable u2 atom y-f_ATC[2]
variable u3 atom z-f_ATC[3]
variable rho atom mass*f_ATC[4]
dump CONFIG all custom 1 read_xref.dmp id type x y z v_u1 v_u2 v_u3 v_rho
run 1

83
examples/USER/atc/cauchy_born/read_xref.screen Normal file
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
variable lattice_constant equal 5.256227487
variable c equal 4
variable L equal (${lattice_constant}*$c)
variable L equal (5.2562274870000003091*$c)
variable L equal (5.2562274870000003091*4)
# create system
lattice fcc ${lattice_constant}
lattice fcc 5.2562274870000003091
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 4 0 $c 0 $c
region box block 0 4 0 4 0 $c
region box block 0 4 0 4 0 4
boundary p p p
# the stretched configuration of the atoms
read_data read_xref_1.data
Reading data file ...
orthogonal box = (-1.05125 -1.05125 -1.05125) to (22.0762 22.0762 22.0762)
1 by 2 by 2 MPI processor grid
256 atoms
256 velocities
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# define region
neighbor 1.0 bin
neigh_modify delay 1000000
thermo 1
thermo_style custom step vol etotal
timestep 0
fix ATC all atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
# the original configuration of the atoms
fix_modify ATC reset_atomic_reference_positions read_xref_0.data
# "box" is the original box
fix_modify ATC mesh create 1 1 1 box f f f
ATC: created uniform mesh with 8 nodes, 8 unique nodes, and 1 elements
fix_modify ATC fields none
fix_modify ATC fields add mass_density
fix_modify ATC output read_xrefFE 1 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify ATC output index step
variable u1 atom x-f_ATC[1]
variable u2 atom y-f_ATC[2]
variable u3 atom z-f_ATC[3]
variable rho atom mass*f_ATC[4]
dump CONFIG all custom 1 read_xref.dmp id type x y z v_u1 v_u2 v_u3 v_rho
run 1
Setting up run ...
ATC: P0, found 256 atoms in reference file
ATC: P0, read 256 reference positions
ATC: CB stiffness: 7.56717 Einstein freq: 0.355649
Memory usage per processor = 16.0674 Mbytes
Step Volume TotEng
0 12370.307 -416.09102
1 12370.307 -416.09102
Loop time of 0.00229579 on 4 procs for 1 steps with 256 atoms
Pair time (%) = 0.00048399 (21.0816)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000252604 (11.0029)
Outpt time (%) = 0.00147229 (64.1301)
Other time (%) = 8.69036e-05 (3.78534)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1700 ave 1700 max 1700 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 7936 ave 7936 max 7936 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 15872 ave 15872 max 15872 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63488
Ave neighs/atom = 248
Neighbor list builds = 0
Dangerous builds = 0

37
examples/USER/atc/drift_diffusion/Ar_ddm.mat Normal file
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material Ar real
heat_capacity constant
capacity 1.0
end
electron_heat_capacity constant, no density
capacity 1.0
end
effective_mass constant
inv_effective_mass 1.
end
heat_flux linear
conductivity 1.0
end
electron_heat_flux linear
conductivity 1.0
end
electron_phonon_exchange linear
coefficient 1.0
end
electron_flux linear
mobility 400.0
diffusivity 1000.0
end
electron_recombination linear
inv_relaxation_time 0.0
equilibrium_carrier_density 1.0
end
electric_field linear
permittivity 0.2
end
end
material Vacuum real
electric_field linear
permittivity 1.0
end
end

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examples/USER/atc/drift_diffusion/CNT_ddm.mat Normal file
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#######################################################################
material Vacuum metal
electric_field linear
permittivity 1.0 # e/V/L scales electric field vs charge
end
electron_density null
end
#######################################################################
material C metal
#### two temperature ####################
heat_capacity constant
capacity 0.0566081301 # E / L^3
end
electron_heat_capacity linear
capacity 9.03321225e-08 # E / L^3
end
heat_flux linear
conductivity 602.21415 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.4413627505355 # E / t / L / T
end
electron_phonon_exchange power_law
coefficient 2.247e-15 # E / t / T 2.247e-15
exponent 4
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
inv_relaxation_time 0.0 # 1/t HACK
equilibrium_carrier_density 0.0 # e/L^3 HACK
end
electric_field linear
permittivity 0.06 # e/V/L scales electric field vs charge
end
end
end

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examples/USER/atc/drift_diffusion/Cu_cddm.mat Normal file
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#=====================================================
material Vacuum metal
#### two temperature ####################
#### drift diffusion #####################
electric_field linear
#permittivity 1.0
permittivity 1.085 # estimate based on speed of light in Cu and Cu's relative permeability of 1
end
end
#=====================================================
material Cu metal
heat_capacity constant
capacity 0.211977459280654
end
heat_flux linear
conductivity 67.4479848
end
electron_heat_capacity linear no_density
#capacity 6.8439866929411762e-05 # value from TTM paper divided by bulk electron density in Cu
capacity 5.8294334393503992e-05 # source 96.8 J m^-3 K^-2 in Lin & Zhigilei 08 (ref 47), converted to AtC units and divided by bulk electron density in Cu, NOTE: should not be multiplied by electron effective mass, only electron number density
end
electron_heat_flux linear
conductivity 441.362750535
end
electron_phonon_exchange hertel
debeye_temperature 343.5 # source wikipedia
mass_enhancement 0.08 # source Hertel 2002, ref 62
end
electric_field linear
permittivity 1.085 # estimate based on speed of light in Cu and Cu's relative permeability of 1
end
effective_mass constant
inv_effective_mass 0.8997 # source: Tolman & Stewart, 1916
end
electron_drag linear
inv_momentum_relaxation_time 100. # order of magnitude estimate for metals ~ 10^-14 s
end
electron_flux convection
end
end
electron_recombination linear
inv_relaxation_time 0.0
equilibrium_carrier_density 0.0
end
end

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examples/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat Normal file
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# barrier
material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
# inv_relaxation_time 0.0 # 1/t HACK
# equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 11.68 # e/V/L scales electric field vs charge
end
effective_mass constant
inv_effective_mass 1.0 # unit-less
end
electron_density fermi_dirac
fermi_energy 0.0
band_edge 0.5
# reference_temperature 300.0 # HACK
donor_concentration 0.001
# donor_ionization_energy 0.1 # relative to band edge HACK
end
end
# well
material Ge metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
inv_relaxation_time 0.0 # 1/t HACK
equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 11.68 # (SAME AS Si) e/V/L scales electric field vs charge
end
effective_mass constant
inv_effective_mass 1.0 # unit-less (SAME AS Si)
end
electron_density fermi_dirac
fermi_energy 0.0
band_edge -0.5
# reference_temperature 0.0 # HACK
# reference_temperature 300.0 # HACK
# donor_concentration 0.001 # HACK
# donor_ionization_energy 0.1 # relative to band edge HACK
end
end

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#=====================================================
material Vacuum metal
#### two temperature ####################
#### drift diffusion #####################
electric_field linear
permittivity 1.0
end
end
#=====================================================
material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
#diffusivity 14000000.0 # L^2/t
diffusivity 1400.0 # L^2/t
mask_y 1
mask_z 1
end
electron_recombination linear
# inv_relaxation_time 0.0 # 1/t HACK
# equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity
end
effective_mass constant
inv_effective_mass 1.0 # unit-less
end
electron_density fermi_dirac
fermi_energy 0.0 # HACK
band_edge -1.0 # -1.0
# reference_temperature 0.0 # HACK
# donor_concentration 0.001 # HACK
# donor_ionization_energy 0.1 # relative to band edge HACK
end
### convective functions
electron_drag linear
inv_momentum_relaxation_time 100.
end
electron_flux convection
end
end

52
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material Vacuum metal
electric_field linear
permittivity 1.0
end
end
material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
#diffusivity 14000000.0 # L^2/t
diffusivity 1400.0 # L^2/t
mask_y 1
mask_z 1
end
electron_recombination linear
# inv_relaxation_time 0.0 # 1/t HACK
# equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity
end
effective_mass constant
inv_effective_mass 1.0 # unit-less
end
electron_density fermi_dirac
fermi_energy 0.0 # HACK
band_edge -1.0 # -1.0
# reference_temperature 0.0 # HACK
# donor_concentration 0.001 # HACK
# donor_ionization_energy 0.1 # relative to band edge HACK
end
end

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material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
effective_mass constant
inv_effective_mass 1.
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
inv_relaxation_time 0.0 # 1/t HACK
equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 0.06 # e/V/L scales electric field vs charge
end
#donor_concentration 1.0e-4 # e/L^3 HACK must be consistent w/ n0 ?
end

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material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
inv_relaxation_time 0.0 # 1/t HACK
equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
#permittivity 0.06 # e/V/L scales electric field vs charge
permittivity 1.0 # e/V/L scales electric field vs charge
end
effective_mass constant
#inv_effective_mass 2308171.85625180610344519705 # rescale by 1/hbar^2 old bug?
inv_effective_mass 1.0
end
band_edge_potential constant
band_edge 0.0
end
electron_density exponential
intrinsic_energy 0.0 # 1.0 e/L^3 HACK must be consistent w/ n0 ?
intrinsic_concentration 0.0 # 1.0 e/L^3 HACK must be consistent w/ n0 ?
reference_temperature 300.0 # HACK
end
end

41
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material Si metal
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux linear
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
#### drift diffusion #####################
electron_flux linear
mobility 360000.0 # L^2/t/V
diffusivity 14000000.0 # L^2/t
end
electron_recombination linear
# inv_relaxation_time 0.0 # 1/t HACK
# equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity
end
effective_mass constant
inv_effective_mass 1.0 # 0.13123421851033382246725208450724 # unit-less
end
electron_density fermi_dirac
fermi_energy 0.5 # HACK
band_edge 0.0 # -1.0
# reference_temperature 0.0 # HACK
donor_concentration 0.0001 # HACK
# donor_ionization_energy 0.1 # relative to band edge HACK
end
end

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material Si metal
#### drift diffusion #####################
electron_flux thermopower
mobility 360000.0 # L^2/t/V , diffusivity from Einstein rel.
Seebeck 1.0e-9 # HACK order kB
end
end
electron_recombination linear
inv_relaxation_time 0.0 # 1/t HACK
equilibrium_carrier_density 1.0 # e/L^3 HACK
end
electric_field linear
permittivity 0.06 # e/V/L scales electric field vs charge
end
#donor_concentration 1.0 # e/L^3 HACK must be consistent w/ n0 ?
#### two temperature ####################
heat_capacity constant
capacity 0.124578126430817 # E / L^3
end
electron_heat_capacity constant, no density #power_law
#capacity 3.53391324615404e-11
capacity 3.53391324615404e-8 # E / L^3
end
effective_mass constant
inv_effective_mass 1.
end
heat_flux linear
conductivity 722.65698 # E / t / L / T
end
electron_heat_flux thermopower # links to electron_flux
conductivity 0.0441362750535 # E / t / L / T
end
electron_phonon_exchange linear
coefficient 6.0221415e-09 # E / t / T
end
end

144
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LAMMPS (14 Aug 2013)
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dn equal 2.0*0.085000000000000006106
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
timestep 0.00050000000000000001041
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1 1 1
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-50 0 0) to (50 1 1)
4 by 1 by 1 MPI processor grid
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
ATC: constructing convective_drift_diffusion coupling with parameter file Cu_cddm.mat
ATC: peratom PE compute created with ID: 3
ATC: 2 materials defined from Cu_cddm.mat
ATC: creating convective_drift_diffusion extrinsic model
ATC: 2 materials defined from Cu_cddm.mat
ATC: 2 materials defined from Cu_cddm.mat
ATC: 2 materials defined from Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
ATC: created uniform mesh with 404 nodes, 101 unique nodes, and 100 elements
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.17000000000000001221 ${n0}
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.17000000000000001221 0.085000000000000006106
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density lbc 0.085000000000000006106
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electron_density rbc 0.085000000000000006106
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
fix_modify AtC output convective_pulseFE 10 text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
thermo $s
thermo 10
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential lbc -5000
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC source electric_potential all 0.085000000000000006106
fix_modify AtC extrinsic electron_integration implicit 10
run 100
Setting up run ...
ATC: WARNING: material: [vacuum] cannot find heat_flux
ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_flux
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: material: [cu] cannot find electron_recombination
ATC: WARNING: physics model: [convection drift-diffusion], material: [cu] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_drag_coefficient
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_velocity> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_drag_power
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_temperature> physics and will be treated as null
Memory usage per processor = 0.432198 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5]
0 0 0.65909742 300 0.0054411845 300 10.091586
10 3 0.65909742 300 0.0054411845 300 10.091586
20 6 0.65909742 300 0.0054411845 300 10.091586
30 10 0.65909742 300 0.0054411845 300 10.091586
40 14 0.65909742 300 0.0054411845 300 10.091586
50 17 0.65909742 300 0.0054411845 300 10.091586
60 20 0.65909742 300 0.0054411845 300 10.091586
70 23 0.65909742 300 0.0054411845 300 10.091586
80 33 0.65909742 300 0.0054411845 300 10.091586
90 37 0.65909742 300 0.0054411845 300 10.091586
100 40 0.65909742 300 0.0054411845 300 10.091586
Loop time of 39.7392 on 4 procs for 100 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000300825 (0.000756998)
Outpt time (%) = 0.125219 (0.315103)
Other time (%) = 39.6136 (99.6841)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

78
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LAMMPS (14 Aug 2013)
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
timestep 9.9999999999999995475e-08
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1 1 1
region simRegion block 0 $L 0 1 0 1
region simRegion block 0 10 0 1 0 1
boundary f p p
create_box 1 simRegion
Created orthogonal box = (0 0 0) to (10 1 1)
4 by 1 by 1 MPI processor grid
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
ATC: constructing drift_diffusion-schrodinger coupling with parameter file Si_ddm_schrodinger.mat
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from Si_ddm_schrodinger.mat
ATC: creating drift_diffusion extrinsic model
ATC: 1 materials defined from Si_ddm_schrodinger.mat
ATC: 1 materials defined from Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
fix_modify AtC mesh create 40 1 1 simRegion f p p
ATC: created uniform mesh with 164 nodes, 41 unique nodes, and 40 elements
variable a equal $L-0.1
variable a equal 10-0.1
variable b equal $L+0.1
variable b equal 10+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 9.9000000000000003553 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 9.9000000000000003553 10.099999999999999645 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_temperature all 30000
fix_modify AtC fix electron_temperature all $T
fix_modify AtC fix electron_temperature all 30000
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC output ddm_schrodingerFE 1 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
ERROR: Illegal fix_modify command (../fix.cpp:104)

105
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LAMMPS (14 Aug 2013)
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dn equal 2.0*0.00010000000000000000479
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
timestep 9.9999999999999995475e-08
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1 1 1
variable a equal 0.5*$L
variable a equal 0.5*10
region simRegion block -$a $a 0 1 0 1
region simRegion block -5 $a 0 1 0 1
region simRegion block -5 5 0 1 0 1
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-5 0 0) to (5 1 1)
4 by 1 by 1 MPI processor grid
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
ATC: constructing drift_diffusion-schrodinger coupling with parameter file SiGe_ddm_schrodinger.mat
ATC: peratom PE compute created with ID: 3
ATC: 2 materials defined from SiGe_ddm_schrodinger.mat
ATC: creating drift_diffusion extrinsic model
ATC: 2 materials defined from SiGe_ddm_schrodinger.mat
ATC: 2 materials defined from SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
fix_modify AtC mesh create 80 1 1 simRegion f p p
ATC: created uniform mesh with 324 nodes, 81 unique nodes, and 80 elements
variable a equal 0.2*$L+0.001
variable a equal 0.2*10+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_elementset well -2.0009999999999998899 $a -INF INF -INF INF
fix_modify AtC mesh create_elementset well -2.0009999999999998899 2.0009999999999998899 -INF INF -INF INF
ATC: created elementset well with 32 elements
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -2.0009999999999998899 $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -2.0009999999999998899 2.0009999999999998899 -INF INF -INF INF
ATC: created nodeset well with 33 nodes
fix_modify AtC material well Ge
variable b equal $a-0.002
variable b equal 2.0009999999999998899-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -2.0009999999999998899 -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -2.0009999999999998899 -1.9989999999999998881 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 1.9989999999999998881 $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 1.9989999999999998881 2.0009999999999998899 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_temperature all 1000
fix_modify AtC fix electron_temperature all $T
fix_modify AtC fix electron_temperature all 1000
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC output finite_wellFE 1 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
ERROR: Illegal fix_modify command (../fix.cpp:104)

72
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# DESCRIPTION: haynes-schockley
echo both
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
thermo $s
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10
run 100

66
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# needs description
# DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
echo both
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1
variable b equal $L+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all
# ends zero
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0
run 1
# ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1

75
examples/USER/atc/drift_diffusion/in.finite_well Normal file
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#needs description
echo both
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
atom_style atomic
lattice fcc 1.0
variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC material well Ge
variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s
# (A) no field
run $m
# (B) fixed boundary field
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m

65
examples/USER/atc/drift_diffusion/in.no_atoms_ddm Normal file
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# needs description
# DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
# w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x
echo both
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
variable s equal 10
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit
run 40
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10
run 40

79
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# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat
echo both
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
run $m

41
examples/USER/atc/drift_diffusion/in.poisson1d_noatoms Normal file
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# needs description
# note the units
units metal
variable nx equal 40
variable h equal 0.25
variable L equal $h*${nx}
variable T equal 300
variable n0 equal 0.000025
variable V equal 5.
variable E equal -0.0001
variable s equal 0.0001
atom_style atomic
timestep 0.0
boundary f f f
lattice fcc 1.0
region BOX block 0 $L 0 1 0 1
create_box 1 BOX
mass * 1.0
atom_modify sort 0 1
fix AtC all atc drift_diffusion Si_ddm.mat
fix_modify AtC mesh create ${nx} 1 1 BOX f p p
# boundary conditions
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_faceset rbc -INF $L -INF INF -INF INF
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration explicit 1
# fix temperature
fix_modify AtC fix temperature all $T
fix_modify AtC fix electron_temperature all $T
# fix electron density
fix_modify AtC fix electron_density all ${n0}
# bcs for electric potential
fix_modify AtC initial electric_potential all 0
fix_modify AtC fix electric_potential lbc $V
fix_modify AtC fix_flux electric_potential rbc $E
fix_modify AtC source electric_potential all $s
thermo 1
thermo_style custom step cpu
fix_modify AtC output poisson1d_noatomsFE 1 text
run 1

73
examples/USER/atc/drift_diffusion/in.poisson2d_noatoms Normal file
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# needs description
echo both
variable nx equal 80 # 80 # 40
variable ny equal ${nx}
variable nz equal 1
variable h equal 1.0
variable l equal -$h
variable u equal $h
#variable l equal -$h*${nx}
#variable u equal $h*${nx}
variable T equal 300
variable n0 equal 0.005
variable S equal 1
variable V equal 5.
# STEP THE GATE VOLTAGE UP
atom_style atomic
timestep 0.0
boundary f f f
lattice fcc 1.0
region BOX block $l $u $l $u 0 1
create_box 1 BOX
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion CNT_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
#fix_modify AtC extrinsic poisson_solver iterative
# boundary conditions
variable a equal $l-0.1
variable b equal $l+0.1
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
variable a equal $u-0.1
variable b equal $u+0.1
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
variable a equal -0.1
variable b equal 0.1
fix_modify AtC mesh create_nodeset origin -INF INF $a $b -INF INF
variable a equal -2*$h
variable b equal 2*$h
variable a equal -8*$h
variable b equal 8*$h
fix_modify AtC mesh create_elementset wire -INF INF $a $b -INF INF
fix_modify AtC material wire C
# simplify
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration explicit 1
fix_modify AtC extrinsic poisson_solver iterative
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
# fix temperature
fix_modify AtC fix temperature all $T
fix_modify AtC fix electron_temperature all $T
# fix electron density
fix_modify AtC fix electron_density all 0
# NEED TO BE ABLE TO TURN OFF electron integration and just do Poisson solve
fix_modify AtC fix electron_density origin ${n0}
# bcs for electric potential
fix_modify AtC unfix electric_potential all
fix_modify AtC initial electric_potential all 0
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc $V
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output poisson2d_noatomsFE 1 full_text
#fix_modify AtC mesh output poisson2dMESH
run 1

138
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# needs description
# STEP THE GATE VOLTAGE UP
# NEED TO TURN OFF T EQNS FOR VACUUM
# HACK need to define well and open bcs
echo both
#variable iter equal 2 # need two for potential to affect density
variable iter1 equal 4 # NOTE <<<<
variable iter2 equal 25 # NOTE <<<<
variable r equal 1
variable nx equal 12 # 30 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 12 # 30 40
variable my equal 8 # 12 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable l equal -${hx}*${nx}
variable u equal ${hx}*${nx}
variable w equal ${hy}*${my}
variable q equal ${hx}*${mx}
variable y equal ${nx}+1-${mx}
variable T equal 300
variable S equal 1
variable n0 equal 0.00007
variable J0 equal 40.0 # 100.0 40.0
variable Vs equal 1.0
#variable Vg equal 1.0 # 10.0 0.0
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
region BOX block ${l} ${u} ${l} ${u} 0 1
create_box 1 BOX
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
# surfaces & regions
variable a equal $l-${tol}
variable b equal $l+$q+${tol}
variable c equal -$w-${tol}
variable d equal $w+${tol}
variable e equal $l+$q-${tol}
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
variable a equal $u-$q-${tol}
variable b equal $u+${tol}
variable e equal $u-$q+${tol}
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
variable a equal -$w-${tol}
variable b equal $w+${tol}
variable c equal $l+$q-${tol}
variable d equal $u-$q+${tol}
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
variable e equal $c+2*${tol}
variable f equal $c+${tol}
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF
variable e equal $d-2*${tol}
variable f equal $d-${tol}
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF
variable e equal $a+2*${tol}
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
variable e equal $b-2*${tol}
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
#fix_modify AtC extrinsic poisson_solver iterative
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter1}
#fix_modify AtC extrinsic conserve density 10
fix_modify AtC extrinsic schrodinger_poisson_solver conserve flux ${iter2}
fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1
fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1
#fix_modify AtC extrinsic initial_fermi_level 0.5
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
# fix temperature
fix_modify AtC fix temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T # <<<
#fix_modify AtC unfix electron_temperature wire
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
### NOTE there seems to be leakage into the vacuum
# electric potential ic
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc ${Vs}
#fix_modify AtC fix electric_potential bot ${Vg} # remove this if Vg=0
# electron density ic
fix_modify AtC initial electron_density all 0
fix_modify AtC fix electron_density all 0
fix_modify AtC unfix electron_density wire
fix_modify AtC initial electron_density wire ${n0}
fix_modify AtC fix electron_density twire 0.0
fix_modify AtC fix electron_density bwire 0.0
fix_modify AtC fix electron_density lwire ${n0}
fix_modify AtC fix electron_density rwire ${n0}
#fix_modify AtC fix electron_density lbc ${n0}
#fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC unfix electron_density lwire
fix_modify AtC unfix electron_density rwire
fix_modify AtC fix_flux electron_density lwire -${J0} # <<<<
fix_modify AtC fix_flux electron_density rwire ${J0} # <<<<
# HACK
#fix_modify AtC fix electron_density all 0
# electron wavefunction ic/bcs
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction top 0.0
fix_modify AtC fix electron_wavefunction bot 0.0
fix_modify AtC fix electron_wavefunction all 0
fix_modify AtC unfix electron_wavefunction wire
#fix_modify AtC fix electron_wavefunction lwire 0.0 # <<<< bit of hack
#fix_modify AtC fix electron_wavefunction rwire 0.0 # <<<< bit of hack
fix_modify AtC fix electron_wavefunction twire 0.0
fix_modify AtC fix electron_wavefunction bwire 0.0
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output schrodinger-poisson2d_JconstraintFE $r full_text binary tensor_components
fix_modify AtC mesh output schrodinger-poisson2dMESH
run $r
# NOW BIAS

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examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective Normal file
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# needs description
# STEP THE GATE VOLTAGE UP
# NEED TO TURN OFF T EQNS FOR VACUUM
# HACK need to define well and open bcs
echo both
#variable iter equal 2 # need two for potential to affect density
variable iter1 equal 4 # NOTE <<<<
variable iter2 equal 25 # NOTE <<<<
variable r equal 1
variable nx equal 12 # 30 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 12 # 30 40
variable my equal 8 # 12 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable l equal -${hx}*${nx}
variable u equal ${hx}*${nx}
variable w equal ${hy}*${my}
variable q equal ${hx}*${mx}
variable y equal ${nx}+1-${mx}
variable T equal 300
variable S equal 1
variable n0 equal 0.00007
variable v0 equal 1000.0
variable J0 equal ${n0}*${v0}
print "prescribed flux: ${J0}"
variable Vs equal 1.0
#variable Vg equal 1.0 # 10.0 0.0
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
region BOX block ${l} ${u} ${l} ${u} 0 1
create_box 1 BOX
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion-schrodinger SiVacuum_cddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
# surfaces & regions
variable a equal $l-${tol}
variable b equal $l+$q+${tol}
variable c equal -$w-${tol}
variable d equal $w+${tol}
variable e equal $l+$q-${tol}
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
variable a equal $u-$q-${tol}
variable b equal $u+${tol}
variable e equal $u-$q+${tol}
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
variable a equal -$w-${tol}
variable b equal $w+${tol}
variable c equal $l+$q-${tol}
variable d equal $u-$q+${tol}
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
variable e equal $c+2*${tol}
variable f equal $c+${tol}
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF
variable e equal $d-2*${tol}
variable f equal $d-${tol}
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF
variable e equal $a+2*${tol}
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
variable e equal $b-2*${tol}
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
#fix_modify AtC extrinsic poisson_solver iterative
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter1}
#fix_modify AtC extrinsic conserve density 10
fix_modify AtC extrinsic schrodinger_poisson_solver conserve flux ${iter2}
fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1
fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1
#fix_modify AtC extrinsic initial_fermi_level 0.5
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
# fix temperature
fix_modify AtC fix temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T # <<<
#fix_modify AtC unfix electron_temperature wire
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
### NOTE there seems to be leakage into the vacuum
# electric potential ic
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc ${Vs}
#fix_modify AtC fix electric_potential bot ${Vg} # remove this if Vg=0
# electron density ic
fix_modify AtC initial electron_density all 0
fix_modify AtC fix electron_density all 0
fix_modify AtC unfix electron_density wire
fix_modify AtC initial electron_density wire ${n0}
fix_modify AtC fix electron_density twire 0.0
fix_modify AtC fix electron_density bwire 0.0
fix_modify AtC fix electron_density lwire ${n0}
fix_modify AtC fix electron_density rwire ${n0}
#fix_modify AtC fix electron_density lbc ${n0}
#fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC unfix electron_density lwire
fix_modify AtC unfix electron_density rwire
fix_modify AtC fix_flux electron_density lwire ${J0} # <<<<
fix_modify AtC fix_flux electron_density rwire -${J0} # <<<<
# HACK
#fix_modify AtC fix electron_density all 0
# electron wavefunction ic/bcs
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction top 0.0
fix_modify AtC fix electron_wavefunction bot 0.0
fix_modify AtC fix electron_wavefunction all 0
fix_modify AtC unfix electron_wavefunction wire
#fix_modify AtC fix electron_wavefunction lwire 0.0 # <<<< bit of hack
#fix_modify AtC fix electron_wavefunction rwire 0.0 # <<<< bit of hack
fix_modify AtC fix electron_wavefunction twire 0.0
fix_modify AtC fix electron_wavefunction bwire 0.0
fix_modify AtC initial electron_velocity x all 0.0
fix_modify AtC initial electron_velocity y all 0.0
fix_modify AtC initial electron_velocity z all 0.0
fix_modify AtC fix electron_velocity x all ${v0}
fix_modify AtC fix electron_velocity y all 0.0
fix_modify AtC fix electron_velocity z all 0.0
fix_modify AtC initial electron_velocity x wire ${v0}
fix_modify AtC fix electron_velocity x wire ${v0}
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output schrodinger-poisson2d_convectiveFE $r full_text binary tensor_components
fix_modify AtC mesh output schrodinger-poisson2dMESH
run $r
# NOW BIAS

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# needs description
# MOVE/COPY this to .._noatoms for bmark
# STEP THE GATE VOLTAGE UP
# NEED TO TURN OFF T EQNS FOR VACUUM
# HACK need to define well and open bcs
echo both
#variable iter equal 2 # need two for potential to affect density
variable iter equal 1 # NOTE <<<<
variable r equal 1
variable nx equal 30 # 30 # 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 30 # 40
variable my equal 12 # 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable l equal -${hx}*${nx}
variable u equal ${hx}*${nx}
variable w equal ${hy}*${my}
variable q equal ${hx}*${mx}
variable y equal ${nx}+1-${mx}
variable T equal 300
variable E equal 0.1
variable S equal 1
variable n0 equal 0.01
variable V equal 5.
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
region BOX block ${l} ${u} ${l} ${u} 0 1
create_box 1 BOX
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
# surfaces & regions
variable a equal $l-${tol}
variable b equal $l+$q+${tol}
variable c equal -$w-${tol}
variable d equal $w+${tol}
variable e equal $l+$q-${tol}
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
variable a equal $u-$q-${tol}
variable b equal $u+${tol}
variable e equal $u-$q+${tol}
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
variable a equal -$w-${tol}
variable b equal $w+${tol}
variable c equal $l+$q-${tol}
variable d equal $u-$q+${tol}
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
variable e equal $c+2*${tol}
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
variable e equal $d-2*${tol}
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
variable e equal $a+2*${tol}
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
variable e equal $b-2*${tol}
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
#fix_modify AtC extrinsic poisson_solver iterative
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter}
fix_modify AtC extrinsic schrodinger_poisson_solver conserve density 10
fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1
fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
# fix temperature
fix_modify AtC fix temperature all $T
fix_modify AtC initial electron_temperature all $T
#fix_modify AtC fix electron_temperature all $T
#fix_modify AtC unfix electron_temperature wire
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
### NOTE there seems to be leakage into the vacuum
# electric potential ic
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 1
# electron density ic
fix_modify AtC initial electron_density all 0
fix_modify AtC fix electron_density all 0
fix_modify AtC unfix electron_density wire
fix_modify AtC initial electron_density wire ${n0}
fix_modify AtC fix electron_density lwire ${n0}
fix_modify AtC fix electron_density rwire ${n0}
fix_modify AtC fix electron_density twire 0.0
fix_modify AtC fix electron_density bwire 0.0
# HACK
#fix_modify AtC fix electron_density all 0
# electron wavefunction ic/bcs
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction top 0.0
fix_modify AtC fix electron_wavefunction bot 0.0
fix_modify AtC fix electron_wavefunction all 0
fix_modify AtC unfix electron_wavefunction wire
fix_modify AtC fix electron_wavefunction lwire 0.0 # dummy value
fix_modify AtC fix electron_wavefunction rwire 0.0 # dummy value
fix_modify AtC fix electron_wavefunction twire 0.0
fix_modify AtC fix electron_wavefunction bwire 0.0
thermo 1
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output schrodinger-poisson2d_noatomsFE $r full_text binary tensor_components
fix_modify AtC mesh output schrodinger-poisson2dMESH
run $r
# NOW BIAS

142
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LAMMPS (14 Aug 2013)
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dn equal 2.0*0.00010000000000000000479
variable dt equal 0.0000001
timestep ${dt}
timestep 9.9999999999999995475e-08
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1 1 1
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-50 0 0) to (50 1 1)
4 by 1 by 1 MPI processor grid
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
ATC: constructing drift_diffusion coupling with parameter file Si_ddm.mat
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from Si_ddm.mat
ATC: creating drift_diffusion extrinsic model
ATC: 1 materials defined from Si_ddm.mat
ATC: 1 materials defined from Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
ATC: created uniform mesh with 404 nodes, 101 unique nodes, and 100 elements
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.00020000000000000000958 ${n0}
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.00020000000000000000958 0.00010000000000000000479
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density lbc 0.00010000000000000000479
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electron_density rbc 0.00010000000000000000479
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential all linear 0 0 0 10 0 0 1
ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0)
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
fix_modify AtC source electric_potential all 0.00010000000000000000479
variable s equal 10
thermo $s
thermo 10
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC output no_atoms_ddmFE 10 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC extrinsic electron_integration implicit
run 40
Setting up run ...
Memory usage per processor = 0.432198 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5]
0 0 0.38734836 300 1.0987928e-07 300 0.011872454
10 2.3 0.3873484 300.00003 0.42381602 1.1554067e+09 0.011872454
20 3.8 0.38734851 300.00011 0.84762424 2.3107922e+09 0.011872453
30 4.9 0.38734869 300.00025 1.2714314 3.4661766e+09 0.011872354
40 6.2 0.38734894 300.00045 1.6952106 4.6215141e+09 0.011870471
Loop time of 6.19604 on 4 procs for 40 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 5.73993e-05 (0.000926387)
Outpt time (%) = 0.0347454 (0.560768)
Other time (%) = 6.16123 (99.4383)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential lbc linear 0 0 0 10 0 0 1
ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0)
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 10 0 0 1
ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0)
fix_modify AtC extrinsic electron_integration implicit 10
run 40
Setting up run ...
Memory usage per processor = 0.432198 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5]
40 0 0.38734894 300.00045 1.6952106 4.6215141e+09 0.011870471
50 6.1 0.38734927 300.0007 2.127197 5.798188e+09 0.012062369
60 20 0.38734967 300.00101 2.5636712 6.9867833e+09 0.01226417
70 26 0.38735014 300.00137 3.0038699 8.1852725e+09 0.01246759
80 32 0.38735069 300.0018 3.4468819 9.3912166e+09 0.012666742
Loop time of 32.1279 on 4 procs for 40 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 9.63807e-05 (0.000299991)
Outpt time (%) = 0.0351226 (0.109321)
Other time (%) = 32.0926 (99.8904)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (14 Aug 2013)
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
Created orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215)
2 by 2 by 1 MPI processor grid
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
thermo 100
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
ATC: constructing drift_diffusion coupling with parameter file Ar_ddm.mat
ATC: peratom PE compute created with ID: 3
ATC: WARNING: material units real do not match lammps
ATC: WARNING: material units real do not match lammps
ATC: 2 materials defined from Ar_ddm.mat
ATC: creating drift_diffusion extrinsic model
ATC: WARNING: material units real do not match lammps
ATC: WARNING: material units real do not match lammps
ATC: 2 materials defined from Ar_ddm.mat
ATC: WARNING: material units real do not match lammps
ATC: WARNING: material units real do not match lammps
ATC: 2 materials defined from Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
ATC: created uniform mesh with 50 nodes, 25 unique nodes, and 16 elements
variable a equal $W+${tol}
variable a equal 1000+${tol}
variable a equal 1000+0.10000000000000000555
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset wire -1000.1000000000000227 $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF 0.10000000000000000555 -INF INF
ATC: created elementset wire with 8 elements
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
fix_modify AtC mesh create_elementset gap -1000.1000000000000227 $a -${tol} INF -INF INF
fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -${tol} INF -INF INF
fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -0.10000000000000000555 INF -INF INF
ATC: created elementset gap with 8 elements
# void is the complement of the wire nodeset
variable a equal $W-${tol}
variable a equal 1000-${tol}
variable a equal 1000-0.10000000000000000555
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh create_nodeset void -999.89999999999997726 $a ${tol} INF -INF INF
fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 ${tol} INF -INF INF
fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 0.10000000000000000555 INF -INF INF
ATC: created nodeset void with 10 nodes
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial temperature all 20
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_temperature all 20
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electron_density all 3.999999999999999819e-06
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC output null_material_ddmFE 100 full_text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
ATC: created nodeset lbc with 5 nodes
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
ATC: created nodeset rbc with 5 nodes
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature lbc 20
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_temperature rbc 20
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electron_density lbc 3.999999999999999819e-06
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
variable m equal 100*10
run $m
run 1000
Setting up run ...
ATC: WARNING: material: [vacuum] cannot find heat_flux
ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_flux
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: material: [vacuum] cannot find electron_heat_capacity
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_temperature> physics and will be treated as null
Memory usage per processor = 0.432121 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4]
0 0 94.264519 12 94.264519 20
100 1.0169871 94.267978 12.000392 94.299245 20.003477
200 1.9957042 94.276498 12.001352 94.329947 20.006513
300 2.9752631 94.289291 12.002784 94.363814 20.009841
400 3.9508462 94.306379 12.004683 94.403041 20.013675
500 4.92396 94.328129 12.007084 94.449527 20.018196
600 5.896678 94.355216 12.010055 94.505534 20.023614
700 7.0118601 94.388659 12.0137 94.573962 20.030199
800 8.0023661 94.429901 12.01817 94.65867 20.03831
900 10.193833 94.480951 12.023673 94.764998 20.048448
1000 11.610713 94.544631 12.030506 94.900724 20.061365
Loop time of 11.6118 on 4 procs for 1000 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00087744 (0.00755644)
Outpt time (%) = 0.0343485 (0.295807)
Other time (%) = 11.5766 (99.6966)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

41
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LAMMPS (14 Aug 2013)
Lattice spacing in x,y,z = 1 1 1
Created orthogonal box = (0 0 0) to (10 1 1)
4 by 1 by 1 MPI processor grid
ATC: constructing drift_diffusion coupling with parameter file Si_ddm.mat
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from Si_ddm.mat
ATC: creating drift_diffusion extrinsic model
ATC: 1 materials defined from Si_ddm.mat
ATC: 1 materials defined from Si_ddm.mat
ATC: created uniform mesh with 164 nodes, 41 unique nodes, and 40 elements
ATC: created nodeset lbc with 1 nodes
ATC: created faceset rbc with 1 faces
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
Setting up run ...
Memory usage per processor = 0.416939 Mbytes
Step CPU
0 0
1 0.12138891
Loop time of 0.132908 on 4 procs for 1 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 2.08616e-06 (0.00156963)
Outpt time (%) = 0.0033738 (2.53845)
Other time (%) = 0.129532 (97.46)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

109
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LAMMPS (14 Aug 2013)
variable nx equal 80 # 80 # 40
variable ny equal ${nx}
variable ny equal 80
variable nz equal 1
variable h equal 1.0
variable l equal -$h
variable l equal -1
variable u equal $h
variable u equal 1
#variable l equal -$h*${nx}
#variable u equal $h*${nx}
variable T equal 300
variable n0 equal 0.005
variable S equal 1
variable V equal 5.
# STEP THE GATE VOLTAGE UP
atom_style atomic
timestep 0.0
boundary f f f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region BOX block $l $u $l $u 0 1
region BOX block -1 $u $l $u 0 1
region BOX block -1 1 $l $u 0 1
region BOX block -1 1 -1 $u 0 1
region BOX block -1 1 -1 1 0 1
create_box 1 BOX
Created orthogonal box = (-1.5874 -1.5874 0) to (1.5874 1.5874 1.5874)
2 by 2 by 1 MPI processor grid
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion CNT_ddm.mat
ATC: constructing drift_diffusion coupling with parameter file CNT_ddm.mat
ATC: peratom PE compute created with ID: 3
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from CNT_ddm.mat
ATC: creating drift_diffusion extrinsic model
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from CNT_ddm.mat
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from CNT_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 80 ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 80 80 ${nz} BOX f f p
fix_modify AtC mesh create 80 80 1 BOX f f p
ATC: created uniform mesh with 13122 nodes, 6561 unique nodes, and 6400 elements
#fix_modify AtC extrinsic poisson_solver iterative
# boundary conditions
variable a equal $l-0.1
variable a equal -1-0.1
variable b equal $l+0.1
variable b equal -1+0.1
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -1.1000000000000000888 $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -1.1000000000000000888 -0.9000000000000000222 -INF INF
ATC: created nodeset bot with 324 nodes
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc -1.1000000000000000888 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc -1.1000000000000000888 -0.9000000000000000222 -INF INF -INF INF
ATC: created nodeset rbc with 324 nodes
variable a equal $u-0.1
variable a equal 1-0.1
variable b equal $u+0.1
variable b equal 1+0.1
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 0.9000000000000000222 $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 0.9000000000000000222 1.1000000000000000888 -INF INF
ATC: created nodeset top with 324 nodes
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc 0.9000000000000000222 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc 0.9000000000000000222 1.1000000000000000888 -INF INF -INF INF
ATC: created nodeset lbc with 324 nodes
variable a equal -0.1
variable b equal 0.1
fix_modify AtC mesh create_nodeset origin -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset origin -INF INF -0.10000000000000000555 $b -INF INF
fix_modify AtC mesh create_nodeset origin -INF INF -0.10000000000000000555 0.10000000000000000555 -INF INF
ATC: created nodeset origin with 648 nodes
variable a equal -2*$h
variable a equal -2*1
variable b equal 2*$h
variable b equal 2*1
variable a equal -8*$h
variable a equal -8*1
variable b equal 8*$h
variable b equal 8*1
fix_modify AtC mesh create_elementset wire -INF INF $a $b -INF INF
fix_modify AtC mesh create_elementset wire -INF INF -8 $b -INF INF
fix_modify AtC mesh create_elementset wire -INF INF -8 8 -INF INF
ATC: created elementset wire with 6400 elements
fix_modify AtC material wire C
# simplify
fix_modify AtC internal_quadrature off
fix_modify AtC control thermal none
fix_modify AtC extrinsic electron_integration explicit 1
fix_modify AtC extrinsic poisson_solver iterative
ERROR: Illegal fix_modify command (../fix.cpp:104)

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LAMMPS (14 Aug 2013)
#variable iter equal 2 # need two for potential to affect density
variable iter1 equal 4 # NOTE <<<<
variable iter2 equal 25 # NOTE <<<<
variable r equal 1
variable nx equal 12 # 30 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 12 # 30 40
variable my equal 8 # 12 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable hy equal 1*${nx}/${ny}
variable hy equal 1*12/${ny}
variable hy equal 1*12/12
variable l equal -${hx}*${nx}
variable l equal -1*${nx}
variable l equal -1*12
variable u equal ${hx}*${nx}
variable u equal 1*${nx}
variable u equal 1*12
variable w equal ${hy}*${my}
variable w equal 1*${my}
variable w equal 1*8
variable q equal ${hx}*${mx}
variable q equal 1*${mx}
variable q equal 1*4
variable y equal ${nx}+1-${mx}
variable y equal 12+1-${mx}
variable y equal 12+1-4
variable T equal 300
variable S equal 1
variable n0 equal 0.00007
variable J0 equal 40.0 # 100.0 40.0
variable Vs equal 1.0
#variable Vg equal 1.0 # 10.0 0.0
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region BOX block ${l} ${u} ${l} ${u} 0 1
region BOX block -12 ${u} ${l} ${u} 0 1
region BOX block -12 12 ${l} ${u} 0 1
region BOX block -12 12 -12 ${u} 0 1
region BOX block -12 12 -12 12 0 1
create_box 1 BOX
Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874)
2 by 2 by 1 MPI processor grid
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat
ATC: peratom PE compute created with ID: 3
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
ATC: creating drift_diffusion extrinsic model
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 12 12 ${nz} BOX f f p
fix_modify AtC mesh create 12 12 1 BOX f f p
ATC: created uniform mesh with 338 nodes, 169 unique nodes, and 144 elements
# surfaces & regions
variable a equal $l-${tol}
variable a equal -12-${tol}
variable a equal -12-0.010000000000000000208
variable b equal $l+$q+${tol}
variable b equal -12+$q+${tol}
variable b equal -12+4+${tol}
variable b equal -12+4+0.010000000000000000208
variable c equal -$w-${tol}
variable c equal -8-${tol}
variable c equal -8-0.010000000000000000208
variable d equal $w+${tol}
variable d equal 8+${tol}
variable d equal 8+0.010000000000000000208
variable e equal $l+$q-${tol}
variable e equal -12+$q-${tol}
variable e equal -12+4-${tol}
variable e equal -12+4-0.010000000000000000208
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 -7.9900000000000002132 -INF INF
ATC: created nodeset bot with 39 nodes
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 -7.9900000000000002132 -INF INF -INF INF
ATC: created nodeset lbc with 39 nodes
variable a equal $u-$q-${tol}
variable a equal 12-$q-${tol}
variable a equal 12-4-${tol}
variable a equal 12-4-0.010000000000000000208
variable b equal $u+${tol}
variable b equal 12+${tol}
variable b equal 12+0.010000000000000000208
variable e equal $u-$q+${tol}
variable e equal 12-$q+${tol}
variable e equal 12-4+${tol}
variable e equal 12-4+0.010000000000000000208
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 12.009999999999999787 -INF INF
ATC: created nodeset top with 39 nodes
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 12.009999999999999787 -INF INF -INF INF
ATC: created nodeset rbc with 39 nodes
variable a equal -$w-${tol}
variable a equal -8-${tol}
variable a equal -8-0.010000000000000000208
variable b equal $w+${tol}
variable b equal 8+${tol}
variable b equal 8+0.010000000000000000208
variable c equal $l+$q-${tol}
variable c equal -12+$q-${tol}
variable c equal -12+4-${tol}
variable c equal -12+4-0.010000000000000000208
variable d equal $u-$q+${tol}
variable d equal 12-$q+${tol}
variable d equal 12-4+${tol}
variable d equal 12-4+0.010000000000000000208
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created elementset wire with 64 elements
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset wire with 81 nodes
variable e equal $c+2*${tol}
variable e equal -8.0099999999999997868+2*${tol}
variable e equal -8.0099999999999997868+2*0.010000000000000000208
variable f equal $c+${tol}
variable f equal -8.0099999999999997868+${tol}
variable f equal -8.0099999999999997868+0.010000000000000000208
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset lwire with 9 nodes
fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF $a $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created faceset lwire with 8 faces
variable e equal $d-2*${tol}
variable e equal 8.0099999999999997868-2*${tol}
variable e equal 8.0099999999999997868-2*0.010000000000000000208
variable f equal $d-${tol}
variable f equal 8.0099999999999997868-${tol}
variable f equal 8.0099999999999997868-0.010000000000000000208
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset rwire with 9 nodes
fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created faceset rwire with 8 faces
variable e equal $a+2*${tol}
variable e equal -8.0099999999999997868+2*${tol}
variable e equal -8.0099999999999997868+2*0.010000000000000000208
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 -7.9900000000000002132 -INF INF
ATC: created nodeset bwire with 9 nodes
variable e equal $b-2*${tol}
variable e equal 8.0099999999999997868-2*${tol}
variable e equal 8.0099999999999997868-2*0.010000000000000000208
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 8.0099999999999997868 -INF INF
ATC: created nodeset twire with 9 nodes
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
fix_modify AtC extrinsic one_dimensional x wire 9
ERROR: Illegal fix_modify command (../fix.cpp:104)

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LAMMPS (14 Aug 2013)
#variable iter equal 2 # need two for potential to affect density
variable iter1 equal 4 # NOTE <<<<
variable iter2 equal 25 # NOTE <<<<
variable r equal 1
variable nx equal 12 # 30 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 12 # 30 40
variable my equal 8 # 12 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable hy equal 1*${nx}/${ny}
variable hy equal 1*12/${ny}
variable hy equal 1*12/12
variable l equal -${hx}*${nx}
variable l equal -1*${nx}
variable l equal -1*12
variable u equal ${hx}*${nx}
variable u equal 1*${nx}
variable u equal 1*12
variable w equal ${hy}*${my}
variable w equal 1*${my}
variable w equal 1*8
variable q equal ${hx}*${mx}
variable q equal 1*${mx}
variable q equal 1*4
variable y equal ${nx}+1-${mx}
variable y equal 12+1-${mx}
variable y equal 12+1-4
variable T equal 300
variable S equal 1
variable n0 equal 0.00007
variable v0 equal 1000.0
variable J0 equal ${n0}*${v0}
variable J0 equal 6.9999999999999993868e-05*${v0}
variable J0 equal 6.9999999999999993868e-05*1000
print "prescribed flux: ${J0}"
prescribed flux: 0.069999999999999992784
variable Vs equal 1.0
#variable Vg equal 1.0 # 10.0 0.0
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region BOX block ${l} ${u} ${l} ${u} 0 1
region BOX block -12 ${u} ${l} ${u} 0 1
region BOX block -12 12 ${l} ${u} 0 1
region BOX block -12 12 -12 ${u} 0 1
region BOX block -12 12 -12 12 0 1
create_box 1 BOX
Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874)
2 by 2 by 1 MPI processor grid
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion-schrodinger SiVacuum_cddm_schrodinger.mat
ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file SiVacuum_cddm_schrodinger.mat
ATC: peratom PE compute created with ID: 3
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat
ATC: creating convective_drift_diffusion extrinsic model
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 12 12 ${nz} BOX f f p
fix_modify AtC mesh create 12 12 1 BOX f f p
ATC: created uniform mesh with 338 nodes, 169 unique nodes, and 144 elements
# surfaces & regions
variable a equal $l-${tol}
variable a equal -12-${tol}
variable a equal -12-0.010000000000000000208
variable b equal $l+$q+${tol}
variable b equal -12+$q+${tol}
variable b equal -12+4+${tol}
variable b equal -12+4+0.010000000000000000208
variable c equal -$w-${tol}
variable c equal -8-${tol}
variable c equal -8-0.010000000000000000208
variable d equal $w+${tol}
variable d equal 8+${tol}
variable d equal 8+0.010000000000000000208
variable e equal $l+$q-${tol}
variable e equal -12+$q-${tol}
variable e equal -12+4-${tol}
variable e equal -12+4-0.010000000000000000208
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 -7.9900000000000002132 -INF INF
ATC: created nodeset bot with 39 nodes
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 -7.9900000000000002132 -INF INF -INF INF
ATC: created nodeset lbc with 39 nodes
variable a equal $u-$q-${tol}
variable a equal 12-$q-${tol}
variable a equal 12-4-${tol}
variable a equal 12-4-0.010000000000000000208
variable b equal $u+${tol}
variable b equal 12+${tol}
variable b equal 12+0.010000000000000000208
variable e equal $u-$q+${tol}
variable e equal 12-$q+${tol}
variable e equal 12-4+${tol}
variable e equal 12-4+0.010000000000000000208
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 12.009999999999999787 -INF INF
ATC: created nodeset top with 39 nodes
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 12.009999999999999787 -INF INF -INF INF
ATC: created nodeset rbc with 39 nodes
variable a equal -$w-${tol}
variable a equal -8-${tol}
variable a equal -8-0.010000000000000000208
variable b equal $w+${tol}
variable b equal 8+${tol}
variable b equal 8+0.010000000000000000208
variable c equal $l+$q-${tol}
variable c equal -12+$q-${tol}
variable c equal -12+4-${tol}
variable c equal -12+4-0.010000000000000000208
variable d equal $u-$q+${tol}
variable d equal 12-$q+${tol}
variable d equal 12-4+${tol}
variable d equal 12-4+0.010000000000000000208
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created elementset wire with 64 elements
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset wire with 81 nodes
variable e equal $c+2*${tol}
variable e equal -8.0099999999999997868+2*${tol}
variable e equal -8.0099999999999997868+2*0.010000000000000000208
variable f equal $c+${tol}
variable f equal -8.0099999999999997868+${tol}
variable f equal -8.0099999999999997868+0.010000000000000000208
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset lwire with 9 nodes
fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF $a $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created faceset lwire with 8 faces
variable e equal $d-2*${tol}
variable e equal 8.0099999999999997868-2*${tol}
variable e equal 8.0099999999999997868-2*0.010000000000000000208
variable f equal $d-${tol}
variable f equal 8.0099999999999997868-${tol}
variable f equal 8.0099999999999997868-0.010000000000000000208
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created nodeset rwire with 9 nodes
fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 $a $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 $b -INF INF
fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 8.0099999999999997868 -INF INF
ATC: created faceset rwire with 8 faces
variable e equal $a+2*${tol}
variable e equal -8.0099999999999997868+2*${tol}
variable e equal -8.0099999999999997868+2*0.010000000000000000208
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $e -INF INF
fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 -7.9900000000000002132 -INF INF
ATC: created nodeset bwire with 9 nodes
variable e equal $b-2*${tol}
variable e equal 8.0099999999999997868-2*${tol}
variable e equal 8.0099999999999997868-2*0.010000000000000000208
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 $b -INF INF
fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 8.0099999999999997868 -INF INF
ATC: created nodeset twire with 9 nodes
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
fix_modify AtC extrinsic one_dimensional x wire 9
ERROR: Illegal fix_modify command (../fix.cpp:104)

191
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LAMMPS (14 Aug 2013)
#variable iter equal 2 # need two for potential to affect density
variable iter equal 1 # NOTE <<<<
variable r equal 1
variable nx equal 30 # 30 # 40 10
variable mx equal 4 # 4 2
#variable ny equal ${nx}
variable ny equal 30 # 40
variable my equal 12 # 6
variable nz equal 1
variable hx equal 1.0
variable hy equal ${hx}*${nx}/${ny}
variable hy equal 1*${nx}/${ny}
variable hy equal 1*30/${ny}
variable hy equal 1*30/30
variable l equal -${hx}*${nx}
variable l equal -1*${nx}
variable l equal -1*30
variable u equal ${hx}*${nx}
variable u equal 1*${nx}
variable u equal 1*30
variable w equal ${hy}*${my}
variable w equal 1*${my}
variable w equal 1*12
variable q equal ${hx}*${mx}
variable q equal 1*${mx}
variable q equal 1*4
variable y equal ${nx}+1-${mx}
variable y equal 30+1-${mx}
variable y equal 30+1-4
variable T equal 300
variable E equal 0.1
variable S equal 1
variable n0 equal 0.01
variable V equal 5.
variable tol equal 0.01
#################################################
atom_style atomic
timestep 0.001
boundary f f f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region BOX block ${l} ${u} ${l} ${u} 0 1
region BOX block -30 ${u} ${l} ${u} 0 1
region BOX block -30 30 ${l} ${u} 0 1
region BOX block -30 30 -30 ${u} 0 1
region BOX block -30 30 -30 30 0 1
create_box 1 BOX
Created orthogonal box = (-47.622 -47.622 0) to (47.622 47.622 1.5874)
2 by 2 by 1 MPI processor grid
mass * 12.01
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat
ATC: peratom PE compute created with ID: 3
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
ATC: creating drift_diffusion extrinsic model
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
ATC: WARNING: material units metal do not match lammps
ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 30 ${ny} ${nz} BOX f f p
fix_modify AtC mesh create 30 30 ${nz} BOX f f p
fix_modify AtC mesh create 30 30 1 BOX f f p
ATC: created uniform mesh with 1922 nodes, 961 unique nodes, and 900 elements
# surfaces & regions
variable a equal $l-${tol}
variable a equal -30-${tol}
variable a equal -30-0.010000000000000000208
variable b equal $l+$q+${tol}
variable b equal -30+$q+${tol}
variable b equal -30+4+${tol}
variable b equal -30+4+0.010000000000000000208
variable c equal -$w-${tol}
variable c equal -12-${tol}
variable c equal -12-0.010000000000000000208
variable d equal $w+${tol}
variable d equal 12+${tol}
variable d equal 12+0.010000000000000000208
variable e equal $l+$q-${tol}
variable e equal -30+$q-${tol}
variable e equal -30+4-${tol}
variable e equal -30+4-0.010000000000000000208
fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 $b -INF INF
fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 -25.989999999999998437 -INF INF
ATC: created nodeset bot with 93 nodes
fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 -25.989999999999998437 -INF INF -INF INF
ATC: created nodeset lbc with 93 nodes
variable a equal $u-$q-${tol}
variable a equal 30-$q-${tol}
variable a equal 30-4-${tol}
variable a equal 30-4-0.010000000000000000208
variable b equal $u+${tol}
variable b equal 30+${tol}
variable b equal 30+0.010000000000000000208
variable e equal $u-$q+${tol}
variable e equal 30-$q+${tol}
variable e equal 30-4+${tol}
variable e equal 30-4+0.010000000000000000208
fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 $b -INF INF
fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 30.010000000000001563 -INF INF
ATC: created nodeset top with 93 nodes
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 $b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 30.010000000000001563 -INF INF -INF INF
ATC: created nodeset rbc with 93 nodes
variable a equal -$w-${tol}
variable a equal -12-${tol}
variable a equal -12-0.010000000000000000208
variable b equal $w+${tol}
variable b equal 12+${tol}
variable b equal 12+0.010000000000000000208
variable c equal $l+$q-${tol}
variable c equal -30+$q-${tol}
variable c equal -30+4-${tol}
variable c equal -30+4-0.010000000000000000208
variable d equal $u-$q+${tol}
variable d equal 30-$q+${tol}
variable d equal 30-4+${tol}
variable d equal 30-4+0.010000000000000000208
fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -26.010000000000001563 $d $a $b -INF INF
fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF
fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
ATC: created elementset wire with 312 elements
fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -26.010000000000001563 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF
fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
ATC: created nodeset wire with 351 nodes
variable e equal $c+2*${tol}
variable e equal -26.010000000000001563+2*${tol}
variable e equal -26.010000000000001563+2*0.010000000000000000208
fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 $e $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 $a $b -INF INF
fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 12.009999999999999787 -INF INF
ATC: created nodeset lwire with 13 nodes
variable e equal $d-2*${tol}
variable e equal 26.010000000000001563-2*${tol}
variable e equal 26.010000000000001563-2*0.010000000000000000208
fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 $d $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 $a $b -INF INF
fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 $b -INF INF
fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
ATC: created nodeset rwire with 13 nodes
variable e equal $a+2*${tol}
variable e equal -12.009999999999999787+2*${tol}
variable e equal -12.009999999999999787+2*0.010000000000000000208
fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 $d $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 $a $e -INF INF
fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $e -INF INF
fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 -11.990000000000000213 -INF INF
ATC: created nodeset bwire with 27 nodes
variable e equal $b-2*${tol}
variable e equal 12.009999999999999787-2*${tol}
variable e equal 12.009999999999999787-2*0.010000000000000000208
fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -26.010000000000001563 $d $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 $e $b -INF INF
fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 $b -INF INF
fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 12.009999999999999787 -INF INF
ATC: created nodeset twire with 27 nodes
# new material
fix_modify AtC material wire Si
# simplify
fix_modify AtC extrinsic one_dimensional x wire $y
fix_modify AtC extrinsic one_dimensional x wire 27
ERROR: Illegal fix_modify command (../fix.cpp:104)

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echo both
### PARAMETERS -----------------------------------------------
# NOTE: dislocation and stacking fault formation occurs
# at frame 21
variable frame equal 21
log eam_tension_frame.log
variable origLx equal 10 # 10 40
variable Ly equal 10 # 10 40
variable Lz equal 3 # 3 4 5
variable hx equal 10 # 4 10 20
variable hy equal 10 # 4 10 20
variable L equal 2
variable tol equal 1.e-4
variable n equal 25 # 2 25 20
variable delta equal 0.005*${origLx}
variable totdelta equal ${delta}*${frame}
variable Lx equal ${origLx}+${totdelta}
variable alat equal 4.08
variable Rc equal (${origLx}/${hx}+${Ly}/${hy})*${alat}
variable rtol equal 0.5*(1.0+1.0/sqrt(2.0))*${alat}
### ----------------------------------------------------------
boundary p p p
atom_style atomic
units metal
dimension 3
# create system
lattice fcc ${alat} origin 0.01 0.01 0.01 orient x 1 1 0 orient y 0 0 1 orient z 1 -1 0
region SYSTEM block -${Lx} ${Lx} -${Ly} ${Ly} 0 ${Lz}
region REFSYSTEM block -${origLx} ${origLx} -${Ly} ${Ly} 0 ${Lz}
read_data eam_tension_${frame}.data
group internal region SYSTEM
pair_style eam/alloy
pair_coeff * * au2.set Au Au
# define "roller" region
variable a equal -${Ly}+$L
region ROLLER1 block INF INF INF $a INF INF
variable a equal ${Ly}-$L
region ROLLER2 block INF INF $a INF INF INF
region ROLLER union 2 ROLLER1 ROLLER2
group ROLLER region ROLLER
fix ROLLER ROLLER setforce NULL 0.0 NULL
group free subtract internal ROLLER
neighbor 1.0 bin
neigh_modify delay 1000000
atom_modify sort 0 1
thermo 20
variable pe equal pe/count(all)
thermo_style custom step cpu pe press lx v_pe
timestep 0.0
fix PK1 internal atc hardy
fix_modify PK1 kernel quartic_cylinder ${Rc}
fix_modify PK1 mesh create ${hx} ${hy} 1 SYSTEM f p p
fix_modify PK1 reset_atomic_reference_positions eam_tension_0.data
fix_modify PK1 set reference_potential_energy
fix_modify PK1 atom_element_map eulerian 1
fix_modify PK1 fields add mass_density energy displacement
fix_modify PK1 fields add dislocation_density
fix_modify PK1 output eam_tension_frameFE 1 text binary tensor_components
fix_modify PK1 output index step
fix_modify PK1 on_the_fly bond on
fix_modify PK1 dxa_exact_mode on
variable u1 atom x-f_PK1[1]
variable u2 atom y-f_PK1[2]
variable u3 atom z-f_PK1[3]
compute CS all centro/atom fcc
compute CNA all cna/atom ${rtol}
dump CONFIG all custom 1 eam_tension_frame.dump id type x y z v_u1 v_u2 v_u3 c_CS c_CNA
# fix myDXA all dxa 1 ${rtol} eam_tension_frame${frame}.dxa # NOTE: dxa fix is NOT needed to use within ATC
run 1

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echo both
### PARAMETERS -----------------------------------------------
# NOTE: dislocation and stacking fault formation occurs
# at frame 21
variable frame equal 21
log eam_tension_mesh_frame.log
variable origLx equal 10 # 10 40
variable Ly equal 10 # 10 40
variable Lz equal 3 # 3 4 5
variable hx equal 10 # 4 10 20
variable hy equal 10 # 4 10 20
variable L equal 2
variable tol equal 1.e-4
variable n equal 25 # 2 25 20
variable delta equal 0.005*${origLx}
variable totdelta equal ${delta}*${frame}
variable Lx equal ${origLx}+${totdelta}
variable alat equal 4.08
variable rtol equal 0.5*(1.0+1.0/sqrt(2.0))*${alat}
### ----------------------------------------------------------
boundary p p p
atom_style atomic
units metal
dimension 3
# create system
lattice fcc ${alat} origin 0.01 0.01 0.01 orient x 1 1 0 orient y 0 0 1 orient z 1 -1 0
region SYSTEM block -${Lx} ${Lx} -${Ly} ${Ly} 0 ${Lz}
region REFSYSTEM block -${origLx} ${origLx} -${Ly} ${Ly} 0 ${Lz}
read_data eam_tension_${frame}.data
group internal region SYSTEM
pair_style eam/alloy
pair_coeff * * au2.set Au Au
# define "roller" region
variable a equal -${Ly}+$L
region ROLLER1 block INF INF INF $a INF INF
variable a equal ${Ly}-$L
region ROLLER2 block INF INF $a INF INF INF
region ROLLER union 2 ROLLER1 ROLLER2
group ROLLER region ROLLER
fix ROLLER ROLLER setforce NULL 0.0 NULL
group free subtract internal ROLLER
neighbor 1.0 bin
neigh_modify delay 1000000
atom_modify sort 0 1
thermo 20
variable pe equal pe/count(all)
thermo_style custom step cpu pe press lx v_pe
timestep 0.0
fix PK1 internal atc field
fix_modify PK1 mesh create ${hx} ${hy} 1 SYSTEM p p p
fix_modify PK1 reset_atomic_reference_positions eam_tension_0.data
fix_modify PK1 set reference_potential_energy
fix_modify PK1 atom_element_map eulerian 1
fix_modify PK1 fields add mass_density energy displacement
fix_modify PK1 fields add dislocation_density
fix_modify PK1 output eam_tension_mesh_frameFE 1 text binary tensor_components
fix_modify PK1 output index step
# fix_modify PK1 on_the_fly bond on
fix_modify PK1 dxa_exact_mode on
variable u1 atom x-f_PK1[1]
variable u2 atom y-f_PK1[2]
variable u3 atom z-f_PK1[3]
compute CS all centro/atom fcc
compute CNA all cna/atom ${rtol}
dump CONFIG all custom 1 eam_tension_mesh_frame.dump id type x y z v_u1 v_u2 v_u3 c_CS c_CNA
# fix myDXA all dxa 1 ${rtol} eam_tension_mesh_frame${frame}.dxa # NOTE: dxa fix is NOT needed to use within ATC
run 1

8
examples/USER/atc/elastic/Ar_CauchyBorn.mat Normal file
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@ -0,0 +1,8 @@
material Ar real
stress cauchy-born
pair_style lj/cut 13.5 #pair_style lj/cut r_cut
pair_coeff 0.238 3.405 #pair_coeff epsilon sigma
end
mass_density
body_force
end

9
examples/USER/atc/elastic/Ar_CauchyBornLinear.mat Normal file
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@ -0,0 +1,9 @@
material Ar real
stress cauchy-born
pair_style lj/cut 13.5 #pair_style lj/cut r_cut
pair_coeff 0.238 3.405 #pair_coeff epsilon sigma
linear
end
mass_density
body_force
end

37
examples/USER/atc/elastic/Ar_damped.mat Normal file
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@ -0,0 +1,37 @@
material Ar metal
stress linear
modulus 0.00025e6
possions_ratio 0.25
end
mass_density constant
density 1.01202
end
body_force
end
material cubic metal
stress cubic
c11 0.00030e6
c12 0.00010e6
c44 0.00010e6
end
mass_density constant
density 1.01202
end
body_force viscous
gamma 1e0
end
end
material damped metal
stress damped_cubic
c11 0.00030e6
c12 0.00010e6
c44 0.00010e6
gamma 0.1e3
end
mass_density constant
density 1.01202
end
body_force
end

29
examples/USER/atc/elastic/Ar_elastic.mat Normal file
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@ -0,0 +1,29 @@
material Ar real
stress linear
modulus 0.00025
possions_ratio 0.25
end
mass_density
body_force
end
material cubic real
stress cubic
c11 0.00030
c12 0.00010
c44 0.00010
end
mass_density
body_force
end
material damped real
stress damped_cubic
c11 0.00030
c12 0.00010
c44 0.00010
gamma 0.1
end
mass_density
body_force
end

11
examples/USER/atc/elastic/Ar_thermo_elastic.mat Normal file
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@ -0,0 +1,11 @@
material Ar real
stress linear
modulus 0.00025
possions_ratio 0.25
end
heat_flux linear
conductivity .00000000168
end
mass_density
body_force
end

18
examples/USER/atc/elastic/Au_elastic.mat Normal file
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@ -0,0 +1,18 @@
material Au metal
stress cauchy-born
pair_style eam
#linear
end
mass_density
body_force
end
material Au_cubic metal
stress cubic
c11 11020.5189657531
c12 9575.20500303137
c44 2709.96368010322
end
mass_density
body_force
end

1315
examples/USER/atc/elastic/CNT.mat Normal file
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File diff suppressed because it is too large Load Diff

18
examples/USER/atc/elastic/CNT_electrostatic.mat Normal file
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@ -0,0 +1,18 @@
material CNT metal
stress linear
modulus 0.00025
possions_ratio 0.25
end
electric_field linear
permittivity 1.0
end
##electron_density identity
##end
mass_density
#electron_density exponential
# intrinsic_concentration 0.0001
# intrinsic_energy 1.0
# reference_temperature 300
#end
body_force
end

20
examples/USER/atc/elastic/CNT_electrostatic2.mat Normal file
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@ -0,0 +1,20 @@
material CNT metal
stress linear
modulus 0.0
possions_ratio 0.25
end
electric_field linear
permittivity 1.0
end
electron_density linear
coefficient -1.e-2 # NOTE will not converge with +0.01, try smaller pos
end
mass_density
#electron_density interpolation
# number_of_points 3
# 0 0 1.e-4
# 1.e0 1.e-4 1.e-4
# 3.e0 3.e-4 1.e-4
#end
body_force
end

11
examples/USER/atc/elastic/CNT_id.mat Normal file
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@ -0,0 +1,11 @@
material CNT0 metal
stress linear
modulus 0.00025
possions_ratio 0.25
end
electric_field linear
permittivity 1.0
end
mass_density
body_force
end

269
examples/USER/atc/elastic/bar1d.screen Normal file
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.01202
ATC: computed mass density : 1.01202
ATC: computed mass density : 1.01202
ATC: 3 materials defined from Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 93.2479 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4406.6687 0 -4406.6687 -1155.1752
100 3.8434911e-14 -4406.6687 0 -4406.6687 -1155.1752
200 2.634669e-11 -4406.6687 0 -4406.6687 -1155.1754
300 6.909135e-10 -4406.6685 0 -4406.6685 -1155.1763
400 3.9413859e-09 -4406.6682 0 -4406.6682 -1155.1783
500 8.5603227e-09 -4406.6676 0 -4406.6676 -1155.181
600 1.0143684e-08 -4406.6671 0 -4406.6671 -1155.1835
700 9.8473676e-09 -4406.6667 0 -4406.6667 -1155.1854
800 9.9628095e-09 -4406.6663 0 -4406.6663 -1155.1871
900 1.1034555e-08 -4406.6659 0 -4406.6659 -1155.189
1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191
Loop time of 71.7602 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 8.28353 (11.5433)
Neigh time (%) = 4.8737 (6.79165)
Comm time (%) = 23.4869 (32.7296)
Outpt time (%) = 0.14537 (0.202577)
Other time (%) = 34.9708 (48.7328)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288628 max 68417 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# run to equilibrium
timestep 5
thermo 100
run 10000
Setting up run ...
Memory usage per processor = 93.2479 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191
1100 1.3961782e-08 -4406.665 0 -4406.665 -1155.1929
1200 1.4156541e-08 -4406.6646 0 -4406.6646 -1155.1947
1300 1.1743161e-08 -4406.6643 0 -4406.6643 -1155.1961
1400 7.6261191e-09 -4406.6643 0 -4406.6643 -1155.1964
1500 5.4918861e-09 -4406.6644 0 -4406.6644 -1155.1955
1600 3.2067753e-09 -4406.6647 0 -4406.6647 -1155.1942
1700 1.5798693e-09 -4406.6649 0 -4406.6649 -1155.1933
1800 3.4267061e-09 -4406.6649 0 -4406.6649 -1155.1932
1900 5.7984811e-09 -4406.6649 0 -4406.6649 -1155.1934
2000 4.4702416e-09 -4406.6648 0 -4406.6648 -1155.1937
2100 4.110363e-09 -4406.6647 0 -4406.6647 -1155.1943
2200 7.7448231e-09 -4406.6646 0 -4406.6646 -1155.1949
2300 8.9174139e-09 -4406.6645 0 -4406.6645 -1155.1953
2400 4.2475131e-09 -4406.6645 0 -4406.6645 -1155.1951
2500 3.9593952e-09 -4406.6646 0 -4406.6646 -1155.1947
2600 5.0490897e-09 -4406.6646 0 -4406.6646 -1155.1945
2700 3.0091882e-09 -4406.6645 0 -4406.6645 -1155.195
2800 2.8396053e-09 -4406.6644 0 -4406.6644 -1155.1955
2900 3.3590465e-09 -4406.6644 0 -4406.6644 -1155.1957
3000 2.6186659e-09 -4406.6644 0 -4406.6644 -1155.1955
3100 2.8276402e-09 -4406.6645 0 -4406.6645 -1155.1953
3200 3.3651448e-09 -4406.6645 0 -4406.6645 -1155.195
3300 4.8200774e-09 -4406.6647 0 -4406.6647 -1155.1944
3400 2.7178e-09 -4406.6648 0 -4406.6648 -1155.1938
3500 2.8250408e-09 -4406.6648 0 -4406.6648 -1155.1938
3600 4.4426525e-09 -4406.6646 0 -4406.6646 -1155.1946
3700 2.3093452e-09 -4406.6644 0 -4406.6644 -1155.1954
3800 1.0139576e-09 -4406.6644 0 -4406.6644 -1155.1958
3900 3.33486e-09 -4406.6644 0 -4406.6644 -1155.1958
4000 3.6153069e-09 -4406.6644 0 -4406.6644 -1155.1956
4100 4.6993593e-10 -4406.6644 0 -4406.6644 -1155.1954
4200 1.1808552e-09 -4406.6645 0 -4406.6645 -1155.1948
4300 3.1059162e-09 -4406.6647 0 -4406.6647 -1155.1942
4400 2.2356994e-09 -4406.6647 0 -4406.6647 -1155.1942
4500 1.0832e-09 -4406.6646 0 -4406.6646 -1155.1947
4600 3.4691005e-09 -4406.6645 0 -4406.6645 -1155.1954
4700 2.6640925e-09 -4406.6644 0 -4406.6644 -1155.1956
4800 1.8105324e-09 -4406.6644 0 -4406.6644 -1155.1954
4900 3.2865681e-09 -4406.6645 0 -4406.6645 -1155.1951
5000 3.2647654e-09 -4406.6645 0 -4406.6645 -1155.1949
5100 1.9703065e-09 -4406.6646 0 -4406.6646 -1155.1947
5200 1.242015e-09 -4406.6646 0 -4406.6646 -1155.1945
5300 3.0457424e-09 -4406.6646 0 -4406.6646 -1155.1946
5400 1.9560942e-09 -4406.6645 0 -4406.6645 -1155.1951
5500 4.3058633e-10 -4406.6644 0 -4406.6644 -1155.1957
5600 2.3184519e-09 -4406.6644 0 -4406.6644 -1155.1957
5700 3.0207566e-09 -4406.6645 0 -4406.6645 -1155.1953
5800 6.8689369e-10 -4406.6646 0 -4406.6646 -1155.1948
5900 1.5170252e-09 -4406.6646 0 -4406.6646 -1155.1946
6000 3.0629191e-09 -4406.6646 0 -4406.6646 -1155.1946
6100 1.842967e-09 -4406.6646 0 -4406.6646 -1155.1945
6200 6.0033688e-10 -4406.6646 0 -4406.6646 -1155.1946
6300 2.0883931e-09 -4406.6645 0 -4406.6645 -1155.1952
6400 1.8269083e-09 -4406.6644 0 -4406.6644 -1155.1957
6500 5.5810474e-10 -4406.6644 0 -4406.6644 -1155.1957
6600 1.7356452e-09 -4406.6645 0 -4406.6645 -1155.1952
6700 2.6958998e-09 -4406.6646 0 -4406.6646 -1155.1947
6800 8.964107e-10 -4406.6646 0 -4406.6646 -1155.1946
6900 1.1426076e-09 -4406.6646 0 -4406.6646 -1155.1947
7000 2.9188626e-09 -4406.6646 0 -4406.6646 -1155.1947
7100 1.8115562e-09 -4406.6645 0 -4406.6645 -1155.1948
7200 7.4087342e-10 -4406.6645 0 -4406.6645 -1155.1952
7300 1.5779154e-09 -4406.6644 0 -4406.6644 -1155.1956
7400 2.7467977e-09 -4406.6644 0 -4406.6644 -1155.1955
7500 4.2123447e-10 -4406.6645 0 -4406.6645 -1155.195
7600 1.1615418e-09 -4406.6646 0 -4406.6646 -1155.1946
7700 2.5380373e-09 -4406.6646 0 -4406.6646 -1155.1945
7800 1.5068282e-09 -4406.6646 0 -4406.6646 -1155.1948
7900 6.0931799e-10 -4406.6645 0 -4406.6645 -1155.195
8000 2.0802965e-09 -4406.6645 0 -4406.6645 -1155.1951
8100 2.1544428e-09 -4406.6645 0 -4406.6645 -1155.1953
8200 4.4375899e-10 -4406.6644 0 -4406.6644 -1155.1955
8300 1.5879866e-09 -4406.6644 0 -4406.6644 -1155.1954
8400 2.1255967e-09 -4406.6645 0 -4406.6645 -1155.1949
8500 8.5066547e-10 -4406.6646 0 -4406.6646 -1155.1945
8600 4.9764713e-10 -4406.6646 0 -4406.6646 -1155.1945
8700 2.4032931e-09 -4406.6646 0 -4406.6646 -1155.1949
8800 1.5506272e-09 -4406.6645 0 -4406.6645 -1155.1951
8900 2.156996e-10 -4406.6645 0 -4406.6645 -1155.1952
9000 1.5053583e-09 -4406.6645 0 -4406.6645 -1155.1953
9100 2.2313062e-09 -4406.6645 0 -4406.6645 -1155.1954
9200 6.5295769e-10 -4406.6645 0 -4406.6645 -1155.1953
9300 7.1214495e-10 -4406.6646 0 -4406.6646 -1155.1949
9400 2.2525879e-09 -4406.6646 0 -4406.6646 -1155.1945
9500 1.2940878e-09 -4406.6646 0 -4406.6646 -1155.1945
9600 3.7619117e-10 -4406.6645 0 -4406.6645 -1155.195
9700 1.9605412e-09 -4406.6645 0 -4406.6645 -1155.1953
9800 1.7828694e-09 -4406.6645 0 -4406.6645 -1155.1953
9900 5.2324205e-10 -4406.6645 0 -4406.6645 -1155.1952
10000 1.1770899e-09 -4406.6645 0 -4406.6645 -1155.1952
10100 2.0621304e-09 -4406.6645 0 -4406.6645 -1155.1951
10200 9.4046414e-10 -4406.6646 0 -4406.6646 -1155.1948
10300 3.3301061e-10 -4406.6646 0 -4406.6646 -1155.1945
10400 2.2075407e-09 -4406.6646 0 -4406.6646 -1155.1946
10500 1.3556476e-09 -4406.6645 0 -4406.6645 -1155.1951
10600 3.1056944e-10 -4406.6645 0 -4406.6645 -1155.1954
10700 1.2113659e-09 -4406.6645 0 -4406.6645 -1155.1953
10800 2.0914266e-09 -4406.6645 0 -4406.6645 -1155.1951
10900 5.1353017e-10 -4406.6645 0 -4406.6645 -1155.1951
11000 5.4707109e-10 -4406.6645 0 -4406.6645 -1155.195
Loop time of 354.654 on 4 procs for 10000 steps with 2304 atoms
Pair time (%) = 67.9127 (19.149)
Neigh time (%) = 31.8455 (8.97932)
Comm time (%) = 122.402 (34.513)
Outpt time (%) = 0.360688 (0.101702)
Other time (%) = 132.133 (37.2569)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 289342 max 67274 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 1000
Dangerous builds = 0

379
examples/USER/atc/elastic/bar1d_damped.screen Normal file
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@ -0,0 +1,379 @@
LAMMPS (14 Aug 2013)
units metal
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 2304 atoms
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
ATC: constructing elastic coupling with parameter file Ar_damped.mat
ATC: peratom PE compute created with ID: 3
ATC: 3 materials defined from Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
variable u equal 4.0000000000000003272e-05*$n*${dt}
variable u equal 4.0000000000000003272e-05*1000*${dt}
variable u equal 4.0000000000000003272e-05*1000*0.0050000000000000001041
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix velocity x rbc 4.0000000000000003272e-05
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
Setting up run ...
Memory usage per processor = 93.2479 Mbytes
Step CPU KinEng PotEng
0 0 0 -191.1377
Loop time of 6.3777e-06 on 4 procs for 0 steps with 2304 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 6.3777e-06 (100)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288576 max 68400 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 0
Dangerous builds = 0
variable pe0 equal pe
variable pe equal pe-${pe0}
variable pe equal pe--191.13770127444766445
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
run 1000
Setting up run ...
Memory usage per processor = 93.2479 Mbytes
Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5]
0 0 0 -191.1377 0 0 0 0 0
100 8.0390151 1.055851e-16 -191.1377 5.3847288e-08 5.5210093e-10 4.8838395e-10 5.5210086e-10 4.8838395e-10
200 11.493128 2.7309802e-13 -191.1377 1.505559e-06 1.1639949e-09 1.2827565e-09 1.1637935e-09 1.2827433e-09
300 19.35353 1.7311896e-11 -191.13769 8.8450898e-06 2.0715862e-09 2.022604e-09 2.0579272e-09 2.020558e-09
400 28.928974 2.1239086e-10 -191.13768 2.6114181e-05 2.9481123e-09 2.7362141e-09 2.7703215e-09 2.6871501e-09
500 33.919009 9.6058596e-10 -191.13765 5.1722206e-05 4.1041211e-09 3.33188e-09 3.253095e-09 2.9376729e-09
600 43.879017 2.2037311e-09 -191.13762 8.020941e-05 5.6140713e-09 4.0767895e-09 3.5687157e-09 2.5638486e-09
700 53.458615 3.2720323e-09 -191.13759 0.00010864588 6.9461579e-09 5.4103466e-09 3.8327109e-09 1.9736115e-09
800 59.149139 3.9667277e-09 -191.13756 0.0001382309 7.930912e-09 7.0706824e-09 4.1286537e-09 1.5663212e-09
900 65.676015 4.6276406e-09 -191.13753 0.00016977721 8.7852e-09 8.6120146e-09 4.3243149e-09 1.3090105e-09
1000 76.426912 5.4647857e-09 -191.1375 0.00020107009 9.4089083e-09 1.0142471e-08 4.111432e-09 1.1470431e-09
Loop time of 76.4282 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 8.25247 (10.7977)
Neigh time (%) = 4.72959 (6.18828)
Comm time (%) = 23.9356 (31.3178)
Outpt time (%) = 0.304101 (0.397891)
Other time (%) = 39.2064 (51.2984)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 289722 max 67420 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
fix_modify AtC output bar1d_dampedFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
fix_modify AtC fix displacement x rbc 0.00020000000000000000958
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
Setting up run ...
Memory usage per processor = 93.4533 Mbytes
Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5]
1000 0 5.4647857e-09 -191.1375 0.00020107009 9.4089083e-09 0 4.111432e-09 -8.9954275e-09
1100 3.4263639 6.3421646e-09 -191.13747 0.00022971709 8.75085e-09 1.4153048e-09 2.5767395e-09 -9.3569477e-09
1200 10.368947 6.9778939e-09 -191.13745 0.00025458471 8.1727552e-09 3.1204783e-09 1.3697518e-09 -9.4201182e-09
1300 14.878477 7.1529752e-09 -191.13743 0.00027170434 7.5897544e-09 4.5095316e-09 6.3357843e-10 -9.4773618e-09
1400 24.373178 6.6395813e-09 -191.13743 0.00027466413 6.747478e-09 5.4996207e-09 2.8850325e-10 -9.1651904e-09
1500 26.945583 5.6922363e-09 -191.13744 0.00026126097 6.2562137e-09 5.3958429e-09 7.4259589e-10 -8.7642657e-09
1600 29.179645 4.7135957e-09 -191.13747 0.00023620822 5.9708984e-09 4.7989197e-09 1.5108282e-09 -8.165151e-09
1700 32.158633 3.4710553e-09 -191.1375 0.00020618074 5.3956633e-09 4.5850559e-09 2.1370382e-09 -7.4317528e-09
1800 34.59477 2.4145542e-09 -191.13753 0.0001751612 4.4014655e-09 4.6172904e-09 2.1438377e-09 -6.2667582e-09
1900 36.481867 2.1438948e-09 -191.13756 0.00014569893 3.408323e-09 4.1360716e-09 1.4726957e-09 -4.5311799e-09
2000 38.402959 2.1864605e-09 -191.13758 0.00012155208 2.5555543e-09 3.2626157e-09 6.5555529e-10 -2.5834443e-09
2100 40.302963 1.9032904e-09 -191.13759 0.00010654531 2.0211043e-09 2.3634891e-09 3.1602374e-10 -1.1813128e-09
2200 42.169921 1.9875147e-09 -191.1376 0.00010189892 2.0066398e-09 1.5638553e-09 1.4805596e-10 -4.8955277e-10
2300 44.033215 3.2414453e-09 -191.13759 0.00010629042 3.4949611e-09 6.0884607e-11 3.7071553e-10 -1.2166095e-09
2400 45.904622 5.4666452e-09 -191.13758 0.00011815334 6.4739473e-09 -2.0744242e-09 1.1628627e-09 -3.4626277e-09
2500 47.797741 7.1143087e-09 -191.13756 0.00013705246 9.1384443e-09 -3.3784529e-09 2.1796903e-09 -5.9902478e-09
2600 51.178232 7.1885602e-09 -191.13754 0.00016288238 1.0502632e-08 -3.4468822e-09 3.4466305e-09 -8.0921646e-09
2700 53.509233 6.4420688e-09 -191.13751 0.00019390227 1.0708869e-08 -2.5391386e-09 4.4412335e-09 -9.5081141e-09
2800 55.372385 5.6029945e-09 -191.13748 0.00022551631 9.3553209e-09 7.5058192e-11 3.8587617e-09 -9.3943471e-09
2900 57.239711 5.099105e-09 -191.13745 0.00025162655 6.936034e-09 3.8584367e-09 1.8989273e-09 -7.959387e-09
3000 59.118431 4.5349913e-09 -191.13743 0.00026783371 5.1180916e-09 6.6034959e-09 6.6351749e-10 -7.0089177e-09
Loop time of 59.1197 on 4 procs for 2000 steps with 2304 atoms
Pair time (%) = 13.3157 (22.5233)
Neigh time (%) = 5.97997 (10.115)
Comm time (%) = 17.5956 (29.7626)
Outpt time (%) = 0.0869119 (0.14701)
Other time (%) = 22.1415 (37.452)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288868 max 65686 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 200
Dangerous builds = 0
fix_modify AtC material all cubic # M damping
run 2000
Setting up run ...
Memory usage per processor = 93.4533 Mbytes
Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5]
3000 0 4.5349913e-09 -191.13743 0.00026783371 5.1180916e-09 0 6.6351749e-10 -1.3612414e-08
3100 1.884902 3.1627635e-09 -191.13743 0.00027166541 3.3508276e-09 1.5163376e-09 2.9822385e-10 -1.3169543e-08
3200 3.7543039 2.1305486e-09 -191.13744 0.00026502967 2.292755e-09 1.9348144e-09 2.9322733e-10 -1.2923953e-08
3300 6.005461 1.7622321e-09 -191.13745 0.00025028487 2.1709597e-09 1.2092749e-09 5.6848039e-10 -1.3098658e-08
3400 16.302727 1.4627886e-09 -191.13747 0.00022947204 2.0542491e-09 2.4241837e-10 7.6881831e-10 -1.3269991e-08
3500 18.647849 1.1457596e-09 -191.13749 0.0002071953 1.7022137e-09 -6.8412058e-10 6.5328081e-10 -1.3186597e-08
3600 20.526815 1.5322847e-09 -191.13751 0.00018851151 1.9578951e-09 -2.5376549e-09 5.0945853e-10 -1.3161338e-08
3700 22.404343 2.7199727e-09 -191.13753 0.00017501297 2.8551124e-09 -5.3147303e-09 3.5995471e-10 -1.317891e-08
3800 24.280314 3.8255198e-09 -191.13754 0.00016517255 3.776711e-09 -7.8091811e-09 1.9270828e-10 -1.3125415e-08
3900 26.155669 4.7080092e-09 -191.13754 0.00015798858 4.6102461e-09 -9.4550009e-09 1.2287245e-10 -1.3138835e-08
4000 28.039841 5.3603485e-09 -191.13755 0.00015424854 5.3157594e-09 -1.0203778e-08 1.5542087e-10 -1.3330611e-08
4100 29.917995 5.3407666e-09 -191.13755 0.00015459539 5.6318354e-09 -1.0223896e-08 3.9327183e-10 -1.3777619e-08
4200 31.791416 4.5200859e-09 -191.13754 0.000158412 5.2283097e-09 -9.7612848e-09 7.3695415e-10 -1.4260955e-08
4300 33.665959 3.248288e-09 -191.13754 0.00016494668 4.2434602e-09 -9.1569844e-09 1.0215962e-09 -1.4755402e-08
4400 35.538211 1.9718426e-09 -191.13753 0.00017370613 3.0004575e-09 -8.5412539e-09 1.0485714e-09 -1.5191473e-08
4500 37.426718 1.0175326e-09 -191.13752 0.00018301345 1.8277045e-09 -8.0355833e-09 8.1451769e-10 -1.5385018e-08
4600 39.941118 4.528091e-10 -191.13751 0.00019011125 8.8800708e-10 -7.698949e-09 4.3848726e-10 -1.5198592e-08
4700 41.926014 1.813047e-10 -191.13751 0.00019345531 3.2820899e-10 -7.6270177e-09 1.6240525e-10 -1.4863017e-08
4800 43.768896 1.0257178e-10 -191.13751 0.00019385828 1.3812287e-10 -7.7900766e-09 5.3812979e-11 -1.4605952e-08
4900 46.766592 1.9853801e-10 -191.13751 0.00019285378 1.955715e-10 -8.0515951e-09 1.5537909e-11 -1.4450335e-08
5000 51.661613 4.4499498e-10 -191.13751 0.00019101535 4.6651548e-10 -8.4263349e-09 3.2542828e-11 -1.4479894e-08
Loop time of 51.6629 on 4 procs for 2000 steps with 2304 atoms
Pair time (%) = 12.642 (24.4702)
Neigh time (%) = 5.57654 (10.7941)
Comm time (%) = 15.4191 (29.8455)
Outpt time (%) = 0.130104 (0.251833)
Other time (%) = 17.8952 (34.6384)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288868 max 65664 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 200
Dangerous builds = 0
fix_modify AtC material all damped # K damping
run 2000
Setting up run ...
Memory usage per processor = 93.4533 Mbytes
Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5]
5000 0 4.4499498e-10 -191.13751 0.00019101535 4.6651548e-10 0 3.2542828e-11 -6.0535591e-09
5100 4.6635571 7.7530221e-10 -191.13751 0.00018808779 8.8219827e-10 -5.1894954e-10 1.1477898e-10 -6.2656816e-09
5200 7.9799862 1.0914185e-09 -191.13752 0.00018469909 1.3356438e-09 -1.1167463e-09 2.5090286e-10 -6.5437879e-09
5300 9.832078 1.3329143e-09 -191.13752 0.00018160964 1.7365431e-09 -1.6964741e-09 4.0718828e-10 -6.8217529e-09
5400 16.735786 1.504171e-09 -191.13752 0.00017917616 1.9911092e-09 -2.1593835e-09 4.9328931e-10 -7.0385998e-09
5500 21.043345 1.594802e-09 -191.13752 0.00017766571 2.0494572e-09 -2.4260642e-09 4.6275872e-10 -7.138857e-09
5600 23.746816 1.5743105e-09 -191.13752 0.00017717238 1.929034e-09 -2.4892277e-09 3.6487504e-10 -7.1146385e-09
5700 25.625748 1.4221294e-09 -191.13752 0.00017729486 1.6665332e-09 -2.3656166e-09 2.5500829e-10 -6.9804167e-09
5800 30.389402 1.1720493e-09 -191.13752 0.00017753363 1.3116581e-09 -2.0608866e-09 1.5433624e-10 -6.7800184e-09
5900 32.585614 8.6077652e-10 -191.13752 0.00017794528 9.2235699e-10 -1.6102419e-09 7.7989231e-11 -6.5963868e-09
6000 35.173423 5.2708656e-10 -191.13752 0.0001789751 5.4942864e-10 -1.0882941e-09 3.5646667e-11 -6.4862104e-09
6100 40.119008 2.325476e-10 -191.13752 0.0001807569 2.4150687e-10 -5.8295363e-10 1.6542883e-11 -6.4439488e-09
6200 41.993394 4.6103001e-11 -191.13752 0.00018302227 5.3284568e-11 -2.125555e-10 9.264294e-12 -6.4611762e-09
6300 45.873721 1.6246443e-11 -191.13752 0.00018541173 2.4386805e-11 -8.566705e-11 9.9387033e-12 -6.5339312e-09
6400 49.424723 1.4744476e-10 -191.13751 0.00018750725 1.5460292e-10 -2.1854704e-10 1.2454671e-11 -6.6323029e-09
6500 52.764808 4.0670554e-10 -191.13751 0.00018887546 4.1540944e-10 -5.5265965e-10 2.0454523e-11 -6.7446848e-09
6600 57.161516 7.1997609e-10 -191.13751 0.00018914788 7.4785363e-10 -9.9312474e-10 4.429436e-11 -6.8751447e-09
6700 60.044641 1.011863e-09 -191.13751 0.00018817658 1.080257e-09 -1.4281411e-09 8.7264316e-11 -7.0103089e-09
6800 63.731949 1.2214055e-09 -191.13751 0.00018635915 1.3481402e-09 -1.7820613e-09 1.4383303e-10 -7.1419056e-09
6900 65.622758 1.3150127e-09 -191.13752 0.00018434046 1.5093341e-09 -2.0332173e-09 2.0695782e-10 -7.2501404e-09
7000 67.990237 1.2853182e-09 -191.13752 0.0001825143 1.5377643e-09 -2.1694031e-09 2.6084212e-10 -7.2971336e-09
Loop time of 67.9915 on 4 procs for 2000 steps with 2304 atoms
Pair time (%) = 13.7916 (20.2843)
Neigh time (%) = 6.20275 (9.12283)
Comm time (%) = 22.365 (32.8938)
Outpt time (%) = 0.24604 (0.361868)
Other time (%) = 25.3861 (37.3372)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288864 max 65670 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 200
Dangerous builds = 0
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 0.75*0.355649e3*0.043360000000000002707
variable m equal 0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 $g $m
fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 11.56570548000000187 $m
fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 11.56570548000000187 19.975000000000001421
run 2000
Setting up run ...
Memory usage per processor = 93.4533 Mbytes
Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5]
7000 0 1.2853182e-09 -191.13752 0.0001825143 1.5377643e-09 0 2.6084212e-10 -5.1277305e-09
7100 3.8653619 2.8903751e-05 -191.1374 0.00029857456 1.4261761e-09 -1.214748e-11 2.7859112e-10 -5.084773e-09
7200 5.7172129 3.8761799e-06 -191.13735 0.00035025356 1.1959825e-09 8.5346682e-11 2.5313036e-10 -4.9584954e-09
7300 7.596113 1.8769484e-06 -191.13737 0.0003337536 8.9086284e-10 2.6798239e-10 2.0084283e-10 -4.7692463e-09
7400 12.42461 1.245935e-05 -191.13743 0.00026909159 5.6202829e-10 5.0489219e-10 1.2878586e-10 -4.5511096e-09
7500 15.114735 1.6301032e-05 -191.13751 0.00018830281 2.7560343e-10 7.5207256e-10 5.694786e-11 -4.362424e-09
7600 19.876048 9.4676227e-06 -191.13758 0.00012208357 8.4877207e-11 9.6782588e-10 1.2617604e-11 -4.2488453e-09
7700 21.707406 1.6567809e-06 -191.13761 8.9858261e-05 1.0099305e-11 1.1176649e-09 1.4916291e-12 -4.2369828e-09
7800 24.205287 3.0391321e-07 -191.13761 9.5611994e-05 5.1427805e-11 1.1674588e-09 1.7611917e-11 -4.3302492e-09
7900 27.866901 3.2726602e-06 -191.13757 0.0001295863 1.905123e-10 1.1057791e-09 4.8229373e-11 -4.4960207e-09
8000 29.84634 4.7851826e-06 -191.13753 0.00017453181 3.9524144e-10 9.4866146e-10 7.738243e-11 -4.6918777e-09
8100 32.731688 3.0560115e-06 -191.13749 0.00021322134 6.2989738e-10 7.2412128e-10 9.7353433e-11 -4.8834384e-09
8200 36.727295 6.6407027e-07 -191.13747 0.00023416094 8.5464088e-10 4.6942869e-10 1.1187578e-10 -5.0480909e-09
8300 38.564577 3.8165674e-08 -191.13747 0.00023410509 1.0268939e-09 2.3847444e-10 1.2118336e-10 -5.1639054e-09
8400 41.031069 8.4495007e-07 -191.13748 0.00021748415 1.1122546e-09 8.8553406e-11 1.2219945e-10 -5.2187642e-09
8500 44.303455 1.3915225e-06 -191.13751 0.0001932998 1.0989984e-09 5.0075534e-11 1.2293817e-10 -5.2142527e-09
8600 46.136877 9.7448077e-07 -191.13753 0.00017115059 9.8587454e-10 1.1774103e-10 1.2176493e-10 -5.1569143e-09
8700 49.565115 2.5400881e-07 -191.13754 0.00015791542 7.9484554e-10 2.5817073e-10 1.1156472e-10 -5.0569238e-09
8800 52.407452 2.6471441e-09 -191.13755 0.00015589474 5.6635938e-10 4.2847179e-10 9.4176403e-11 -4.9223096e-09
8900 54.820348 2.1367306e-07 -191.13754 0.00016308046 3.4009704e-10 5.9208385e-10 7.0443086e-11 -4.7692236e-09
9000 59.598561 4.0089918e-07 -191.13753 0.00017492322 1.5426704e-10 7.172267e-10 4.311796e-11 -4.6253241e-09
Loop time of 59.5999 on 4 procs for 2000 steps with 2304 atoms
Pair time (%) = 13.6404 (22.8866)
Neigh time (%) = 5.86772 (9.84519)
Comm time (%) = 19.3873 (32.5292)
Outpt time (%) = 0.201972 (0.338879)
Other time (%) = 20.5024 (34.4001)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288850 max 65677 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 200
Dangerous builds = 0

280
examples/USER/atc/elastic/bar1d_flux.screen Normal file
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@ -0,0 +1,280 @@
LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: 3 materials defined from Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
ATC: created faceset obndy with 2 faces
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 93.0953 Mbytes
Step myTemp myPres PotEng
0 0 -0.00072339042 -4509.8851
100 1.7485737e-12 -0.00065677838 -4509.8851
200 2.1209236e-12 -0.00058835409 -4509.8851
300 3.1757662e-11 -0.00088336321 -4509.8851
400 4.4437682e-10 -0.0022808215 -4509.8852
500 2.1276171e-09 -0.0055205162 -4509.8852
600 5.3746766e-09 -0.010513144 -4509.8852
700 9.3752238e-09 -0.016165157 -4509.8852
800 1.3218953e-08 -0.02139071 -4509.8852
900 1.6753544e-08 -0.026203391 -4509.8852
1000 2.0559423e-08 -0.031228823 -4509.8852
Loop time of 77.9631 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 8.02545 (10.2939)
Neigh time (%) = 4.56744 (5.85847)
Comm time (%) = 22.9713 (29.4644)
Outpt time (%) = 0.286932 (0.368036)
Other time (%) = 42.1119 (54.0152)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288102 max 69229 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# run to equilibrium
timestep 5
thermo 100
run 10000
Setting up run ...
Memory usage per processor = 93.5532 Mbytes
Step myTemp myPres PotEng
1000 2.0559423e-08 -0.031228823 -4509.8852
1100 2.4448613e-08 -0.036521719 -4509.8852
1200 2.7029986e-08 -0.040978057 -4509.8852
1300 2.7245337e-08 -0.042998684 -4509.8852
1400 2.5759549e-08 -0.041645718 -4509.8852
1500 2.2667557e-08 -0.037303114 -4509.8852
1600 1.8985753e-08 -0.031463351 -4509.8852
1700 1.6073802e-08 -0.025662764 -4509.8852
1800 1.2763714e-08 -0.020737937 -4509.8852
1900 7.2995795e-09 -0.01675253 -4509.8852
2000 2.1755431e-09 -0.013533314 -4509.8853
2100 1.1934319e-09 -0.011450448 -4509.8853
2200 5.1850465e-09 -0.011687818 -4509.8853
2300 1.1883622e-08 -0.015251299 -4509.8852
2400 1.6266667e-08 -0.021397871 -4509.8852
2500 1.9099042e-08 -0.02792249 -4509.8851
2600 2.184558e-08 -0.033185039 -4509.8852
2700 2.4595817e-08 -0.037175923 -4509.8852
2800 2.6643068e-08 -0.040355693 -4509.8852
2900 2.6394943e-08 -0.042183343 -4509.8852
3000 2.3989422e-08 -0.041411974 -4509.8852
3100 2.0979363e-08 -0.037465063 -4509.8851
3200 1.7427127e-08 -0.031310189 -4509.8852
3300 1.3963242e-08 -0.024887233 -4509.8852
3400 1.0069796e-08 -0.019686777 -4509.8852
3500 4.9395633e-09 -0.01603797 -4509.8853
3600 1.5407167e-09 -0.013620537 -4509.8853
3700 2.5284685e-09 -0.012392513 -4509.8853
3800 7.790979e-09 -0.012777012 -4509.8852
3900 1.3465317e-08 -0.015407232 -4509.8852
4000 1.7796468e-08 -0.02062936 -4509.8852
4100 2.137127e-08 -0.027628973 -4509.8852
4200 2.3606809e-08 -0.034315098 -4509.8852
4300 2.5221837e-08 -0.038703928 -4509.8852
4400 2.6247664e-08 -0.040548555 -4509.8852
4500 2.5017987e-08 -0.040839998 -4509.8852
4600 2.1628404e-08 -0.040012148 -4509.8852
4700 1.7878834e-08 -0.037370745 -4509.8851
4800 1.5934582e-08 -0.032277925 -4509.8851
4900 1.2990149e-08 -0.025549108 -4509.8852
5000 7.8316754e-09 -0.01918358 -4509.8853
5100 3.3266953e-09 -0.014887033 -4509.8853
5200 1.805252e-09 -0.01286358 -4509.8853
5300 4.2912871e-09 -0.012392579 -4509.8852
5400 9.9026848e-09 -0.013257092 -4509.8852
5500 1.6165255e-08 -0.015976619 -4509.8852
5600 2.1206295e-08 -0.020907339 -4509.8852
5700 2.4000025e-08 -0.027469529 -4509.8852
5800 2.5521345e-08 -0.034321126 -4509.8852
5900 2.5894586e-08 -0.039670766 -4509.8852
6000 2.5086791e-08 -0.042046228 -4509.8852
6100 2.360407e-08 -0.041352366 -4509.8852
6200 1.9586346e-08 -0.038824048 -4509.8852
6300 1.6684228e-08 -0.035608606 -4509.8852
6400 1.4893508e-08 -0.031584998 -4509.8852
6500 1.1127507e-08 -0.026164353 -4509.8852
6600 5.9884577e-09 -0.019764802 -4509.8853
6700 2.2391294e-09 -0.014210542 -4509.8853
6800 2.7797654e-09 -0.011431487 -4509.8853
6900 6.7664929e-09 -0.011810438 -4509.8852
7000 1.1980057e-08 -0.014206493 -4509.8852
7100 1.7989445e-08 -0.017536849 -4509.8852
7200 2.3218176e-08 -0.02190877 -4509.8852
7300 2.5628573e-08 -0.027653206 -4509.8852
7400 2.610839e-08 -0.034000347 -4509.8852
7500 2.4944322e-08 -0.039281243 -4509.8852
7600 2.2693765e-08 -0.042058723 -4509.8852
7700 1.9767428e-08 -0.041825858 -4509.8851
7800 1.6504232e-08 -0.039030684 -4509.8851
7900 1.4309561e-08 -0.03485307 -4509.8852
8000 1.3055145e-08 -0.030357952 -4509.8852
8100 9.5625542e-09 -0.025706075 -4509.8852
8200 4.6410355e-09 -0.02054295 -4509.8853
8300 3.2795872e-09 -0.015185677 -4509.8853
8400 5.509246e-09 -0.011181309 -4509.8853
8500 9.2654236e-09 -0.010336847 -4509.8852
8600 1.5169111e-08 -0.013152226 -4509.8852
8700 2.1124719e-08 -0.018237266 -4509.8852
8800 2.5607376e-08 -0.023635507 -4509.8852
8900 2.7829768e-08 -0.028664368 -4509.8853
9000 2.7490864e-08 -0.033752079 -4509.8853
9100 2.4629425e-08 -0.038717883 -4509.8852
9200 1.9856317e-08 -0.042074213 -4509.8851
9300 1.5754223e-08 -0.042397751 -4509.8851
9400 1.4158011e-08 -0.039645985 -4509.8851
9500 1.293562e-08 -0.034905375 -4509.8852
9600 1.0925115e-08 -0.029498287 -4509.8852
9700 8.2117111e-09 -0.024274276 -4509.8853
9800 4.2073503e-09 -0.019498803 -4509.8853
9900 3.6200071e-09 -0.015198764 -4509.8853
10000 7.3205984e-09 -0.011878546 -4509.8852
10100 1.2327605e-08 -0.010695702 -4509.8852
10200 1.7930358e-08 -0.012691556 -4509.8852
10300 2.4534101e-08 -0.017839785 -4509.8852
10400 2.8574489e-08 -0.024561434 -4509.8852
10500 2.944535e-08 -0.030655475 -4509.8852
10600 2.7962098e-08 -0.034958095 -4509.8852
10700 2.3119076e-08 -0.037998711 -4509.8852
10800 1.684499e-08 -0.040493081 -4509.8852
10900 1.2305474e-08 -0.041691151 -4509.8851
11000 1.1330272e-08 -0.040137729 -4509.8851
Loop time of 371.175 on 4 procs for 10000 steps with 2304 atoms
Pair time (%) = 66.4286 (17.8968)
Neigh time (%) = 31.4239 (8.46606)
Comm time (%) = 117.354 (31.617)
Outpt time (%) = 0.685033 (0.184558)
Other time (%) = 155.283 (41.8355)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 289296 max 68184 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 1000
Dangerous builds = 0

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LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
create_atoms 1 region atomRegion
Created 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: 3 materials defined from Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 92.6375 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4509.8851 0 -4509.8851 26.948349
100 4.7374019e-13 -4509.8851 0 -4509.8851 26.94834
200 9.7683427e-13 -4509.8851 0 -4509.8851 26.94803
300 1.9565172e-11 -4509.8851 0 -4509.8851 26.946439
400 2.6411547e-10 -4509.8852 0 -4509.8852 26.942798
500 1.351766e-09 -4509.8852 0 -4509.8852 26.93773
600 3.6802148e-09 -4509.8852 0 -4509.8852 26.932648
700 6.6530697e-09 -4509.8852 0 -4509.8852 26.928033
800 9.5474556e-09 -4509.8852 0 -4509.8852 26.923147
900 1.2412323e-08 -4509.8852 0 -4509.8852 26.917542
1000 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
Loop time of 69.3748 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 8.07954 (11.6462)
Neigh time (%) = 4.407 (6.35245)
Comm time (%) = 22.0263 (31.7496)
Outpt time (%) = 0.19482 (0.280822)
Other time (%) = 34.6672 (49.9709)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288910 max 68513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000
Setting up run ...
Memory usage per processor = 92.6375 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
100 1.809994e-08 -4509.8852 0 -4509.8852 26.907429
200 1.9777109e-08 -4509.8852 0 -4509.8852 26.904241
300 2.0275205e-08 -4509.8852 0 -4509.8852 26.902912
400 1.9266773e-08 -4509.8852 0 -4509.8852 26.904281
500 1.6821974e-08 -4509.8851 0 -4509.8851 26.908126
600 1.370661e-08 -4509.8852 0 -4509.8852 26.912761
700 1.0292223e-08 -4509.8852 0 -4509.8852 26.916838
800 6.5498338e-09 -4509.8853 0 -4509.8853 26.920715
900 3.1643856e-09 -4509.8853 0 -4509.8853 26.925094
1000 1.0112513e-09 -4509.8852 0 -4509.8852 26.928958
1100 4.4564547e-10 -4509.8852 0 -4509.8852 26.930177
1200 2.264627e-09 -4509.8852 0 -4509.8852 26.92803
1300 6.3325706e-09 -4509.8853 0 -4509.8853 26.923952
1400 1.1281983e-08 -4509.8853 0 -4509.8853 26.919616
1500 1.5582979e-08 -4509.8852 0 -4509.8852 26.915411
1600 1.8378446e-08 -4509.8852 0 -4509.8852 26.911278
1700 1.9544417e-08 -4509.8852 0 -4509.8852 26.907886
1800 1.993739e-08 -4509.8851 0 -4509.8851 26.905965
1900 1.9956722e-08 -4509.8851 0 -4509.8851 26.905229
2000 1.9225238e-08 -4509.8852 0 -4509.8852 26.905144
2100 1.6580757e-08 -4509.8853 0 -4509.8853 26.906419
2200 1.2058028e-08 -4509.8853 0 -4509.8853 26.910376
2300 7.4549951e-09 -4509.8852 0 -4509.8852 26.916716
2400 4.0264612e-09 -4509.8852 0 -4509.8852 26.923054
2500 1.8321195e-09 -4509.8852 0 -4509.8852 26.92718
2600 5.8894583e-10 -4509.8852 0 -4509.8852 26.92887
2700 1.1822868e-09 -4509.8853 0 -4509.8853 26.928935
2800 4.1199827e-09 -4509.8853 0 -4509.8853 26.927485
2900 8.3401571e-09 -4509.8853 0 -4509.8853 26.924202
3000 1.2795486e-08 -4509.8852 0 -4509.8852 26.91968
3100 1.656454e-08 -4509.8852 0 -4509.8852 26.915184
3200 1.8809835e-08 -4509.8852 0 -4509.8852 26.911167
3300 1.9524689e-08 -4509.8852 0 -4509.8852 26.907277
3400 1.9239653e-08 -4509.8852 0 -4509.8852 26.904028
3500 1.8306513e-08 -4509.8852 0 -4509.8852 26.903155
3600 1.6715381e-08 -4509.8852 0 -4509.8852 26.905573
3700 1.4633381e-08 -4509.8851 0 -4509.8851 26.909896
3800 1.1933216e-08 -4509.8851 0 -4509.8851 26.913983
3900 8.1608505e-09 -4509.8852 0 -4509.8852 26.917338
4000 4.081711e-09 -4509.8853 0 -4509.8853 26.920926
4100 1.5631282e-09 -4509.8853 0 -4509.8853 26.924958
4200 1.2262219e-09 -4509.8853 0 -4509.8853 26.928167
4300 2.985009e-09 -4509.8852 0 -4509.8852 26.929352
4400 6.8933386e-09 -4509.8852 0 -4509.8852 26.928435
4500 1.1278724e-08 -4509.8852 0 -4509.8852 26.925624
4600 1.4438096e-08 -4509.8852 0 -4509.8852 26.920742
4700 1.6779441e-08 -4509.8852 0 -4509.8852 26.914294
4800 1.8690218e-08 -4509.8853 0 -4509.8853 26.908349
4900 1.9317873e-08 -4509.8852 0 -4509.8852 26.905059
5000 1.8273072e-08 -4509.8851 0 -4509.8851 26.904542
Loop time of 207.618 on 4 procs for 5000 steps with 2304 atoms
Pair time (%) = 33.494 (16.1325)
Neigh time (%) = 16.7803 (8.08228)
Comm time (%) = 59.1908 (28.5094)
Outpt time (%) = 0.143787 (0.0692554)
Other time (%) = 98.0096 (47.2066)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288845 max 67924 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 500
Dangerous builds = 0

208
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: 3 materials defined from Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
ATC: created faceset obndy with 2 faces
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 93.0953 Mbytes
Step myTemp myPres PotEng
0 0 -0.00072339042 -4509.8851
100 7.1225566e-14 -0.00069609188 -4509.8851
200 3.7853133e-13 -0.00065829543 -4509.8851
300 1.6363911e-11 -0.00093014878 -4509.8851
400 2.6679578e-10 -0.0022162027 -4509.8852
500 1.616056e-09 -0.0053039586 -4509.8852
600 5.0333459e-09 -0.010270696 -4509.8852
700 9.7370581e-09 -0.016093983 -4509.8852
800 1.3809125e-08 -0.021486202 -4509.8852
900 1.6783957e-08 -0.026147268 -4509.8852
1000 1.9615527e-08 -0.030744945 -4509.8852
Loop time of 61.3722 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 8.47621 (13.8112)
Neigh time (%) = 4.57113 (7.44821)
Comm time (%) = 21.3849 (34.8445)
Outpt time (%) = 0.0678592 (0.11057)
Other time (%) = 26.8721 (43.7855)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288581 max 68542 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
Setting up run ...
Memory usage per processor = 93.5532 Mbytes
Step myTemp myPres PotEng
1000 1.9615527e-08 -0.030744945 -4509.8852
1100 2.3080841e-08 -0.035570103 -4509.8852
1200 2.6803382e-08 -0.039749355 -4509.8852
1300 2.8836885e-08 -0.041881649 -4509.8852
1400 2.7038886e-08 -0.04118176 -4509.8852
1500 2.247439e-08 -0.037776265 -4509.8852
1600 1.8021787e-08 -0.032491325 -4509.8852
1700 1.4774855e-08 -0.026754505 -4509.8852
1800 1.2061023e-08 -0.022034601 -4509.8852
1900 8.5768539e-09 -0.018709001 -4509.8852
2000 3.6373058e-09 -0.016114748 -4509.8852
2100 5.3669536e-10 -0.014163462 -4509.8853
2200 3.2454928e-09 -0.014205399 -4509.8853
2300 1.030702e-08 -0.017492992 -4509.8853
2400 1.6038797e-08 -0.023210717 -4509.8852
2500 1.7061988e-08 -0.029013462 -4509.8851
2600 1.9296258e-08 -0.03339452 -4509.8852
2700 2.2816944e-08 -0.036626152 -4509.8852
2800 2.6944075e-08 -0.039307649 -4509.8852
2900 2.8170813e-08 -0.040972921 -4509.8852
3000 2.7256286e-08 -0.040327211 -4509.8852
3100 2.445985e-08 -0.036617618 -4509.8852
3200 1.8787648e-08 -0.03049195 -4509.8852
3300 1.4750104e-08 -0.023629006 -4509.8852
3400 1.3515772e-08 -0.017473229 -4509.8852
3500 1.157919e-08 -0.012114855 -4509.8851
3600 9.6213234e-09 -0.0064144434 -4509.8851
3700 9.1781574e-09 0.00062376196 -4509.8851
3800 9.0938842e-09 0.0087100206 -4509.885
3900 7.7454581e-09 0.016669158 -4509.885
4000 9.3314606e-09 0.023405906 -4509.885
Loop time of 109.051 on 4 procs for 3000 steps with 2304 atoms
Pair time (%) = 20.2492 (18.5685)
Neigh time (%) = 9.8419 (9.02501)
Comm time (%) = 37.2858 (34.191)
Outpt time (%) = 0.421606 (0.386612)
Other time (%) = 41.2529 (37.8289)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288933 max 68141 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 300
Dangerous builds = 0

112
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
Reading data file ...
orthogonal box = (-47.3241 -15.7747 -15.7747) to (47.3241 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
2304 atoms
2304 velocities
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_thermo_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: 1 materials defined from Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
ATC: created faceset obndy with 2 faces
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
Setting up run ...
Memory usage per processor = 56.6533 Mbytes
Step Temp E_pair E_mol TotEng Press
0 29.995658 -4509.8851 0 -4303.9707 135.84496
1 29.920966 -4509.8851 0 -4304.4835 135.59617
Loop time of 0.161032 on 4 procs for 1 steps with 2304 atoms
Pair time (%) = 0.013374 (8.3052)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00626355 (3.88963)
Outpt time (%) = 0.027244 (16.9184)
Other time (%) = 0.11415 (70.8868)
Nlocal: 576 ave 648 max 504 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5677 ave 7126 max 4228 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 218376 max 138456 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 436752 max 277776 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 0
Dangerous builds = 0
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
ATC: constructing thermo-mechanical coupling with parameter file Ar_thermo_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: 1 materials defined from Ar_thermo_elastic.mat
ATC: peratom PE compute created with ID: 3
fix_modify AtC boundary ghosts
ERROR: Illegal fix_modify command (../fix.cpp:104)

1212
examples/USER/atc/elastic/cnt_electrostatic.screen Normal file
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LAMMPS (14 Aug 2013)
units metal
atom_style atomic
lattice diamond 3.6
Lattice spacing in x,y,z = 3.6 3.6 3.6
boundary f f f
#region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box
#region box block 0 10 0 10 0 10
#create_box 1 box
#group box region box
#atom_modify sort 0 1
pair_style tersoff
read_data tube_8_4.data
Reading data file ...
orthogonal box = (-4.34588 -4.34588 0) to (4.34588 4.34588 104.296)
1 by 1 by 4 MPI processor grid
1008 atoms
1008 velocities
pair_coeff * * ../../../../potentials/SiC.tersoff C
mass * 12.01
# PARAMETERS-----------------------------
variable L equal zhi-zlo
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xhiFE equal 5.0*6.0499999999999998224
variable xloFE equal -${xhiFE}
variable xloFE equal -30.25
variable yhiFE equal $R
variable yhiFE equal 6.0499999999999998224
variable yloFE equal -${xhiFE}
variable yloFE equal -30.25
variable zhiFE equal zhi
variable zloFE equal zlo+10
print "Length $L [${zloFE}, ${zhiFE}]"
Length 104.29551668000000575 [10, 104.29551668000000575]
variable E equal 0.01 # 1.0 10.0 0.01
variable V equal $E*${zloFE}
variable V equal 0.010000000000000000208*${zloFE}
variable V equal 0.010000000000000000208*10
variable V equal 2
print "Electric field $E ref.voltage $V"
Electric field 0.010000000000000000208 ref.voltage 2
variable s equal 20
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box
region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box
group internal region feRegion
908 atoms in group internal
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
>>> number of stationary ghosts: 100 of 1008
#neighbor 5. bin
#neigh_modify every 10 delay 0 check no
timestep 0.0005
# coupling
fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat
ATC: constructing equilibrium electrostatic coupling with parameter file CNT_electrostatic2.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
ATC: creating electrostatic extrinsic model
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
fix_modify AtC omit atomic_charge
#fix_modify AtC internal_quadrature off <<<< ???
variable alat equal 1.42
variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0
variable w equal 1.4199999999999999289*${alat}*3.*sqrt(3.)/4.0
variable w equal 1.4199999999999999289*1.4199999999999999289*3.*sqrt(3.)/4.0
#variable w equal 10
fix_modify AtC atom_weight constant internal $w
fix_modify AtC atom_weight constant internal 2.6193804362864128166
fix_modify AtC source_integration atom
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC mesh create 5 1 12 feRegion f p f
ATC: created uniform mesh with 156 nodes, 78 unique nodes, and 60 elements
fix_modify AtC control momentum flux
#fix_modify AtC extrinsic poisson_solver max_iterations 5
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
#variable a equal -$R-0.1
#variable b equal $R+0.1
#fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 30.25 ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 ${xhiFE} ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 10 units box
ATC: created nodeset lbc with 6 nodes
fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 30.25 ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 104.29551668000000575 units box
ATC: created nodeset rbc with 6 nodes
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box
ATC: created nodeset bot with 13 nodes
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box
ATC: created nodeset top with 13 nodes
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 $V
fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 2
ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0)
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 $V
fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 2
ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0)
# run
thermo_style custom step cpu etotal ke
thermo $s
thermo 20
fix_modify AtC output cnt_electrostatic2FE $s full_text # binary
fix_modify AtC output cnt_electrostatic2FE 20 full_text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC output index step
# NOTE not recognized as vector by paraview
variable uX atom x-f_AtC[1]
variable uY atom y-f_AtC[2]
variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho
dump CONFIG all custom 20 cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho
log cnt_electrostatic2.log
#run $s
run 100
Setting up run ...
ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
Memory usage per processor = 53.9593 Mbytes
Step CPU TotEng KinEng
0 0 -7315.3918 4.2386027e-06
20 7.0248148 -7315.3918 0.0003453277
40 8.5434699 -7315.3918 0.0012274403
60 14.682407 -7315.3918 0.0026370119
80 21.289801 -7315.3918 0.004552872
100 29.208281 -7315.3918 0.0069472253
Loop time of 29.2009 on 4 procs for 100 steps with 1008 atoms
Pair time (%) = 0.305472 (1.04611)
Neigh time (%) = 0 (0)
Comm time (%) = 0.435163 (1.49024)
Outpt time (%) = 0.202401 (0.693134)
Other time (%) = 28.2578 (96.7705)
Nlocal: 252 ave 256 max 248 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 59 ave 80 max 40 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4456 ave 4608 max 4304 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 17824
Ave neighs/atom = 17.6825
Neighbor list builds = 0
Dangerous builds = 0
# NOTE try fix charge on tip

350
examples/USER/atc/elastic/cnt_fixed_charge.screen Normal file
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@ -0,0 +1,350 @@
LAMMPS (14 Aug 2013)
units metal
atom_style charge
dielectric 1.
variable type string "_charge"
boundary s s f
# read in CNT
read_data cnt_9_0_100${type}.data
read_data cnt_9_0_100_charge.data
Reading data file ...
orthogonal box = (-7.04598 -7.04598 0) to (7.04598 7.04598 100)
1 by 1 by 4 MPI processor grid
846 atoms
lattice diamond 3.6 # NOTE ???
Lattice spacing in x,y,z = 3.6 3.6 3.6
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
# PARAMETERS-----------------------------
variable dt equal 0.0005
variable L equal zhi-zlo
variable zhi equal zhi
variable zTip equal ${zhi}-2.0
variable zTip equal 100-2.0
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xhiFE equal 5.0*6.0499999999999998224
variable xloFE equal -${xhiFE}
variable xloFE equal -30.25
variable yhiFE equal $R
variable yhiFE equal 6.0499999999999998224
variable yloFE equal -${yhiFE}
variable yloFE equal -6.0499999999999998224
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable zhiFE equal zhi+(zhi-10)/12*2
variable Lfree equal zhi-${zloFE}
variable Lfree equal zhi-10
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
Length 100 [10, 115] 98
#variable E equal 0.1 # bias 1.0
variable Vb equal 0.0 # bias
variable Vg equal 0.5 # gate/modulation
print "bias voltage ${Vb}, gate voltage ${Vg}"
bias voltage 0, gate voltage 0.5
variable n equal 100000
variable s equal 250
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box
group internal region feRegion
756 atoms in group internal
group fixed subtract all internal
90 atoms in group fixed
fix FIX fixed setforce 0 0 0
thermo 100
#minimize 0 0 1000 1000
#write_restart cnt_in_box0.rst
region TIP block INF INF INF INF ${zTip} INF units box
region TIP block INF INF INF INF 98 INF units box
group TIP region TIP
9 atoms in group TIP
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
variable nTip equal count(TIP)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
>>> number of stationary ghosts: 90 of 846
print ">>> number of tip atoms : ${nTip}"
>>> number of tip atoms : 9
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep ${dt}
timestep 0.00050000000000000001041
variable tag string "cnt_fixed_charge"
# set charge on tip
variable C equal -0.1 # -0.01 -0.0001102
print "charge $C [e]"
charge -0.10000000000000000555 [e]
variable c equal $C/${nTip}
variable c equal -0.10000000000000000555/${nTip}
variable c equal -0.10000000000000000555/9
set group TIP charge $c
set group TIP charge -0.011111111111111111535
Setting atom values ...
9 settings made for charge
# coupling
fix AtC internal atc electrostatic CNT_id.mat
ATC: constructing electrostatic mechanical coupling with parameter file CNT_id.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
ATC: creating electrostatic extrinsic model
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
fix_modify AtC include atomic_charge
fix_modify AtC internal_quadrature off
# note weights don't affect phi or f
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
#fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 14 feRegion f p f
ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
# node sets
variable t equal 1.1*$R
variable t equal 1.1*6.0499999999999998224
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box
ATC: created nodeset tube with 39 nodes
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box
ATC: created nodeset lefttube with 3 nodes
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box
ATC: created nodeset rbc with 11 nodes
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box
ATC: created nodeset lbc with 11 nodes
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box
ATC: created nodeset top with 15 nodes
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box
ATC: created nodeset bot with 15 nodes
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# ground
fix_modify AtC fix electric_potential lbc 0
# bias
fix_modify AtC fix electric_potential rbc ${Vb}
fix_modify AtC fix electric_potential rbc 0
# gate
fix_modify AtC fix electric_potential bot ${Vg}
fix_modify AtC fix electric_potential bot 0.5
# run
compute CM TIP com
compute q all property/atom q
compute Q all reduce sum c_q
compute FSUM all reduce sum fx fy fz
thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1]
thermo $s
thermo 250
log ${tag}.log
log cnt_fixed_charge.log
#run $n
#run $n
thermo 10
timestep 0.0
min_modify line quadratic
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 54.7522 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1]
0 -6146.2653 0 -1.2222229e-10 1.1111297e-10 98.69 -0.1 0 0 0 -0.00094915808 9.0465829e-16 -2.9442594e-15 8.5762791 0.26756106 -0.00094915808
10 -6148.5953 0 -2.4439829e-05 -2.2098859e-10 98.493704 -0.1 0 0 0 -0.00094915808 1.2097899e-09 -1.5843514e-09 8.9290595 0.26659976 -0.00094915929
20 -6149.6563 0 -0.0001026377 -1.2280254e-10 98.220511 -0.1 0 0 0 -0.00094915808 -1.2490271e-10 1.3882666e-11 9.0170586 0.26585869 -0.00094915796
30 -6150.5918 0 -0.00018409212 -1.5241986e-10 98.082714 -0.1 0 0 0 -0.00094915808 1.1496787e-09 -5.0626918e-10 8.9773134 0.26549134 -0.00094915923
40 -6151.5228 0 -0.00028729352 -1.255161e-10 97.911408 -0.1 0 0 0 -0.00094915808 -7.0229746e-12 2.277342e-10 8.9692427 0.26498393 -0.00094915808
50 -6152.4762 0 -0.00040932626 -1.3818574e-12 97.725058 -0.1 0 0 0 -0.00094915808 6.9526046e-11 1.9786892e-10 8.9900875 0.26449594 -0.00094915815
60 -6153.4274 0 -0.00055067345 1.805009e-10 97.514368 -0.1 0 0 0 -0.00094915808 -2.4739767e-10 5.8424452e-10 8.9790629 0.26387994 -0.00094915784
70 -6154.3557 0 -0.00070066137 1.0114613e-10 97.330744 -0.1 0 0 0 -0.00094915808 -2.6211632e-10 7.052493e-10 8.9849075 0.26339716 -0.00094915782
80 -6155.267 0 -0.00085596687 -1.0710927e-10 97.147959 -0.1 0 0 0 -0.00094915808 4.4143026e-07 1.6718385e-10 5.3206144 0.26285936 -0.00094959951
90 -6155.4335 0 -0.00088765763 -1.7962733e-11 97.118985 -0.1 0 0 0 -0.00094915808 -3.2852156e-07 -2.142539e-10 1.9421081 0.2627935 -0.00094882956
100 -6155.4688 0 -0.00092338115 4.3179489e-12 97.108467 -0.1 0 0 0 -0.00094915808 2.1921637e-06 3.277627e-10 1.8128583 0.26276227 -0.00095135025
110 -6155.4937 0 -0.0009583995 2.7080132e-11 97.099066 -0.1 0 0 0 -0.00094915808 -6.6593497e-07 3.1466135e-10 1.6760028 0.26273976 -0.00094849215
120 -6155.5192 0 -0.0010096681 7.5495905e-12 97.084131 -0.1 0 0 0 -0.00094915808 4.1925486e-06 -3.3057391e-10 0.84688966 0.26269582 -0.00095335063
130 -6155.5475 0 -0.0010984064 -2.2204658e-11 97.037469 -0.1 0 0 0 -0.00094915808 1.6487881e-05 7.877601e-10 -0.24391523 0.26256701 -0.00096564596
140 -6155.5674 0 -0.0011643139 -5.8625528e-12 96.997016 -0.1 0 0 0 -0.00094915808 1.9922307e-05 2.8145019e-10 0.21107429 0.26245307 -0.00096908039
150 -6155.5802 0 -0.0012261174 1.6615978e-12 96.978462 -0.1 0 0 0 -0.00094915808 2.3564757e-05 -6.1453672e-10 0.34197533 0.26240133 -0.00097272284
160 -6155.5842 0 -0.0012567683 4.1015453e-12 96.969841 -0.1 0 0 0 -0.00094915808 -1.8048071e-05 -7.4358615e-10 0.24350595 0.26237804 -0.00093111001
170 -6155.5848 0 -0.0012749252 3.2100637e-12 96.96678 -0.1 0 0 0 -0.00094915808 -5.8709343e-05 -1.0101609e-10 0.23678759 0.26236915 -0.00089044874
180 -6155.5863 0 -0.0013921995 9.5094171e-12 96.955174 -0.1 0 0 0 -0.00094915808 -0.00026288245 2.257e-09 0.27067485 0.2623373 -0.00068627564
190 -6155.5869 0 -0.001448131 2.9297299e-11 96.95023 -0.1 0 0 0 -0.00094915808 -0.00022357532 -5.3015481e-10 0.25119591 0.26232192 -0.00072558276
200 -6155.5875 0 -0.0015072261 1.2995721e-11 96.946996 -0.1 0 0 0 -0.00094915808 3.676363e-06 -1.6247639e-09 0.14855078 0.26231405 -0.00095283445
210 -6155.5884 0 -0.0016446609 -5.6541246e-11 96.941051 -0.1 0 0 0 -0.00094915808 0.00012779831 5.5608749e-09 0.071556101 0.2622972 -0.0010769564
220 -6155.5885 0 -0.0016649389 -1.4916073e-11 96.940172 -0.1 0 0 0 -0.00094915808 2.8769126e-05 7.3325474e-10 0.072836172 0.26229459 -0.00097792721
230 -6155.5886 0 -0.0016840656 3.0271757e-11 96.93972 -0.1 0 0 0 -0.00094915808 -8.2275147e-05 -3.2732419e-09 0.038242471 0.26229362 -0.00086688294
240 -6155.5886 0 -0.0017104776 1.1844187e-12 96.939312 -0.1 0 0 0 -0.00094915808 1.3323934e-06 4.6833365e-10 0.029894245 0.2622922 -0.00095049048
250 -6155.5886 0 -0.001782375 -5.1737556e-11 96.938585 -0.1 0 0 0 -0.00094915808 0.00010776134 5.532132e-09 0.015593573 0.26229021 -0.0010569194
260 -6155.5886 0 -0.0018325003 1.4170213e-11 96.938021 -0.1 0 0 0 -0.00094915808 -0.00011466701 -1.8404319e-09 0.0074676942 0.26228875 -0.00083449107
270 -6155.5887 0 -0.0018909045 4.5008271e-12 96.93745 -0.1 0 0 0 -0.00094915808 0.00013183246 -4.7505827e-10 0.012466474 0.26228709 -0.0010809905
280 -6155.5887 0 -0.0019654593 -2.0855882e-11 96.936554 -0.1 0 0 0 -0.00094915808 0.000169485 -5.926811e-11 -0.0067531896 0.26228461 -0.0011186431
290 -6155.5887 0 -0.0020221999 -8.6767858e-12 96.935891 -0.1 0 0 0 -0.00094915808 -5.3692915e-05 1.0159278e-09 -0.0018194713 0.26228254 -0.00089546517
300 -6155.5887 0 -0.0020344145 -5.607299e-14 96.935775 -0.1 0 0 0 -0.00094915808 -1.5062541e-05 3.3229655e-10 0.0029236218 0.26228228 -0.00093409554
310 -6155.5887 0 -0.0020565506 -8.9663374e-12 96.935684 -0.1 0 0 0 -0.00094915808 0.00020002046 -1.267435e-09 0.003519094 0.26228199 -0.0011491785
320 -6155.5887 0 -0.0021315555 -1.4536397e-11 96.93549 -0.1 0 0 0 -0.00094915808 0.00011130878 1.691832e-10 0.0035264974 0.26228133 -0.0010604669
330 -6155.5887 0 -0.0021892704 2.8975537e-12 96.935359 -0.1 0 0 0 -0.00094915808 2.1304961e-05 -6.0918033e-10 0.0032239388 0.26228087 -0.00097046304
340 -6155.5887 0 -0.002267819 2.8726725e-12 96.935208 -0.1 0 0 0 -0.00094915808 -0.00012295621 1.4278825e-09 0.0015958494 0.26228031 -0.00082620188
350 -6155.5887 0 -0.0023365018 7.5696565e-12 96.935104 -0.1 0 0 0 -0.00094915808 -3.8319531e-05 2.8702501e-10 -0.00070205167 0.26227999 -0.00091083855
360 -6155.5887 0 -0.00237721 -9.4045843e-12 96.935064 -0.1 0 0 0 -0.00094915808 0.00015892958 -1.1733697e-09 -0.0021409156 0.26227985 -0.0011080877
370 -6155.5887 0 -0.0024126534 -1.8974906e-11 96.935058 -0.1 0 0 0 -0.00094915808 0.00013759568 4.1426828e-10 -0.0021373479 0.26227982 -0.0010867538
380 -6155.5887 0 -0.0024420366 3.1870067e-12 96.93505 -0.1 0 0 0 -0.00094915808 6.0222094e-05 -4.9318939e-10 -0.0021696981 0.26227978 -0.0010093802
390 -6155.5887 0 -0.0024987512 -6.1806174e-12 96.935034 -0.1 0 0 0 -0.00094915808 -2.1228292e-06 2.8515227e-10 -0.0022646942 0.2622797 -0.00094703525
400 -6155.5887 0 -0.002653766 -1.4619372e-11 96.93499 -0.1 0 0 0 -0.00094915808 0.00013021546 1.1233177e-09 -0.0033420787 0.26227949 -0.0010793735
410 -6155.5887 0 -0.0028422882 -1.292254e-11 96.934928 -0.1 0 0 0 -0.00094915808 0.00020536826 -5.0886e-10 -0.0049198922 0.26227921 -0.0011545263
420 -6155.5887 0 -0.0030173435 -1.0655446e-11 96.934865 -0.1 0 0 0 -0.00094915808 0.00011114747 -2.5969168e-10 -0.0048225266 0.2622789 -0.0010603056
430 -6155.5887 0 -0.0032602753 -2.4154772e-11 96.934789 -0.1 0 0 0 -0.00094915808 0.00035483493 1.6053604e-10 -0.0043785731 0.26227846 -0.001303993
440 -6155.5887 0 -0.0036112872 -5.6473718e-11 96.934705 -0.1 0 0 0 -0.00094915808 0.00043425018 1.8745787e-10 -0.0038812537 0.26227785 -0.0013834083
450 -6155.5887 0 -0.0038611908 -1.9242305e-12 96.934666 -0.1 0 0 0 -0.00094915808 0.0001243155 -3.6471408e-10 -0.0050455501 0.26227745 -0.0010734736
460 -6155.5887 0 -0.0042622211 -1.1948937e-11 96.93463 -0.1 0 0 0 -0.00094915808 0.00017733896 -5.9650038e-10 -0.005090118 0.26227685 -0.001126497
470 -6155.5887 0 -0.0051704959 -6.5555834e-11 96.93456 -0.1 0 0 0 -0.00094915808 0.00044796055 2.0162891e-09 -0.0063013863 0.26227558 -0.0013971186
480 -6155.5887 0 -0.0058774787 8.0639107e-12 96.934537 -0.1 0 0 0 -0.00094915808 0.00030232037 -4.1063286e-10 -0.0063827796 0.26227474 -0.0012514785
490 -6155.5887 0 -0.0071402115 -4.9061812e-11 96.934554 -0.1 0 0 0 -0.00094915808 0.00014674646 -1.4276993e-09 -0.0085602294 0.26227356 -0.0010959045
500 -6155.5887 0 -0.0089111607 -5.2606473e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646
Loop time of 106.653 on 4 procs for 500 steps with 846 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-6146.26527937 -6155.58874802 -6155.58874805
Force two-norm initial, final = 9.08614 0.00211093
Force max component initial, final = 2.35984 0.000212848
Final line search alpha, max atom move = 1 0.000212848
Iterations, force evaluations = 500 1000
Pair time (%) = 9.67218 (9.06879)
Neigh time (%) = 0 (0)
Comm time (%) = 6.7444 (6.32366)
Outpt time (%) = 2.93299 (2.75002)
Other time (%) = 87.3039 (81.8575)
Nlocal: 211.5 ave 216 max 207 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 191.25 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 47313 ave 52056 max 42570 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 189252
Ave neighs/atom = 223.702
Neighbor list builds = 0
Dangerous builds = 0
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable F equal f_AtC[5]
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0*90*${Lfree}*${Lfree}/3./$u
variable EI equal 0*90*90*${Lfree}/3./$u
variable EI equal 0*90*90*90/3./$u
variable EI equal 0*90*90*90/3./-0.0089111606622158945346
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal -0*${eV2J}*${A2m}
variable EI equal -0*1.6021764600000000642e-19*${A2m}
variable EI equal -0*1.6021764600000000642e-19*1.0000000000000000364e-10
print "flexural rigidity ${EI} [Nm^2] NOTE z force"
flexural rigidity -0 [Nm^2] NOTE z force
# flexural rigidity 6.716732985e-25 [Nm^2]
fix_modify AtC output ${tag}FE 1 full_text
fix_modify AtC output cnt_fixed_chargeFE 1 full_text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC output index step
run 1
Setting up run ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 54.1206 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1]
500 -6155.5887 0 -0.0089111607 -5.2606424e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646
501 -6155.5887 0 -0.0089111607 -5.2606424e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646
Loop time of 0.0591159 on 4 procs for 1 steps with 846 atoms
Pair time (%) = 0.00747705 (12.6481)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000546396 (0.924278)
Outpt time (%) = 0.0172972 (29.2598)
Other time (%) = 0.0337953 (57.1678)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0

333
examples/USER/atc/elastic/eam_energy.screen Normal file
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LAMMPS (14 Aug 2013)
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable l2 equal 0.5*3
variable L equal 10
variable L2 equal 0.5*$L
variable L2 equal 0.5*10
variable h equal $L
variable h equal 10
lattice fcc 4.08 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 4.08 4.08 4.08
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
region BOX block -1.5 ${l2} -${L2} ${L2} -${l2} ${l2}
region BOX block -1.5 1.5 -${L2} ${L2} -${l2} ${l2}
region BOX block -1.5 1.5 -5 ${L2} -${l2} ${l2}
region BOX block -1.5 1.5 -5 5 -${l2} ${l2}
region BOX block -1.5 1.5 -5 5 -1.5 ${l2}
region BOX block -1.5 1.5 -5 5 -1.5 1.5
create_box 1 BOX
Created orthogonal box = (-6.12 -20.4 -6.12) to (6.12 20.4 6.12)
1 by 4 by 1 MPI processor grid
create_atoms 1 region BOX
Created 360 atoms
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
ATC: constructing shape function field estimate with parameter file Au_elastic.mat
ATC: peratom PE compute created with ID: 3
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP mesh create 1 10 1 BOX p f p
ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix ATC all atc elastic Au_elastic.mat
ATC: constructing elastic coupling with parameter file Au_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 11.6006
ATC: computed mass density : 11.6006
ATC: 2 materials defined from Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC mesh create 1 10 1 BOX p f p
ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
Setting up run ...
ATC: CB stiffness: 11.5362 Einstein freq: 4682.34
ATC: CB stiffness: 11.5362 Einstein freq: 4682.34
ATC: WARNING: all initial conditions for displacement have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero
Memory usage per processor = 70.4928 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1414.8 0 -1414.8 0.022463201
Loop time of 5.76973e-05 on 4 procs for 0 steps with 360 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 5.76973e-05 (100)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
variable pe equal pe-${e0}
variable pe equal pe--1414.8000000636002369
variable dL equal ly-${L0}
variable dL equal ly-40.799999999999997158
variable strain equal v_dL/${L0}
variable strain equal v_dL/40.799999999999997158
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
0 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0
1 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0
Loop time of 0.220009 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.010402 (4.72801)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0269095 (12.2311)
Outpt time (%) = 0.0771807 (35.0808)
Other time (%) = 0.105516 (47.9601)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
1 -1414.7633 0 0.036746101 0 0 -19.38 0.1 -19.38 40.8 0 0
2 -1414.7633 0 0.036746101 0.036746101 0 -19.38 0.1 -19.38 40.8 0 0
Loop time of 0.305193 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.0104025 (3.4085)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0294241 (9.64114)
Outpt time (%) = 0.132358 (43.3686)
Other time (%) = 0.133008 (43.5818)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
2 -1414.653 0 0.1469844 0.036746101 0 -19.38 0.2 -19.38 40.8 0 0
3 -1414.653 0 0.1469844 0.1469844 0 -19.38 0.2 -19.38 40.8 0 0
Loop time of 0.49256 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.0226828 (4.60508)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0572202 (11.6169)
Outpt time (%) = 0.15985 (32.4529)
Other time (%) = 0.252807 (51.3251)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
3 -1414.4693 0 0.33071491 0.1469844 0 -19.38 0.3 -19.38 40.8 0 0
4 -1414.4693 0 0.33071491 0.33071491 0 -19.38 0.3 -19.38 40.8 0 0
Loop time of 0.4925 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.0401872 (8.15985)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0840666 (17.0694)
Outpt time (%) = 0.122344 (24.8415)
Other time (%) = 0.245902 (49.9293)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
change_box all y scale 1.01 remap
Changing box ...
orthogonal box = (-6.12 -20.604 -6.12) to (6.12 20.604 6.12)
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
ATC: created function : 0 + 0(x-0)+0.01(y-0)+0(z-0)
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
4 -1414.1262 0.34311553 0.33071491 0.33071491 0 -19.5738 0.3 -19.5738 41.208 0.408 0.01
5 -1414.1262 0.34311553 0.33071491 0.33071491 0.34908704 -19.5738 0.3 -19.5738 41.208 0.408 0.01
Loop time of 0.406034 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.0312375 (7.69333)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0279282 (6.87828)
Outpt time (%) = 0.107298 (26.4259)
Other time (%) = 0.23957 (59.0025)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
change_box all y scale 1.01 remap
Changing box ...
orthogonal box = (-6.12 -20.81 -6.12) to (6.12 20.81 6.12)
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
ATC: created function : 0 + 0(x-0)+0.0201(y-0)+0(z-0)
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
5 -1413.1082 1.3610604 0.33071491 0.33071491 0 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201
6 -1413.1082 1.3610604 0.33071491 0.33071491 1.0612595 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201
Loop time of 0.0288442 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.000436962 (1.5149)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00012219 (0.423618)
Outpt time (%) = 0.0219155 (75.9788)
Other time (%) = 0.00636959 (22.0827)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
change_box all y scale 1.01 remap
Changing box ...
orthogonal box = (-6.12 -21.0181 -6.12) to (6.12 21.0181 6.12)
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
ATC: created function : 0 + 0(x-0)+0.030301(y-0)+0(z-0)
run 1
Setting up run ...
Memory usage per processor = 70.4928 Mbytes
Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
6 -1411.4328 3.0364818 0.33071491 0.33071491 0 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301
7 -1411.4328 3.0364818 0.33071491 0.33071491 1.7947982 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301
Loop time of 0.0317271 on 4 procs for 1 steps with 360 atoms
Pair time (%) = 0.00369978 (11.6613)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00984788 (31.0394)
Outpt time (%) = 0.00181496 (5.72054)
Other time (%) = 0.0163645 (51.5788)
Nlocal: 90 ave 90 max 90 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1184 ave 1184 max 1184 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3870 ave 3870 max 3870 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 7740 ave 7740 max 7740 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30960
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0

266
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LAMMPS (14 Aug 2013)
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
variable V equal 0.00010000000000000000479*$L
variable V equal 0.00010000000000000000479*10
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
Lattice spacing in x,y,z = 1 1 1
boundary f p p
region box block -$L $L 0 1 0 1
region box block -10 $L 0 1 0 1
region box block -10 10 0 1 0 1
create_box 1 box
Created orthogonal box = (-10 0 0) to (10 1 1)
4 by 1 by 1 MPI processor grid
group box region box
0 atoms in group box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
ATC: constructing equilibrium electrostatic coupling with parameter file CNT.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: 7 materials defined from CNT.mat
ATC: creating electrostatic extrinsic model
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: 7 materials defined from CNT.mat
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: computed mass density : 96.08
ATC: 7 materials defined from CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
fix_modify AtC mesh create 4 1 1 box f p p
ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
ATC: created elementset all with 4 elements
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 $V
fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)
# run
thermo_style custom step cpu etotal ke
thermo $s
thermo 1
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output electron_densityFE 1 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
default material - table linear
run $s
run 1
Setting up run ...
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
0 0 0 -0
1 0.01880908 0 -0
Loop time of 0.018833 on 4 procs for 1 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 2.5034e-06 (0.0132926)
Outpt time (%) = 0.017292 (91.8175)
Other time (%) = 0.00153852 (8.16923)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0
# run CNT1 material
print "CNT1 material - analytical linear"
CNT1 material - analytical linear
fix_modify AtC material all CNT1
run $s
run 1
Setting up run ...
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
1 0 0 -0
2 0.11045408 0 -0
Loop time of 0.110485 on 4 procs for 1 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 1.54972e-06 (0.00140265)
Outpt time (%) = 0.00781226 (7.07087)
Other time (%) = 0.102671 (92.9277)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0
# run CNT2 material
print "CNT2 material - analytical exponetial"
CNT2 material - analytical exponetial
fix_modify AtC material all CNT2
run $s
run 1
Setting up run ...
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
2 0 0 -0
3 0.10601687 0 -0
Loop time of 0.123864 on 4 procs for 1 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 2.02656e-06 (0.00163611)
Outpt time (%) = 0.0475852 (38.4172)
Other time (%) = 0.0762771 (61.5812)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0
# run CNT material
print "CNT material - table DOS"
CNT material - table DOS
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s
run 1
Setting up run ...
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt-exp] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: material: [cnt] cannot find body_force
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
3 0 0 -0
4 0.0015778542 0 -0
Loop time of 0.00159025 on 4 procs for 1 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 7.15256e-07 (0.0449775)
Outpt time (%) = 0.00022918 (14.4115)
Other time (%) = 0.00136036 (85.5435)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

845
examples/USER/atc/elastic/electrostatic_bending.screen Normal file
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@ -0,0 +1,845 @@
LAMMPS (14 Aug 2013)
units metal
atom_style charge
dielectric 1.
variable type string "_charge"
boundary s s f
# read in CNT
read_data cnt_9_0_100${type}.data
read_data cnt_9_0_100_charge.data
Reading data file ...
orthogonal box = (-7.04598 -7.04598 0) to (7.04598 7.04598 100)
1 by 1 by 4 MPI processor grid
846 atoms
lattice diamond 3.6 # NOTE ???
Lattice spacing in x,y,z = 3.6 3.6 3.6
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
# PARAMETERS-----------------------------
variable dt equal 0.0005
variable L equal zhi-zlo
variable zhi equal zhi
variable zTip equal ${zhi}-2.0 # 2 4
variable zTip equal 100-2.0
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xhiFE equal 5.0*6.0499999999999998224
variable xloFE equal -${xhiFE}
variable xloFE equal -30.25
variable yhiFE equal $R
variable yhiFE equal 6.0499999999999998224
variable yloFE equal -${yhiFE}
variable yloFE equal -6.0499999999999998224
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable zhiFE equal zhi+(zhi-10)/12*2
variable Lfree equal zhi-${zloFE}
variable Lfree equal zhi-10
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
Length 100 [10, 115] 98
#variable E equal 0.1 # bias 1.0
variable Vb equal 0.1 # 0.1 #0.5 #0.0 # bias
variable Vg equal 0.5 # 1.0 # 5.0 0.5 #50.0 # 0.5 # gate/modulation
print "bias voltage ${Vb}, gate voltage ${Vg}"
bias voltage 0.10000000000000000555, gate voltage 0.5
variable ng equal 20 # 80 # 10
variable nb equal 2 # 3
variable n equal 100000
variable s equal 250
# END -----------------------------------
region TIP block INF INF INF INF ${zTip} INF units box
region TIP block INF INF INF INF 98 INF units box
group TIP region TIP
9 atoms in group TIP
#region FIXED block INF INF INF INF INF ${zLoFE} units box
#group FIXED region FIXED
#group FREE subtract all FIXED
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box
group internal region feRegion
756 atoms in group internal
group FIXED subtract all internal
90 atoms in group FIXED
fix FIX FIXED setforce 0 0 0
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
variable nTip equal count(TIP)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
>>> number of stationary ghosts: 90 of 846
print ">>> number of tip atoms : ${nTip}"
>>> number of tip atoms : 9
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep ${dt}
timestep 0.00050000000000000001041
thermo 100
variable tag string "electrostatic_bending"
# set charge on tip
variable C equal -0.025
print "charge $C [e]"
charge -0.025000000000000001388 [e]
variable c equal $C/${nTip}
variable c equal -0.025000000000000001388/${nTip}
variable c equal -0.025000000000000001388/9
set group TIP charge $c
set group TIP charge -0.0027777777777777778838
Setting atom values ...
9 settings made for charge
# coupling
fix AtC internal atc electrostatic CNT_id.mat
ATC: constructing electrostatic mechanical coupling with parameter file CNT_id.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
ATC: creating electrostatic extrinsic model
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_id.mat
fix_modify AtC include atomic_charge
fix_modify AtC internal_quadrature off
# note weights don't affect phi or f
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
#fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 14 feRegion f p f
ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
# node sets
variable t equal 1.1*$R
variable t equal 1.1*6.0499999999999998224
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box
ATC: created nodeset tube with 39 nodes
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box
ATC: created nodeset lefttube with 3 nodes
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box
ATC: created nodeset rbc with 11 nodes
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box
ATC: created nodeset lbc with 11 nodes
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box
ATC: created nodeset top with 15 nodes
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box
ATC: created nodeset bot with 15 nodes
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# ground
fix_modify AtC fix electric_potential lbc 0
# bias
fix_modify AtC fix electric_potential rbc ${Vb}
fix_modify AtC fix electric_potential rbc 0.10000000000000000555
# gate
fix_modify AtC fix electric_potential bot ${Vg}
fix_modify AtC fix electric_potential bot 0.5
# run
compute CM TIP com
compute q all property/atom q
compute Q all reduce sum c_q
compute FSUM all reduce sum fx fy fz
compute RSUM internal reduce sum fx fy fz
thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] c_RSUM[1]
thermo $s
thermo 250
fix_modify AtC output ${tag}FE 100000000 full_text # $s full_text #binary
fix_modify AtC output electrostatic_bendingFE 100000000 full_text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC output index step
# NOTE not recognized as vector by paraview
variable uX atom x-f_AtC[1]
variable uY atom y-f_AtC[2]
variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom $s ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho
dump CONFIG all custom 250 ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho
dump CONFIG all custom 250 electrostatic_bending.dmp id type x y z v_uX v_uY v_uZ v_rho
reset_timestep 0
log ${tag}.log
log electrostatic_bending.log
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
thermo 10
timestep 0.0
min_modify line quadratic
variable Vg equal 0.1
variable Lx equal 1.0
variable ng equal 4
#compute RSUM FREE reduce sum fx fy fz
#dump CONFIG all custom 10000 ${tag}.dmp id type x y z c_U[1] c_U[2] c_U[3] fx fy fz
variable a equal 0
variable i loop ${ng}
variable i loop 4
label loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (1-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (1-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (1-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (1-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0 0 0 0
ATC: created function : 0 + 0(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.2354 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
0 -6146.5328 0 -1.2222229e-10 1.1111297e-10 98.69 -0.025 0 0 0 0 9.0465829e-16 -2.9442594e-15 8.5762791 0 6.8998626e-16 6.8998626e-16
10 -6148.8618 0 4.940931e-12 -2.2100035e-10 98.493762 -0.025 0 0 0 0 1.2098779e-09 -1.5844069e-09 8.9290499 0 -1.209881e-09 -1.209881e-09
20 -6149.9222 0 2.3540796e-12 -1.2223531e-10 98.220638 -0.025 0 0 0 0 -1.255241e-10 1.3853794e-11 9.0170496 0 1.2552811e-10 1.2552811e-10
30 -6150.857 0 -5.8780008e-12 -1.5206673e-10 98.082897 -0.025 0 0 0 0 1.1490666e-09 -5.0591806e-10 8.9773205 0 -1.149063e-09 -1.149063e-09
40 -6151.7874 0 6.0788906e-12 -1.2585104e-10 97.911664 -0.025 0 0 0 0 -7.6226226e-12 2.2822122e-10 8.969255 0 7.6276741e-12 7.6276741e-12
50 -6152.7403 0 -8.5868587e-12 -2.1662548e-12 97.725384 -0.025 0 0 0 0 6.8901152e-11 1.9872572e-10 8.9900713 0 -6.8910336e-11 -6.8910336e-11
60 -6153.6909 0 -2.3882229e-11 1.8005686e-10 97.514756 -0.025 0 0 0 0 -2.4792216e-10 5.8505025e-10 8.9790647 0 2.4791056e-10 2.4791056e-10
70 -6154.6186 0 -1.4341604e-11 1.0186267e-10 97.331185 -0.025 0 0 0 0 -2.5377242e-10 7.0580372e-10 8.9849053 0 2.5377634e-10 2.5377634e-10
80 -6155.5294 0 3.317641e-12 -1.0628218e-10 97.148448 -0.025 0 0 0 0 -3.6329208e-10 1.6682668e-10 5.3213166 0 3.6329e-10 3.6329e-10
90 -6155.6958 0 -7.4051845e-13 -1.7958969e-11 97.119481 -0.025 0 0 0 0 -2.6610771e-10 -2.1459841e-10 1.9442496 0 2.6610824e-10 2.6610824e-10
100 -6155.7311 0 -1.7366193e-12 4.0895485e-12 97.108958 -0.025 0 0 0 0 -2.2828441e-12 3.2760579e-10 1.8155088 0 2.2768396e-12 2.2768396e-12
110 -6155.7559 0 -3.7182375e-12 2.7076944e-11 97.099557 -0.025 0 0 0 0 -2.7283076e-10 3.148088e-10 1.6786296 0 2.7283883e-10 2.7283883e-10
120 -6155.7815 0 -1.6001509e-12 7.7718611e-12 97.084625 -0.025 0 0 0 0 -2.3085834e-10 -3.3010689e-10 0.84988485 0 2.3084659e-10 2.3084659e-10
130 -6155.8097 0 6.1918255e-12 -2.2013612e-11 97.037986 -0.025 0 0 0 0 3.8781477e-10 7.8589814e-10 -0.24071684 0 -3.8781011e-10 -3.8781011e-10
140 -6155.8296 0 9.1649429e-13 -5.8772777e-12 96.997528 -0.025 0 0 0 0 -2.9271952e-10 2.8177507e-10 0.21373041 0 2.9272128e-10 2.9272128e-10
150 -6155.8424 0 1.2990133e-12 1.6560103e-12 96.978985 -0.025 0 0 0 0 1.8917465e-10 -6.1365804e-10 0.34484179 0 -1.8917478e-10 -1.8917478e-10
160 -6155.8465 0 -8.7514622e-13 4.204932e-12 96.970352 -0.025 0 0 0 0 5.4505837e-10 -7.430968e-10 0.24626587 0 -5.4506486e-10 -5.4506486e-10
170 -6155.8471 0 -3.1964234e-12 3.3010755e-12 96.967294 -0.025 0 0 0 0 2.2410803e-10 -1.016244e-10 0.23959213 0 -2.2410755e-10 -2.2410755e-10
180 -6155.8485 0 -1.5534979e-11 9.5624334e-12 96.955682 -0.025 0 0 0 0 -2.0043328e-09 2.2585906e-09 0.27363173 0 2.0043342e-09 2.0043342e-09
190 -6155.8492 0 -2.0892941e-11 2.9371598e-11 96.950738 -0.025 0 0 0 0 3.8637701e-10 -5.3578627e-10 0.2536299 0 -3.8637116e-10 -3.8637116e-10
200 -6155.8498 0 -7.8964312e-12 1.3090003e-11 96.947508 -0.025 0 0 0 0 1.5603734e-09 -1.6272208e-09 0.15118948 0 -1.5603738e-09 -1.5603738e-09
210 -6155.8506 0 3.2330911e-11 -5.680355e-11 96.941553 -0.025 0 0 0 0 -5.1954511e-09 5.6107173e-09 0.074902549 0 5.1954505e-09 5.1954505e-09
220 -6155.8508 0 1.291125e-11 -1.4639389e-11 96.940685 -0.025 0 0 0 0 -7.2531212e-10 7.1522033e-10 0.075697866 0 7.253091e-10 7.253091e-10
230 -6155.8508 0 -2.1539062e-11 3.0981675e-11 96.940234 -0.025 0 0 0 0 3.4501174e-09 -3.3448009e-09 0.040836048 0 -3.4501143e-09 -3.4501143e-09
240 -6155.8508 0 -2.6136061e-12 1.0779917e-12 96.939825 -0.025 0 0 0 0 -6.485948e-10 4.904014e-10 0.032769742 0 6.4859596e-10 6.4859596e-10
250 -6155.8509 0 5.4062908e-11 -5.4847092e-11 96.939069 -0.025 0 0 0 0 -6.3245546e-09 5.8679399e-09 0.01865975 0 6.3245566e-09 6.3245566e-09
260 -6155.8509 0 1.9938451e-12 1.3745327e-11 96.938535 -0.025 0 0 0 0 2.8230301e-09 -1.7880768e-09 0.010102843 0 -2.8230281e-09 -2.8230281e-09
270 -6155.8509 0 -1.1673108e-11 7.7225918e-12 96.937968 -0.025 0 0 0 0 4.3671364e-10 -8.0304089e-10 0.01529266 0 -4.3670395e-10 -4.3670395e-10
280 -6155.851 0 3.1090928e-11 -2.3740814e-11 96.93705 -0.025 0 0 0 0 -1.2298254e-09 2.371559e-10 -0.0040591525 0 1.2298302e-09 1.2298302e-09
290 -6155.851 0 6.6834666e-12 -9.0749829e-12 96.936403 -0.025 0 0 0 0 -7.3137352e-10 1.0983283e-09 0.0010075626 0 7.3137798e-10 7.3137798e-10
300 -6155.851 0 9.4443218e-13 5.2069655e-13 96.936293 -0.025 0 0 0 0 4.9924787e-12 3.5018175e-10 0.0057823754 0 -4.9956751e-12 -4.9956751e-12
310 -6155.851 0 4.9457364e-11 -2.183241e-11 96.936135 -0.025 0 0 0 0 5.5646397e-10 -3.1013634e-09 0.0066174421 0 -5.5646838e-10 -5.5646838e-10
320 -6155.851 0 1.1303802e-11 -1.5610116e-11 96.935999 -0.025 0 0 0 0 9.3725597e-11 -2.0834063e-10 0.0066461623 0 -9.3720589e-11 -9.3720589e-11
330 -6155.851 0 -8.7492205e-11 5.0132409e-11 96.935781 -0.025 0 0 0 0 1.5034892e-09 4.8824636e-09 0.0058982085 0 -1.5034817e-09 -1.5034817e-09
340 -6155.851 0 1.4386338e-10 -4.2580912e-11 96.935678 -0.025 0 0 0 0 -4.4942366e-09 -4.8008051e-09 0.0019740498 0 4.4942601e-09 4.4942601e-09
350 -6155.851 0 -1.5770775e-12 -1.5554503e-11 96.935641 -0.025 0 0 0 0 -1.789129e-09 4.3210504e-10 0.0016260173 0 1.7891285e-09 1.7891285e-09
360 -6155.851 0 -1.3297897e-10 5.1630323e-11 96.935622 -0.025 0 0 0 0 9.3219024e-09 5.9535856e-10 0.00082004967 0 -9.3218922e-09 -9.3218922e-09
370 -6155.851 0 5.4333939e-11 -2.6192184e-11 96.935617 -0.025 0 0 0 0 -4.3663676e-10 -5.1620423e-10 0.0012789335 0 4.3664737e-10 4.3664737e-10
380 -6155.851 0 -6.6039258e-12 -7.5609136e-12 96.935612 -0.025 0 0 0 0 -8.3813595e-09 4.7199823e-09 0.0011369214 0 8.3813612e-09 8.3813612e-09
390 -6155.851 0 -1.0040056e-10 8.5325014e-11 96.935587 -0.025 0 0 0 0 1.1171651e-08 -1.0037805e-08 0.00012469127 0 -1.1171646e-08 -1.1171646e-08
400 -6155.851 0 5.0853732e-11 -4.2801835e-11 96.935572 -0.025 0 0 0 0 -1.9340418e-09 1.74979e-09 0.00019466711 0 1.9340627e-09 1.9340627e-09
410 -6155.851 0 1.2049586e-10 -9.9618548e-11 96.935543 -0.025 0 0 0 0 -2.0243059e-08 1.9356236e-08 0.0002523799 0 2.0243046e-08 2.0243046e-08
420 -6155.851 0 1.7899642e-11 3.5995836e-12 96.935531 -0.025 0 0 0 0 3.5620666e-09 -2.7057846e-09 0.00024873544 0 -3.5620556e-09 -3.5620556e-09
430 -6155.851 0 -2.3941392e-11 2.3004815e-11 96.935527 -0.025 0 0 0 0 9.3931782e-09 -8.5349023e-09 0.0001591579 0 -9.3931752e-09 -9.3931752e-09
440 -6155.851 0 1.3054108e-10 -1.2689303e-10 96.935522 -0.025 0 0 0 0 -2.63239e-08 2.3190494e-08 0.00014838156 0 2.6323909e-08 2.6323909e-08
450 -6155.851 0 -3.3583974e-12 2.1841662e-11 96.93552 -0.025 0 0 0 0 7.9211719e-09 -6.7971069e-09 0.00012051248 0 -7.921168e-09 -7.921168e-09
460 -6155.851 0 -6.7930456e-10 6.424851e-10 96.935514 -0.025 0 0 0 0 1.2429227e-07 -1.0630871e-07 0.00014409432 0 -1.2429226e-07 -1.2429226e-07
470 -6155.851 0 5.649524e-10 -5.6453071e-10 96.935512 -0.025 0 0 0 0 -1.0735848e-07 8.9872405e-08 0.00010631061 0 1.0735848e-07 1.0735848e-07
480 -6155.851 0 6.13809e-10 -4.9012022e-10 96.935509 -0.025 0 0 0 0 -5.5839534e-08 4.5710027e-08 8.7271236e-05 0 5.5839543e-08 5.5839543e-08
490 -6155.851 0 -6.1673512e-10 5.8106663e-10 96.935508 -0.025 0 0 0 0 8.9417248e-08 -6.795396e-08 4.2860856e-05 0 -8.941724e-08 -8.941724e-08
500 -6155.851 0 -1.4672717e-11 -1.0669776e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116217e-08 1.9116217e-08
Loop time of 100.289 on 4 procs for 500 steps with 846 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-6146.53284043 -6155.85100774 -6155.85100774
Force two-norm initial, final = 9.08523 6.13752e-06
Force max component initial, final = 2.35947 4.97842e-07
Final line search alpha, max atom move = 1 4.97842e-07
Iterations, force evaluations = 500 1000
Pair time (%) = 9.67277 (9.6449)
Neigh time (%) = 0 (0)
Comm time (%) = 6.21171 (6.19381)
Outpt time (%) = 2.68868 (2.68093)
Other time (%) = 81.7159 (81.4804)
Nlocal: 211.5 ave 216 max 207 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 191.25 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 47313 ave 52056 max 42570 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 189252
Ave neighs/atom = 223.702
Neighbor list builds = 0
Dangerous builds = 0
min_style sd
min_modify line backtrack
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
500 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116216e-08 1.9116216e-08
501 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116216e-08 1.9116216e-08
Loop time of 0.124472 on 4 procs for 1 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85100774 -6155.85100774 -6155.85100774
Force two-norm initial, final = 6.13752e-06 6.13752e-06
Force max component initial, final = 4.97842e-07 4.97842e-07
Final line search alpha, max atom move = 0.5 2.48921e-07
Iterations, force evaluations = 1 2
Pair time (%) = 0.0223783 (17.9785)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00169677 (1.36317)
Outpt time (%) = 0 (0)
Other time (%) = 0.100397 (80.6583)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable uz equal c_CM[3]
# variable F equal f_AtC[5]
# variable Fz equal f_AtC[7]
variable F equal c_RSUM[1]
variable Fz equal c_RSUM[3]
variable R equal $F-$C*$b
variable R equal 1.9116216109081213915e-08-$C*$b
variable R equal 1.9116216109081213915e-08--0.025000000000000001388*$b
variable R equal 1.9116216109081213915e-08--0.025000000000000001388*0
variable Rz equal ${Fz}-$C*$a
variable Rz equal -3.2008125606681979403e-05-$C*$a
variable Rz equal -3.2008125606681979403e-05--0.025000000000000001388*$a
variable Rz equal -3.2008125606681979403e-05--0.025000000000000001388*0
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*90/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*90/3./-1.4672651617664272549e-11
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal -316591754.20715177059*${eV2J}*${A2m}
variable EI equal -316591754.20715177059*1.6021764600000000642e-19*${A2m}
variable EI equal -316591754.20715177059*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0 0 F 1.9116216109081213915e-08 -3.2008125606681979403e-05 u -1.4672651617664272549e-11 96.935507997738042718 c -0.0027777777777777778838 phi 0 EI -5.072358560208045613e-21 R 1.9116216109081213915e-08 -3.2008125606681979403e-05
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (2-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 0 0
ATC: created function : 0 + 0.0333333(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
501 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0.00083333333 -1.9116216e-08 1.6870874e-08 3.2008126e-05 1.222715e-14 0.00083335245 0.00083335245
510 -6155.851 0 7.5244067e-05 -1.3502021e-11 96.935508 -0.025 0 0 0 0.00083333333 3.2438701e-08 -3.0416424e-08 -1.4566602e-05 -6.2703389e-08 0.00083330089 0.00083330089
520 -6155.851 0 0.00023596516 2.4216597e-11 96.935508 -0.025 0 0 0 0.00083333333 -9.6655814e-09 1.7834635e-08 3.5959276e-05 -1.9663763e-07 0.000833343 0.000833343
530 -6155.851 0 0.0004521778 -1.8488146e-10 96.935507 -0.025 0 0 0 0.00083333333 -2.8087999e-08 1.4373107e-08 2.6399328e-05 -3.7681483e-07 0.00083336142 0.00083336142
540 -6155.851 0 0.00068686652 2.2560925e-10 96.935506 -0.025 0 0 0 0.00083333333 5.1280851e-08 -4.944283e-08 -2.3516917e-05 -5.7238876e-07 0.00083328205 0.00083328205
550 -6155.851 0 0.00097528387 -6.0249475e-11 96.935505 -0.025 0 0 0 0.00083333333 -3.0869719e-08 4.6053248e-08 -9.2849468e-06 -8.1273656e-07 0.0008333642 0.0008333642
560 -6155.851 0 0.0012888546 -4.7543618e-10 96.935504 -0.025 0 0 0 0.00083333333 -1.4084137e-08 -6.9499793e-09 3.5765609e-05 -1.0740455e-06 0.00083334742 0.00083334742
570 -6155.851 0 0.0016207689 7.8821517e-10 96.935503 -0.025 0 0 0 0.00083333333 2.0767366e-08 -2.5348885e-08 -4.7729297e-05 -1.3506408e-06 0.00083331257 0.00083331257
580 -6155.851 0 0.00198597 -5.3637299e-10 96.935501 -0.025 0 0 0 0.00083333333 -5.4517718e-06 9.2340557e-09 -4.9488581e-05 -1.654975e-06 0.00083878511 0.00083878511
590 -6155.851 0 0.0023856369 -4.1449046e-10 96.9355 -0.025 0 0 0 0.00083333333 -3.8437452e-05 2.7829132e-08 -6.8439705e-05 -1.9880307e-06 0.00087177079 0.00087177079
600 -6155.851 0 0.0028044617 1.0997501e-09 96.935499 -0.025 0 0 0 0.00083333333 2.0036119e-05 -2.8313041e-08 -0.00038373515 -2.3370514e-06 0.00081329721 0.00081329721
610 -6155.851 0 0.0032615703 -9.438232e-10 96.935498 -0.025 0 0 0 0.00083333333 -6.721699e-05 -1.6094486e-08 0.00026852221 -2.7179752e-06 0.00090055032 0.00090055032
620 -6155.851 0 0.0037228155 -9.8658553e-11 96.935498 -0.025 0 0 0 0.00083333333 -5.0356472e-05 6.6220662e-08 -0.00016057488 -3.1023462e-06 0.00088368981 0.00088368981
630 -6155.851 0 0.0042063596 4.5342852e-10 96.935499 -0.025 0 0 0 0.00083333333 -0.00024149697 -6.6311642e-08 -0.00013128121 -3.5052997e-06 0.0010748303 0.0010748303
640 -6155.851 0 0.0047053923 -4.4915583e-12 96.935498 -0.025 0 0 0 0.00083333333 0.00018476866 8.5931516e-09 -1.0920921e-05 -3.9211602e-06 0.00064856468 0.00064856468
650 -6155.851 0 0.0051780729 -5.9267245e-10 96.9355 -0.025 0 0 0 0.00083333333 0.0012250879 4.6153937e-08 0.00016791897 -4.3150607e-06 -0.00039175458 -0.00039175458
660 -6155.851 0 0.005528704 2.0178848e-10 96.935499 -0.025 0 0 0 0.00083333333 0.0023386089 -4.9920568e-08 -0.00030153107 -4.6072533e-06 -0.0015052756 -0.0015052756
670 -6155.851 0 0.0067930159 2.0337825e-09 96.935504 -0.025 0 0 0 0.00083333333 0.00277847 9.6153354e-08 -0.001427071 -5.6608465e-06 -0.0019451367 -0.0019451367
680 -6155.851 0 0.0091353864 -1.2005671e-09 96.935506 -0.025 0 0 0 0.00083333333 -0.00098634606 -5.6084108e-09 -0.0001949811 -7.612822e-06 0.0018196794 0.0018196794
690 -6155.851 0 0.0092720897 -6.6192949e-11 96.935506 -0.025 0 0 0 0.00083333333 -0.0015552585 -8.6270391e-10 9.3688022e-05 -7.7267414e-06 0.0023885919 0.0023885919
699 -6155.851 0 0.0093583676 1.0464746e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017464739 2.5209399e-08 7.7398462e-05 -7.7986397e-06 0.0025798072 0.0025798072
Loop time of 14.1081 on 4 procs for 198 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85100774 -6155.85101159 -6155.85101159
Force two-norm initial, final = 0.000277846 0.0011336
Force max component initial, final = 9.26371e-05 0.00012545
Final line search alpha, max atom move = 0.0078125 9.80074e-07
Iterations, force evaluations = 198 409
Pair time (%) = 3.19903 (22.6752)
Neigh time (%) = 0 (0)
Comm time (%) = 0.348575 (2.47075)
Outpt time (%) = 0.160979 (1.14104)
Other time (%) = 10.3995 (73.713)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
min_style sd
min_modify line backtrack
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
699 -6155.851 0 0.0093583676 1.0464746e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017464739 2.5209399e-08 7.7398462e-05 -7.7986397e-06 0.0025798072 0.0025798072
700 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017544129 2.4247674e-08 5.1686313e-05 -7.7987745e-06 0.0025877462 0.0025877462
701 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017544129 2.4247674e-08 5.1686313e-05 -7.7987745e-06 0.0025877462 0.0025877462
Loop time of 0.5394 on 4 procs for 2 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85101159 -6155.8510116 -6155.8510116
Force two-norm initial, final = 0.0011336 0.000872834
Force max component initial, final = 0.00012545 8.10661e-05
Final line search alpha, max atom move = 0.015625 1.26666e-06
Iterations, force evaluations = 2 14
Pair time (%) = 0.111926 (20.7502)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0156116 (2.89425)
Outpt time (%) = 0.0084697 (1.57021)
Other time (%) = 0.403392 (74.7853)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable uz equal c_CM[3]
# variable F equal f_AtC[5]
# variable Fz equal f_AtC[7]
variable F equal c_RSUM[1]
variable Fz equal c_RSUM[3]
variable R equal $F-$C*$b
variable R equal 0.0025877461923070671154-$C*$b
variable R equal 0.0025877461923070671154--0.025000000000000001388*$b
variable R equal 0.0025877461923070671154--0.025000000000000001388*0.033333333333333332871
variable Rz equal ${Fz}-$C*$a
variable Rz equal -5.16863129458517475e-05-$C*$a
variable Rz equal -5.16863129458517475e-05--0.025000000000000001388*$a
variable Rz equal -5.16863129458517475e-05--0.025000000000000001388*0
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*90*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*90*90/3./$u
variable EI equal 0.0025877461923070671154*90*90*90/3./0.0093585293597155689432
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 67192.429553881200263*${eV2J}*${A2m}
variable EI equal 67192.429553881200263*1.6021764600000000642e-19*${A2m}
variable EI equal 67192.429553881200263*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.033333333333333332871 0 F 0.0025877461923070671154 -5.16863129458517475e-05 u 0.0093585293597155689432 96.935509332376838643 c -0.0027777777777777778838 phi 0 EI 1.0765412892143675813e-24 R 0.0034210795256404006107 -5.16863129458517475e-05
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (3-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 0 0
ATC: created function : 0 + 0.0666667(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
701 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.0016666667 -0.0017544129 2.4247674e-08 5.1686313e-05 -1.5597549e-05 0.0034210795 0.0034210795
710 -6155.851 0 0.0093927498 -5.1805658e-10 96.935509 -0.025 0 0 0 0.0016666667 -0.001496399 -1.5573071e-08 7.0866631e-05 -1.5654583e-05 0.0031630657 0.0031630657
720 -6155.851 0 0.0095888777 -5.6216657e-11 96.935505 -0.025 0 0 0 0.0016666667 -0.0012004213 3.8090266e-08 -0.00014799652 -1.5981463e-05 0.002867088 0.002867088
730 -6155.851 0 0.0099072785 4.4310767e-10 96.935503 -0.025 0 0 0 0.0016666667 -0.0012734816 3.5022383e-09 -0.00014979591 -1.6512131e-05 0.0029401483 0.0029401483
740 -6155.851 0 0.010283518 -1.5173013e-09 96.935504 -0.025 0 0 0 0.0016666667 -0.0010070513 -1.0777316e-07 8.9852513e-05 -1.7139197e-05 0.0026737179 0.0026737179
750 -6155.851 0 0.010683953 1.4747556e-09 96.935501 -0.025 0 0 0 0.0016666667 -0.00089533919 1.3811485e-07 -6.6972671e-05 -1.7806589e-05 0.0025620059 0.0025620059
760 -6155.851 0 0.011131302 -8.2231093e-10 96.9355 -0.025 0 0 0 0.0016666667 -0.00011238797 -3.2303593e-08 -3.3022463e-06 -1.855217e-05 0.0017790546 0.0017790546
770 -6155.851 0 0.011585226 1.1357581e-10 96.9355 -0.025 0 0 0 0.0016666667 -0.0008139296 -1.0279988e-07 7.672706e-05 -1.9308709e-05 0.0024805963 0.0024805963
780 -6155.851 0 0.012015856 -1.7079649e-11 96.935492 -0.025 0 0 0 0.0016666667 -0.00011750039 1.4724756e-07 2.6085857e-05 -2.0026427e-05 0.0017841671 0.0017841671
790 -6155.851 0 0.012432647 -5.7454545e-10 96.935489 -0.025 0 0 0 0.0016666667 -2.6583326e-05 -5.8164597e-08 -0.00024192986 -2.0721078e-05 0.00169325 0.00169325
800 -6155.851 0 0.012864332 1.1612045e-09 96.935494 -0.025 0 0 0 0.0016666667 -0.00013922996 -7.3129958e-08 0.00017322782 -2.1440553e-05 0.0018058966 0.0018058966
810 -6155.851 0 0.013534631 -1.599629e-09 96.935497 -0.025 0 0 0 0.0016666667 0.00021713244 2.0110132e-07 -0.00011691578 -2.2557718e-05 0.0014495342 0.0014495342
820 -6155.851 0 0.014473048 1.4920287e-09 96.935488 -0.025 0 0 0 0.0016666667 0.00072740903 -2.2264896e-07 -0.00025826088 -2.4121746e-05 0.00093925764 0.00093925764
830 -6155.851 0 0.015814165 9.9540852e-10 96.935488 -0.025 0 0 0 0.0016666667 -0.00020150428 -1.4648382e-07 5.1213137e-05 -2.6356941e-05 0.0018681709 0.0018681709
840 -6155.851 0 0.017960316 -3.6691752e-09 96.935483 -0.025 0 0 0 0.0016666667 0.00095321447 6.0691053e-07 0.00078150564 -2.993386e-05 0.0007134522 0.0007134522
850 -6155.851 0 0.020433235 1.5826068e-09 96.935477 -0.025 0 0 0 0.0016666667 0.0035255313 -2.7216094e-07 -0.0011364529 -3.4055392e-05 -0.0018588646 -0.0018588646
860 -6155.851 0 0.023085812 3.1475892e-09 96.935486 -0.025 0 0 0 0.0016666667 0.01015645 -5.3450364e-07 -0.00055909791 -3.8476354e-05 -0.0084897836 -0.0084897836
870 -6155.851 0 0.027552884 -1.0798686e-08 96.935526 -0.025 0 0 0 0.0016666667 0.016481473 2.2189423e-06 0.0016007847 -4.5921473e-05 -0.014814807 -0.014814807
880 -6155.8511 0 0.055457179 -1.535611e-08 96.935606 -0.025 0 0 0 0.0016666667 0.013469024 1.8368724e-06 0.007644777 -9.2428631e-05 -0.011802357 -0.011802357
890 -6155.8511 0 0.070355074 3.8023025e-09 96.93559 -0.025 0 0 0 0.0016666667 0.0045123223 -1.0894883e-06 0.0012650095 -0.00011725846 -0.0028456556 -0.0028456556
900 -6155.8511 0 0.071239511 -9.5003883e-11 96.935566 -0.025 0 0 0 0.0016666667 0.0041482123 5.3052778e-08 0.0013631978 -0.00011873252 -0.0024815456 -0.0024815456
910 -6155.8511 0 0.071770633 1.2925244e-09 96.935508 -0.025 0 0 0 0.0016666667 0.0041066236 3.455464e-07 -4.7637007e-05 -0.00011961772 -0.0024399569 -0.0024399569
920 -6155.8511 0 0.07241886 -3.7163732e-10 96.935444 -0.025 0 0 0 0.0016666667 0.0043614531 -4.0071843e-07 -0.0020847574 -0.0001206981 -0.0026947864 -0.0026947864
930 -6155.8511 0 0.08035653 -8.2019055e-09 96.935169 -0.025 0 0 0 0.0016666667 0.0030840679 -1.6577238e-06 -0.0028722541 -0.00013392755 -0.0014174012 -0.0014174012
940 -6155.8511 0 0.10233759 1.4658533e-09 96.934738 -0.025 0 0 0 0.0016666667 0.0030986023 6.3718151e-07 0.0075147368 -0.00017056265 -0.0014319357 -0.0014319357
950 -6155.8511 0 0.1091589 4.8592844e-10 96.934799 -0.025 0 0 0 0.0016666667 0.0019854702 -1.4318185e-07 0.012415464 -0.00018193149 -0.00031880356 -0.00031880356
960 -6155.8511 0 0.12158268 2.8258211e-09 96.935015 -0.025 0 0 0 0.0016666667 0.0013596908 -1.5767032e-06 0.0030979015 -0.00020263779 0.00030697591 0.00030697591
970 -6155.8511 0 0.12403838 -1.3425882e-09 96.935054 -0.025 0 0 0 0.0016666667 0.0017582125 -2.2550336e-07 -0.0026021546 -0.00020673063 -9.1545869e-05 -9.1545869e-05
972 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487
Loop time of 25.365 on 4 procs for 271 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.8510194 -6155.85111851 -6155.85111851
Force two-norm initial, final = 0.000910877 0.000855978
Force max component initial, final = 9.24024e-05 8.83791e-05
Final line search alpha, max atom move = 0.015625 1.38092e-06
Iterations, force evaluations = 271 553
Pair time (%) = 4.51795 (17.8118)
Neigh time (%) = 0 (0)
Comm time (%) = 1.02193 (4.0289)
Outpt time (%) = 0.702078 (2.7679)
Other time (%) = 19.123 (75.3914)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
min_style sd
min_modify line backtrack
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
972 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487
973 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487
Loop time of 0.277416 on 4 procs for 1 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85111851 -6155.85111851 -6155.85111851
Force two-norm initial, final = 0.000855978 0.000855978
Force max component initial, final = 8.83791e-05 8.83791e-05
Final line search alpha, max atom move = 0.015625 1.38092e-06
Iterations, force evaluations = 1 7
Pair time (%) = 0.0593559 (21.396)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00413132 (1.48921)
Outpt time (%) = 0 (0)
Other time (%) = 0.213929 (77.1148)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable uz equal c_CM[3]
# variable F equal f_AtC[5]
# variable Fz equal f_AtC[7]
variable F equal c_RSUM[1]
variable Fz equal c_RSUM[3]
variable R equal $F-$C*$b
variable R equal -0.00010577487498249815213-$C*$b
variable R equal -0.00010577487498249815213--0.025000000000000001388*$b
variable R equal -0.00010577487498249815213--0.025000000000000001388*0.066666666666666665741
variable Rz equal ${Fz}-$C*$a
variable Rz equal 0.0025842016931355718881-$C*$a
variable Rz equal 0.0025842016931355718881--0.025000000000000001388*$a
variable Rz equal 0.0025842016931355718881--0.025000000000000001388*0
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*90*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*90*90/3./$u
variable EI equal -0.00010577487498249815213*90*90*90/3./0.12405404654784669971
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal -207.1943264731270915*${eV2J}*${A2m}
variable EI equal -207.1943264731270915*1.6021764600000000642e-19*${A2m}
variable EI equal -207.1943264731270915*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.066666666666666665741 0 F -0.00010577487498249815213 0.0025842016931355718881 u 0.12405404654784669971 96.935053768033569099 c -0.0027777777777777778838 phi 0 EI -3.3196187252079907596e-27 R 0.0015608917916841685402 0.0025842016931355718881
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (4-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 0 0
ATC: created function : 0 + 0.1(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
973 -6155.8512 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0025 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00031013512 0.00072755846 0.00072755846
977 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508
Loop time of 1.007 on 4 procs for 4 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85122189 -6155.85122188 -6155.85122188
Force two-norm initial, final = 0.000891466 0.000702795
Force max component initial, final = 0.000104825 6.49275e-05
Final line search alpha, max atom move = 0.015625 1.01449e-06
Iterations, force evaluations = 4 19
Pair time (%) = 0.155607 (15.4525)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0349094 (3.46666)
Outpt time (%) = 0 (0)
Other time (%) = 0.816487 (81.0808)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
min_style sd
min_modify line backtrack
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt0] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 55.3135 Mbytes
Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1]
977 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508
978 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508
Loop time of 0.277741 on 4 procs for 1 steps with 846 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6155.85122188 -6155.85122188 -6155.85122188
Force two-norm initial, final = 0.000702795 0.000702795
Force max component initial, final = 6.49275e-05 6.49275e-05
Final line search alpha, max atom move = 0.015625 1.01449e-06
Iterations, force evaluations = 1 7
Pair time (%) = 0.0594354 (21.3995)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00418288 (1.50603)
Outpt time (%) = 0 (0)
Other time (%) = 0.214123 (77.0944)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable uz equal c_CM[3]
# variable F equal f_AtC[5]
# variable Fz equal f_AtC[7]
variable F equal c_RSUM[1]
variable Fz equal c_RSUM[3]
variable R equal $F-$C*$b
variable R equal 0.00077379508410631867108-$C*$b
variable R equal 0.00077379508410631867108--0.025000000000000001388*$b
variable R equal 0.00077379508410631867108--0.025000000000000001388*0.10000000000000001943
variable Rz equal ${Fz}-$C*$a
variable Rz equal 0.0026622076933775122923-$C*$a
variable Rz equal 0.0026622076933775122923--0.025000000000000001388*$a
variable Rz equal 0.0026622076933775122923--0.025000000000000001388*0
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*90*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*90*90/3./$u
variable EI equal 0.00077379508410631867108*90*90*90/3./0.12406087903930071437
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 1515.6446326506320474*${eV2J}*${A2m}
variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*${A2m}
variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.10000000000000001943 0 F 0.00077379508410631867108 0.0026622076933775122923 u 0.12406087903930071437 96.935055022011525239 c -0.0027777777777777778838 phi 0 EI 2.4283301521581904147e-26 R 0.0032737950841063190484 0.0026622076933775122923
next i
jump SELF loop_i

632
examples/USER/atc/elastic/electrostatic_bending_dos.screen Normal file
View File

@ -0,0 +1,632 @@
LAMMPS (14 Aug 2013)
units metal
atom_style charge
dielectric 1.
boundary s s f
# read in CNT
read_data min_CNT_dos.data
Reading data file ...
orthogonal box = (-3.72623 -3.66963 0) to (3.60284 3.66963 100)
1 by 1 by 4 MPI processor grid
846 atoms
846 velocities
set group all charge 0
Setting atom values ...
846 settings made for charge
lattice diamond 3.6
Lattice spacing in x,y,z = 3.6 3.6 3.6
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
compute q all property/atom q
compute Q all reduce sum c_q
# PARAMETERS-----------------------------
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
variable Lx equal xhi-xlo
variable L equal zhi-zlo
variable zTip equal zhi-3.5
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xhiFE equal 5.0*6.0499999999999998224
variable xloFE equal -${xhiFE}
variable xloFE equal -30.25
variable yhiFE equal $R
variable yhiFE equal 6.0499999999999998224
variable yloFE equal -${yhiFE}
variable yloFE equal -6.0499999999999998224
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable zhiFE equal zhi+(zhi-10)/12*2
variable Lfree equal zhi-${zloFE}
variable Lfree equal zhi-10
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
Length 100 [10, 115] 96.5
variable Vb equal 0.1
variable Vg equal 0.15
variable V0 equal 1. # 2.
print "bias voltage ${Vb}, gate voltage ${Vg}"
bias voltage 0.10000000000000000555, gate voltage 0.14999999999999999445
variable ng equal 3
variable n equal 100000
variable s equal 250
# END -----------------------------------
region TIP block INF INF INF INF ${zTip} INF units box
region TIP block INF INF INF INF 96.5 INF units box
group TIP region TIP
9 atoms in group TIP
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box
region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box
group internal region feRegion
756 atoms in group internal
group FIXED subtract all internal
90 atoms in group FIXED
fix FIX FIXED setforce 0 0 0
thermo 10
set group all image 0 0 0
Setting atom values ...
846 settings made for image
compute CM TIP com
thermo_style custom step c_Q etotal c_CM[1] c_CM[3]
#minimize 0 0 1000 1000
#write_restart min_CNT_dos.rst
run 0
Setting up run ...
Memory usage per processor = 2.45103 Mbytes
Step Q TotEng CM[1] CM[3]
0 0 -6155.851 -3752.4867 -51103.063
Loop time of 0.00996494 on 4 procs for 0 steps with 846 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 0.00996494 (100)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 159.75 ave 216 max 108 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 37714.5 ave 40824 max 32904 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 150858
Ave neighs/atom = 178.319
Neighbor list builds = 0
Dangerous builds = 0
#EXIT
variable L equal c_CM[1]
variable Lx equal $L
variable Lx equal -3752.4866657778384251
variable dx equal c_CM[1]-${Lx}
variable dx equal c_CM[1]--3752.4866657778384251
variable L equal c_CM[3]
variable Lz equal $L
variable Lz equal -51103.063299276320322
variable dz equal c_CM[3]-${Lz}
variable dz equal c_CM[3]--51103.063299276320322
print "initial ${Lx} ${Lz} "
initial -3752.4866657778384251 -51103.063299276320322
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
>>> number of stationary ghosts: 90 of 846
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep 0
thermo 100
# coupling ............................................................
fix AtC internal atc electrostatic CNT_electrostatic2.mat
ATC: constructing electrostatic mechanical coupling with parameter file CNT_electrostatic2.mat
ATC: peratom PE compute created with ID: 6
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
ATC: creating electrostatic extrinsic model
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
ATC: computed mass density : 2.05933
ATC: 1 materials defined from CNT_electrostatic2.mat
fix_modify AtC omit atomic_charge
#fix_modify AtC internal_quadrature off ## NOTE active -> error
# note weights don't affect phi or f i.e. they divide out
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
fix_modify AtC source_integration atom
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum none # flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 ${nz} feRegion f p f
fix_modify AtC mesh create 10 1 14 feRegion f p f
ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements
# node sets ............................................................
variable t equal 1.1*$R
variable t equal 1.1*6.0499999999999998224
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box
fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box
ATC: created nodeset tube with 39 nodes
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box
ATC: created nodeset lefttube with 3 nodes
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box
ATC: created nodeset rbc with 11 nodes
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box
ATC: created nodeset lbc with 11 nodes
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box
ATC: created nodeset top with 15 nodes
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box
ATC: created nodeset bot with 15 nodes
# boundary conditions ..................................................
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# minimize .............................................................
compute FSUM all reduce sum fx fy fz
compute RSUM internal reduce sum fx fy fz
thermo $s
thermo 250
fix_modify AtC output electrostatic_bending_dosFE 100000000 full_text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC output index step
# store original (reference) coordinates
fix X all store/state 0 x y z
# NOTE not recognized as vector by paraview - due to dump2ensight
variable uX atom x-f_X[1]
variable uY atom y-f_X[2]
variable uZ atom z-f_X[3]
#variable uX atom x-f_AtC[1]
#variable uY atom y-f_AtC[2]
#variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom 100000 electrostatic_bending_dos.dmp id type x y z c_q v_uX v_uY v_uZ v_rho
reset_timestep 0
log electrostatic_bending_dos.log
thermo 10 # 1 # 10
min_modify line quadratic
variable a equal 0
variable i loop ${ng}
variable i loop 3
thermo_style custom step c_Q pe v_dx v_dz f_FIX[1] f_FIX[3]
label loop_i
variable b equal ($i-1)*${Vg}/${ng}/${Lz}
variable b equal (1-1)*${Vg}/${ng}/${Lz}
variable b equal (1-1)*0.14999999999999999445/${ng}/${Lz}
variable b equal (1-1)*0.14999999999999999445/3/${Lz}
variable b equal (1-1)*0.14999999999999999445/3/-51103.063299276320322
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
fix_modify AtC fix electric_potential all linear 0 0 0 -0 0 $a ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -0 0 0 ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -0 0 0 1
ATC: created function : 1 + -0(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: all initial conditions for displacement have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
ATC: WARNING: material: [cnt] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 51.8077 Mbytes
Step Q PotEng dx dz FIX[1] FIX[3]
0 0 -6155.851 0 0 2.2200304e-11 0.010686876
10 0 -6155.851 2.7284841e-12 -0.00060946523 5.7770455e-11 0.0091922227
20 0 -6155.851 4.0927262e-12 -0.0011905579 -4.4327736e-13 0.0001153156
30 0 -6155.851 4.5474735e-12 -0.0011946243 2.1081175e-11 1.3099811e-05
40 0 -6155.851 4.5474735e-12 -0.0011946457 2.2032078e-11 6.8020645e-06
50 0 -6155.851 5.4569682e-12 -0.0011947265 2.2896851e-11 6.476084e-06
60 0 -6155.851 7.730705e-12 -0.0011953427 2.2953812e-11 3.5758304e-06
70 0 -6155.851 8.1854523e-12 -0.0011954794 1.9801188e-11 8.3950483e-07
80 0 -6155.851 8.1854523e-12 -0.0011954783 1.8441963e-11 2.9804539e-07
90 0 -6155.851 7.2759576e-12 -0.0011954747 2.1744013e-11 -3.8789192e-08
100 0 -6155.851 7.730705e-12 -0.0011954732 1.9237549e-11 -2.8935894e-09
110 0 -6155.851 7.2759576e-12 -0.0011954716 1.9095805e-11 1.6112378e-09
120 0 -6155.851 8.1854523e-12 -0.0011954714 1.9817977e-11 4.6976383e-09
130 0 -6155.851 7.730705e-12 -0.0011954714 1.7488642e-11 3.2517748e-09
140 0 -6155.851 1.0004442e-11 -0.0011954717 1.5207016e-11 2.7887026e-11
150 0 -6155.851 1.0459189e-11 -0.0011954718 1.7530141e-11 6.6725403e-11
160 0 -6155.851 1.0913936e-11 -0.0011954718 1.7545739e-11 8.9193097e-12
170 0 -6155.851 1.0913936e-11 -0.0011954718 1.7562698e-11 8.2844842e-12
180 0 -6155.851 1.0913936e-11 -0.0011954718 1.7454236e-11 8.3764107e-12
190 0 -6155.851 1.0913936e-11 -0.0011954718 1.7391744e-11 8.3804075e-12
200 0 -6155.851 1.0913936e-11 -0.0011954718 1.7363343e-11 8.2092111e-12
210 0 -6155.851 1.0913936e-11 -0.0011954718 1.7510129e-11 8.3804075e-12
220 0 -6155.851 1.0913936e-11 -0.0011954718 1.7388087e-11 8.3107965e-12
230 0 -6155.851 1.0913936e-11 -0.0011954718 1.7328517e-11 8.3658636e-12
240 0 -6155.851 1.0913936e-11 -0.0011954718 1.7553941e-11 8.2239771e-12
250 0 -6155.851 1.0913936e-11 -0.0011954718 1.7431705e-11 7.9389828e-12
260 0 -6155.851 1.0913936e-11 -0.0011954718 1.7440851e-11 8.2803764e-12
270 0 -6155.851 1.0913936e-11 -0.0011954718 1.7502551e-11 8.4340313e-12
280 0 -6155.851 1.0913936e-11 -0.0011954718 1.7509039e-11 8.2114315e-12
290 0 -6155.851 1.0913936e-11 -0.0011954718 1.7563475e-11 8.2074347e-12
300 0 -6155.851 1.0913936e-11 -0.0011954718 1.7385805e-11 8.4339202e-12
310 0 -6155.851 1.0913936e-11 -0.0011954718 1.7432996e-11 8.3754115e-12
320 0 -6155.851 1.0913936e-11 -0.0011954718 1.7523174e-11 8.472778e-12
330 0 -6155.851 1.0913936e-11 -0.0011954718 1.7343221e-11 8.1784579e-12
340 0 -6155.851 1.0913936e-11 -0.0011954718 1.7426002e-11 8.1481488e-12
350 0 -6155.851 1.0913936e-11 -0.0011954718 1.74698e-11 8.3067997e-12
360 0 -6155.851 1.0913936e-11 -0.0011954718 1.738067e-11 8.5164098e-12
370 0 -6155.851 1.0913936e-11 -0.0011954718 1.753599e-11 8.3784091e-12
380 0 -6155.851 1.0913936e-11 -0.0011954718 1.7339446e-11 8.3465457e-12
390 0 -6155.851 1.0913936e-11 -0.0011954718 1.7437576e-11 8.5182972e-12
400 0 -6155.851 1.0913936e-11 -0.0011954718 1.7300047e-11 8.1350482e-12
410 0 -6155.851 1.0913936e-11 -0.0011954718 1.7222838e-11 8.2779339e-12
420 0 -6155.851 1.0913936e-11 -0.0011954718 1.7421602e-11 8.0918605e-12
430 0 -6155.851 1.0913936e-11 -0.0011954718 1.7416773e-11 8.3816287e-12
440 0 -6155.851 1.0913936e-11 -0.0011954718 1.7347863e-11 8.4523499e-12
450 0 -6155.851 1.0913936e-11 -0.0011954718 1.7408828e-11 8.1795681e-12
460 0 -6155.851 1.0913936e-11 -0.0011954718 1.7534991e-11 8.308576e-12
470 0 -6155.851 1.0913936e-11 -0.0011954718 1.7459565e-11 8.2645002e-12
480 0 -6155.851 1.0913936e-11 -0.0011954718 1.7273457e-11 8.5179641e-12
490 0 -6155.851 1.0913936e-11 -0.0011954718 1.7452029e-11 8.4042773e-12
500 0 -6155.851 1.0913936e-11 -0.0011954718 1.7463576e-11 8.1070706e-12
Loop time of 154.975 on 4 procs for 500 steps with 846 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-6155.85097822 -6155.8510078 -6155.8510078
Force two-norm initial, final = 0.00144775 6.46495e-12
Force max component initial, final = 0.000150789 6.70891e-13
Final line search alpha, max atom move = 1 6.70891e-13
Iterations, force evaluations = 500 1000
Pair time (%) = 10.2259 (6.59839)
Neigh time (%) = 0 (0)
Comm time (%) = 7.76684 (5.01167)
Outpt time (%) = 0.783488 (0.505557)
Other time (%) = 136.199 (87.8844)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
#min_style sd
#min_modify line backtrack
#minimize 0 0 1000 1000
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable Q equal c_Q
variable ux equal ${dx}
variable ux equal 1.0913936421275138855e-11
variable uz equal ${dz}
variable uz equal -0.0011954718283959664404
variable Fx equal f_FIX[1]
variable Fz equal f_FIX[3]
variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7463575724407931489e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7463575724407931489e-11*90*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7463575724407931489e-11*90*90*${Lfree}/3./${ux}
variable EI equal 1.7463575724407931489e-11*90*90*90/3./${ux}
variable EI equal 1.7463575724407931489e-11*90*90*90/3./1.0913936421275138855e-11
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 388828.44257354736328*${eV2J}*${A2m}
variable EI equal 388828.44257354736328*1.6021764600000000642e-19*${A2m}
variable EI equal 388828.44257354736328*1.6021764600000000642e-19*1.0000000000000000364e-10
print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
>> V -0 0 F 1.7463575724407931489e-11 8.1070705704178180895e-12 u 1.0913936421275138855e-11 -0.0011954718283959664404 Q 0 EI 6.2297177766979946381e-24
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/${ng}/${Lz}
variable b equal (2-1)*${Vg}/${ng}/${Lz}
variable b equal (2-1)*0.14999999999999999445/${ng}/${Lz}
variable b equal (2-1)*0.14999999999999999445/3/${Lz}
variable b equal (2-1)*0.14999999999999999445/3/-51103.063299276320322
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 $a ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 0 ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 0 1
ATC: created function : 1 + -9.78415e-07(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 51.8077 Mbytes
Step Q PotEng dx dz FIX[1] FIX[3]
500 0 -6155.851 0.0003179655 -0.0011954718 1.7463576e-11 8.1070706e-12
510 0 -6155.851 0.0003179655 -0.0011954718 1.7251516e-11 8.5466079e-12
520 0 -6155.851 0.0003179655 -0.0011954718 1.7276357e-11 8.2207574e-12
530 0 -6155.851 0.0003179655 -0.0011954718 1.75636e-11 8.4386942e-12
540 0 -6155.851 0.0003179655 -0.0011954718 1.7522834e-11 8.5189633e-12
550 0 -6155.851 0.0003179655 -0.0011954718 1.7338121e-11 8.1677998e-12
560 0 -6155.851 0.0003179655 -0.0011954718 1.7448248e-11 8.4081631e-12
570 0 -6155.851 0.0003179655 -0.0011954718 1.7392986e-11 8.5064178e-12
580 0 -6155.851 0.0003179655 -0.0011954718 1.7444438e-11 8.5607077e-12
590 0 -6155.851 0.0003179655 -0.0011954718 1.7296425e-11 8.4051655e-12
600 0 -6155.851 0.0003179655 -0.0011954718 1.7447616e-11 8.3621998e-12
610 0 -6155.851 0.0003179655 -0.0011954718 1.7417904e-11 8.3870688e-12
620 0 -6155.851 0.0003179655 -0.0011954718 1.7328212e-11 8.6393115e-12
630 0 -6155.851 0.0003179655 -0.0011954718 1.7411971e-11 8.4993124e-12
640 0 -6155.851 0.0003179655 -0.0011954718 1.7426383e-11 8.6461949e-12
650 0 -6155.851 0.0003179655 -0.0011954718 1.7399009e-11 8.3740792e-12
660 0 -6155.851 0.0003179655 -0.0011954718 1.737387e-11 8.4294793e-12
670 0 -6155.851 0.0003179655 -0.0011954718 1.7378914e-11 8.7023722e-12
680 0 -6155.851 0.0003179655 -0.0011954718 1.734771e-11 8.80096e-12
690 0 -6155.851 0.0003179655 -0.0011954718 1.7320447e-11 8.8147267e-12
700 0 -6155.851 0.0003179655 -0.0011954718 1.7359548e-11 8.7029273e-12
710 0 -6155.851 0.0003179655 -0.0011954718 1.7191474e-11 8.8338226e-12
720 0 -6155.851 0.0003179655 -0.0011954718 1.7362872e-11 8.7141405e-12
730 0 -6155.851 0.0003179655 -0.0011954718 1.7459898e-11 8.5019769e-12
740 0 -6155.851 0.0003179655 -0.0011954718 1.724575e-11 8.7195806e-12
750 0 -6155.851 0.0003179655 -0.0011954718 1.7368686e-11 8.9750429e-12
760 0 -6155.851 0.0003179655 -0.0011954718 1.7282762e-11 8.5165208e-12
770 0 -6155.851 0.0003179655 -0.0011954718 1.7351915e-11 8.6922691e-12
780 0 -6155.851 0.0003179655 -0.0011954718 1.7261335e-11 8.8746788e-12
790 0 -6155.851 0.0003179655 -0.0011954718 1.7332431e-11 8.4021679e-12
800 0 -6155.851 0.0003179655 -0.0011954718 1.7336011e-11 8.6323171e-12
810 0 -6155.851 0.0003179655 -0.0011954718 1.7329544e-11 8.656631e-12
820 0 -6155.851 0.0003179655 -0.0011954718 1.7118616e-11 8.7636565e-12
830 0 -6155.851 0.0003179655 -0.0011954718 1.7304474e-11 8.7291285e-12
840 0 -6155.851 0.0003179655 -0.0011954718 1.7398697e-11 8.7205798e-12
850 0 -6155.851 0.0003179655 -0.0011954718 1.7366813e-11 8.8165031e-12
860 0 -6155.851 0.0003179655 -0.0011954718 1.7268856e-11 8.8138385e-12
870 0 -6155.851 0.0003179655 -0.0011954718 1.7315867e-11 9.0394359e-12
880 0 -6155.851 0.0003179655 -0.0011954718 1.7205706e-11 8.9996899e-12
890 0 -6155.851 0.0003179655 -0.0011954718 1.7218945e-11 9.0571994e-12
900 0 -6155.851 0.0003179655 -0.0011954718 1.7313557e-11 8.9475094e-12
910 0 -6155.851 0.0003179655 -0.0011954718 1.7205095e-11 8.8882235e-12
920 0 -6155.851 0.0003179655 -0.0011954718 1.7258906e-11 8.6174401e-12
930 0 -6155.851 0.0003179655 -0.0011954718 1.7300519e-11 9.1007202e-12
940 0 -6155.851 0.0003179655 -0.0011954718 1.7295516e-11 8.8616892e-12
950 0 -6155.851 0.0003179655 -0.0011954718 1.7298798e-11 8.9259711e-12
960 0 -6155.851 0.0003179655 -0.0011954718 1.7154941e-11 8.7637675e-12
970 0 -6155.851 0.0003179655 -0.0011954718 1.7201674e-11 9.0283336e-12
980 0 -6155.851 0.0003179655 -0.0011954718 1.7269717e-11 8.5640384e-12
990 0 -6155.851 0.0003179655 -0.0011954718 1.7215684e-11 8.985479e-12
1000 0 -6155.851 0.0003179655 -0.0011954718 1.7359402e-11 9.1016084e-12
Loop time of 58.7288 on 4 procs for 500 steps with 846 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-6155.8510078 -6155.8510078 -6155.8510078
Force two-norm initial, final = 6.46495e-12 6.71492e-12
Force max component initial, final = 6.70891e-13 6.69757e-13
Final line search alpha, max atom move = 1 6.69757e-13
Iterations, force evaluations = 500 1000
Pair time (%) = 7.65567 (13.0356)
Neigh time (%) = 0 (0)
Comm time (%) = 1.17538 (2.00138)
Outpt time (%) = 0.144858 (0.246656)
Other time (%) = 49.7529 (84.7163)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
#min_style sd
#min_modify line backtrack
#minimize 0 0 1000 1000
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable Q equal c_Q
variable ux equal ${dx}
variable ux equal 0.0003179654981977364514
variable uz equal ${dz}
variable uz equal -0.0011954718283959664404
variable Fx equal f_FIX[1]
variable Fz equal f_FIX[3]
variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7359402110228572269e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7359402110228572269e-11*90*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.7359402110228572269e-11*90*90*${Lfree}/3./${ux}
variable EI equal 1.7359402110228572269e-11*90*90*90/3./${ux}
variable EI equal 1.7359402110228572269e-11*90*90*90/3./0.0003179654981977364514
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 0.013266642880109728517*${eV2J}*${A2m}
variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*${A2m}
variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*1.0000000000000000364e-10
print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
>> V -9.7841492802855238901e-07 0 F 1.7359402110228572269e-11 9.1016083558770333184e-12 u 0.0003179654981977364514 -0.0011954718283959664404 Q 0 EI 2.125550292573840973e-31
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/${ng}/${Lz}
variable b equal (3-1)*${Vg}/${ng}/${Lz}
variable b equal (3-1)*0.14999999999999999445/${ng}/${Lz}
variable b equal (3-1)*0.14999999999999999445/3/${Lz}
variable b equal (3-1)*0.14999999999999999445/3/-51103.063299276320322
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 $a ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 0 ${V0}
fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 0 1
ATC: created function : 1 + -1.95683e-06(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
ATC: WARNING: material: [cnt] cannot find electron_flux
ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 51.8077 Mbytes
Step Q PotEng dx dz FIX[1] FIX[3]
1000 0 -6155.851 0.00031796548 -0.0011954718 1.7359402e-11 9.1016084e-12
1010 0 -6155.851 0.00031796548 -0.0011954718 1.72647e-11 8.9737107e-12
1020 0 -6155.851 0.00031796548 -0.0011954718 1.7298243e-11 9.3161034e-12
1030 0 -6155.851 0.00031796548 -0.0011954718 1.7292941e-11 8.7504448e-12
1040 0 -6155.851 0.00031796548 -0.0011954718 1.7324222e-11 8.9780405e-12
1050 0 -6155.851 0.00031796548 -0.0011954718 1.7239831e-11 8.8595797e-12
1060 0 -6155.851 0.00031796548 -0.0011954718 1.7318608e-11 8.6920471e-12
1070 0 -6155.851 0.00031796548 -0.0011954718 1.7192938e-11 8.8485885e-12
1080 0 -6155.851 0.00031796548 -0.0011954718 1.7274428e-11 8.8733465e-12
1090 0 -6155.851 0.00031796548 -0.0011954718 1.7129246e-11 9.0292218e-12
1100 0 -6155.851 0.00031796548 -0.0011954718 1.7195401e-11 9.1879837e-12
1110 0 -6155.851 0.00031796548 -0.0011954718 1.7221478e-11 8.9610541e-12
1120 0 -6155.851 0.00031796548 -0.0011954718 1.7302357e-11 9.2608143e-12
1130 0 -6155.851 0.00031796548 -0.0011954718 1.7290416e-11 9.0714103e-12
1140 0 -6155.851 0.00031796548 -0.0011954718 1.7198343e-11 9.21907e-12
1150 0 -6155.851 0.00031796548 -0.0011954718 1.7163059e-11 9.2147401e-12
1160 0 -6155.851 0.00031796548 -0.0011954718 1.7186443e-11 9.0759622e-12
1170 0 -6155.851 0.00031796548 -0.0011954718 1.7350291e-11 9.0307761e-12
1180 0 -6155.851 0.00031796548 -0.0011954718 1.7178033e-11 8.9124264e-12
1190 0 -6155.851 0.00031796548 -0.0011954718 1.7142825e-11 9.4578789e-12
1200 0 -6155.851 0.00031796548 -0.0011954718 1.7238853e-11 8.9984686e-12
1210 0 -6155.851 0.00031796548 -0.0011954718 1.7307909e-11 8.8733465e-12
1220 0 -6155.851 0.00031796548 -0.0011954718 1.7251884e-11 9.2414965e-12
1230 0 -6155.851 0.00031796548 -0.0011954718 1.7304682e-11 9.1451291e-12
1240 0 -6155.851 0.00031796548 -0.0011954718 1.7177992e-11 9.1870955e-12
1250 0 -6155.851 0.00031796548 -0.0011954718 1.7087293e-11 9.1605612e-12
1260 0 -6155.851 0.00031796548 -0.0011954718 1.7135144e-11 9.0688568e-12
1270 0 -6155.851 0.00031796548 -0.0011954718 1.7224919e-11 9.0758512e-12
1280 0 -6155.851 0.00031796548 -0.0011954718 1.7203346e-11 9.1016084e-12
1290 0 -6155.851 0.00031796548 -0.0011954718 1.7203673e-11 9.2676977e-12
1300 0 -6155.851 0.00031796548 -0.0011954718 1.7155246e-11 9.1611163e-12
1310 0 -6155.851 0.00031796548 -0.0011954718 1.7048158e-11 9.2623686e-12
1320 0 -6155.851 0.00031796548 -0.0011954718 1.7049185e-11 9.2745811e-12
1330 0 -6155.851 0.00031796548 -0.0011954718 1.7226918e-11 9.383605e-12
1340 0 -6155.851 0.00031796548 -0.0011954718 1.7146114e-11 9.0593089e-12
1350 0 -6155.851 0.00031796548 -0.0011954718 1.7130807e-11 9.2582608e-12
1360 0 -6155.851 0.00031796548 -0.0011954718 1.7170206e-11 9.4171337e-12
1370 0 -6155.851 0.00031796548 -0.0011954718 1.7139155e-11 9.0635277e-12
1380 0 -6155.851 0.00031796548 -0.0011954718 1.7048789e-11 9.1849861e-12
1390 0 -6155.851 0.00031796548 -0.0011954718 1.7176548e-11 9.2297281e-12
1400 0 -6155.851 0.00031796548 -0.0011954718 1.7135373e-11 9.2431618e-12
1410 0 -6155.851 0.00031796548 -0.0011954718 1.7186665e-11 9.3181018e-12
1420 0 -6155.851 0.00031796548 -0.0011954718 1.7178928e-11 9.4295682e-12
1430 0 -6155.851 0.00031796548 -0.0011954718 1.7148834e-11 9.4859676e-12
1440 0 -6155.851 0.00031796548 -0.0011954718 1.715662e-11 9.3871577e-12
1450 0 -6155.851 0.00031796548 -0.0011954718 1.7190711e-11 9.3713926e-12
1460 0 -6155.851 0.00031796548 -0.0011954718 1.7210958e-11 9.5933261e-12
1470 0 -6155.851 0.00031796548 -0.0011954718 1.7199183e-11 9.4561026e-12
1480 0 -6155.851 0.00031796548 -0.0011954718 1.7054681e-11 9.3104413e-12
1490 0 -6155.851 0.00031796548 -0.0011954718 1.722188e-11 9.3294261e-12
1500 0 -6155.851 0.00031796548 -0.0011954718 1.7142694e-11 9.3715036e-12
Loop time of 76.7522 on 4 procs for 500 steps with 846 atoms
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-6155.8510078 -6155.8510078 -6155.8510078
Force two-norm initial, final = 6.71492e-12 6.81183e-12
Force max component initial, final = 6.69757e-13 8.93204e-13
Final line search alpha, max atom move = 1 8.93204e-13
Iterations, force evaluations = 500 1000
Pair time (%) = 8.35572 (10.8866)
Neigh time (%) = 0 (0)
Comm time (%) = 2.23788 (2.91572)
Outpt time (%) = 0.0837539 (0.109123)
Other time (%) = 66.0748 (86.0885)
Nlocal: 211.5 ave 216 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 195.75 ave 261 max 126 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 48199.5 ave 53136 max 41085 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 192798
Ave neighs/atom = 227.894
Neighbor list builds = 0
Dangerous builds = 0
#min_style sd
#min_modify line backtrack
#minimize 0 0 1000 1000
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable Q equal c_Q
variable ux equal ${dx}
variable ux equal 0.0003179654813720844686
variable uz equal ${dz}
variable uz equal -0.0011954718283959664404
variable Fx equal f_FIX[1]
variable Fz equal f_FIX[3]
variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.714269351471564562e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.714269351471564562e-11*90*${Lfree}*${Lfree}/3./${ux}
variable EI equal 1.714269351471564562e-11*90*90*${Lfree}/3./${ux}
variable EI equal 1.714269351471564562e-11*90*90*90/3./${ux}
variable EI equal 1.714269351471564562e-11*90*90*90/3./0.0003179654813720844686
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 0.013101027526950992722*${eV2J}*${A2m}
variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*${A2m}
variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*1.0000000000000000364e-10
print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
>> V -1.956829856057104778e-06 0 F 1.714269351471564562e-11 9.3715035731634088734e-12 u 0.0003179654813720844686 -0.0011954718283959664404 Q 0 EI 2.0990157905492896479e-31
next i
jump SELF loop_i

91
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# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

112
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# needs description
echo both
units metal
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
variable g equal 0.75*0.355649e3*${kCal2eV}
variable m equal 0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000

98
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# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

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# needs description
#AtC Elastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region atomRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000

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# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

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# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

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# needs description
# E = - grad \phi
# f = q E
echo both
units metal
atom_style atomic
lattice diamond 3.6
pair_style tersoff
boundary s s f
read_data tube_8_4.data
# PARAMETERS-----------------------------
variable L equal zhi-zlo
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${xhiFE}
variable zhiFE equal zhi
variable zloFE equal zlo+10
print "Length $L [${zloFE}, ${zhiFE}]"
variable E equal 10.0
print "Electric field $E"
variable drhodx equal 0.0001
variable s equal 50
# END -----------------------------------
#pair_coeff * * SiC.tersoff C
pair_coeff * * ../../../../potentials/SiC.tersoff C
mass * 12.01
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep 0.0005
# coupling
fix AtC internal atc electrostatic CNT_electrostatic.mat
fix_modify AtC internal_quadrature off
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create 5 1 12 feRegion f p f
# initial & boundary conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
variable a equal -$R-0.1
variable b equal $R+0.1
fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box
variable a equal ${zloFE}-0.1
variable b equal ${zloFE}+0.1
fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} $a $b units box
variable a equal ${xhiFE}-0.1
variable b equal ${xhiFE}+0.1
fix_modify AtC mesh create_nodeset top $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
variable a equal ${xloFE}-0.1
variable b equal ${xloFE}+0.1
fix_modify AtC mesh create_nodeset bot $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
fix_modify AtC fix electron_density all 0.0
#fix_modify AtC fix electron_density tube 0.2
fix_modify AtC fix electron_density tube linear 0 0 0 0 0 ${drhodx} 0
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 0 0
fix_modify AtC control momentum flux
# run
thermo_style custom step cpu etotal ke
thermo 1#$s
fix_modify AtC output cnt_electrostaticFE $s full_text
fix_modify AtC output index step
# NOTE not recognized as vector by paraview
variable uX atom x-f_AtC[1]
variable uY atom y-f_AtC[2]
variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom $s cnt_electrostatic.dmp id type x y z v_uX v_uY v_uZ v_rho
log cnt_electrostatic.log
#run 1000
# fixed charge, bc on potential
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0 0
fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 0 0
fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 0 0
run 1000

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# needs description
# E = - grad \phi
# f = q E
# NOTE tangent is constant for LAGRANGIAN but not exact...
# NOTE try one atom and one free node
# issue is one of magnitude of E since
# tangent = perm BB - dn/dphi NN
# CHECK CONDITIONING?
echo both
units metal
atom_style atomic
lattice diamond 3.6
boundary f f f
#region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box
#region box block 0 10 0 10 0 10
#create_box 1 box
#group box region box
#atom_modify sort 0 1
pair_style tersoff
read_data tube_8_4.data
pair_coeff * * ../../../../potentials/SiC.tersoff C
mass * 12.01
# PARAMETERS-----------------------------
variable L equal zhi-zlo
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${xhiFE}
variable zhiFE equal zhi
variable zloFE equal zlo+10
print "Length $L [${zloFE}, ${zhiFE}]"
variable E equal 0.01 # 1.0 10.0 0.01
variable V equal $E*${zloFE}
variable V equal 2
print "Electric field $E ref.voltage $V"
variable s equal 20
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
#neighbor 5. bin
#neigh_modify every 10 delay 0 check no
timestep 0.0005
# coupling
fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat
fix_modify AtC omit atomic_charge
#fix_modify AtC internal_quadrature off <<<< ???
variable alat equal 1.42
variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0
#variable w equal 10
fix_modify AtC atom_weight constant internal $w
fix_modify AtC source_integration atom
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC mesh create 5 1 12 feRegion f p f
fix_modify AtC control momentum flux
#fix_modify AtC extrinsic poisson_solver max_iterations 5
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
#variable a equal -$R-0.1
#variable b equal $R+0.1
#fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output cnt_electrostatic2FE $s full_text # binary
fix_modify AtC output index step
# NOTE not recognized as vector by paraview
variable uX atom x-f_AtC[1]
variable uY atom y-f_AtC[2]
variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho
log cnt_electrostatic2.log
#run $s
run 100
# NOTE try fix charge on tip

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echo both
units metal
atom_style charge
dielectric 1.
variable type string "_charge"
boundary s s f
# read in CNT
read_data cnt_9_0_100${type}.data
lattice diamond 3.6 # NOTE ???
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
# PARAMETERS-----------------------------
variable dt equal 0.0005
variable L equal zhi-zlo
variable zhi equal zhi
variable zTip equal ${zhi}-2.0
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${yhiFE}
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable Lfree equal zhi-${zloFE}
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
#variable E equal 0.1 # bias 1.0
variable Vb equal 0.0 # bias
variable Vg equal 0.5 # gate/modulation
print "bias voltage ${Vb}, gate voltage ${Vg}"
variable n equal 100000
variable s equal 250
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
group fixed subtract all internal
fix FIX fixed setforce 0 0 0
thermo 100
#minimize 0 0 1000 1000
#write_restart cnt_in_box0.rst
region TIP block INF INF INF INF ${zTip} INF units box
group TIP region TIP
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
variable nTip equal count(TIP)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
print ">>> number of tip atoms : ${nTip}"
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep ${dt}
variable tag string "cnt_fixed_charge"
# set charge on tip
variable C equal -0.1 # -0.01 -0.0001102
print "charge $C [e]"
variable c equal $C/${nTip}
set group TIP charge $c
# coupling
fix AtC internal atc electrostatic CNT_id.mat
fix_modify AtC include atomic_charge
fix_modify AtC internal_quadrature off
# note weights don't affect phi or f
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
#fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
# node sets
variable t equal 1.1*$R
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# ground
fix_modify AtC fix electric_potential lbc 0
# bias
fix_modify AtC fix electric_potential rbc ${Vb}
# gate
fix_modify AtC fix electric_potential bot ${Vg}
# run
compute CM TIP com
compute q all property/atom q
compute Q all reduce sum c_q
compute FSUM all reduce sum fx fy fz
thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] &
c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1]
thermo $s
log ${tag}.log
#run $n
#run $n
thermo 10
timestep 0.0
min_modify line quadratic
minimize 0 0 1000 1000
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable F equal f_AtC[5]
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal ${EI}*${eV2J}*${A2m}
print "flexural rigidity ${EI} [Nm^2] NOTE z force"
# flexural rigidity 6.716732985e-25 [Nm^2]
fix_modify AtC output ${tag}FE 1 full_text
fix_modify AtC output index step
run 1

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echo both
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable L equal 10
variable L2 equal 0.5*$L
variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX
create_atoms 1 region BOX
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
variable pe equal pe-${e0}
variable dL equal ly-${L0}
variable strain equal v_dL/${L0}
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1

74
examples/USER/atc/elastic/in.electron_density Normal file
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# needs description
echo both
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
boundary f p p
region box block -$L $L 0 1 0 1
create_box 1 box
group box region box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
run $s
# run CNT1 material
print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1
run $s
# run CNT2 material
print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2
run $s
# run CNT material
print "CNT material - table DOS"
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s

186
examples/USER/atc/elastic/in.electrostatic_bending Normal file
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echo both
units metal
atom_style charge
dielectric 1.
variable type string "_charge"
boundary s s f
# read in CNT
read_data cnt_9_0_100${type}.data
lattice diamond 3.6 # NOTE ???
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
# PARAMETERS-----------------------------
variable dt equal 0.0005
variable L equal zhi-zlo
variable zhi equal zhi
variable zTip equal ${zhi}-2.0 # 2 4
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${yhiFE}
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable Lfree equal zhi-${zloFE}
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
#variable E equal 0.1 # bias 1.0
variable Vb equal 0.1 # 0.1 #0.5 #0.0 # bias
variable Vg equal 0.5 # 1.0 # 5.0 0.5 #50.0 # 0.5 # gate/modulation
print "bias voltage ${Vb}, gate voltage ${Vg}"
variable ng equal 20 # 80 # 10
variable nb equal 2 # 3
variable n equal 100000
variable s equal 250
# END -----------------------------------
region TIP block INF INF INF INF ${zTip} INF units box
group TIP region TIP
#region FIXED block INF INF INF INF INF ${zLoFE} units box
#group FIXED region FIXED
#group FREE subtract all FIXED
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
group FIXED subtract all internal
fix FIX FIXED setforce 0 0 0
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
variable nTip equal count(TIP)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
print ">>> number of tip atoms : ${nTip}"
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep ${dt}
thermo 100
variable tag string "electrostatic_bending"
# set charge on tip
variable C equal -0.025
print "charge $C [e]"
variable c equal $C/${nTip}
set group TIP charge $c
# coupling
fix AtC internal atc electrostatic CNT_id.mat
fix_modify AtC include atomic_charge
fix_modify AtC internal_quadrature off
# note weights don't affect phi or f
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
#fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
# node sets
variable t equal 1.1*$R
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
# boundary conditions
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# ground
fix_modify AtC fix electric_potential lbc 0
# bias
fix_modify AtC fix electric_potential rbc ${Vb}
# gate
fix_modify AtC fix electric_potential bot ${Vg}
# run
compute CM TIP com
compute q all property/atom q
compute Q all reduce sum c_q
compute FSUM all reduce sum fx fy fz
compute RSUM internal reduce sum fx fy fz
thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] &
c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] c_RSUM[1]
thermo $s
fix_modify AtC output ${tag}FE 100000000 full_text # $s full_text #binary
fix_modify AtC output index step
# NOTE not recognized as vector by paraview
variable uX atom x-f_AtC[1]
variable uY atom y-f_AtC[2]
variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom $s ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho
reset_timestep 0
log ${tag}.log
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
thermo 10
timestep 0.0
min_modify line quadratic
variable Vg equal 0.1
variable Lx equal 1.0
variable ng equal 4
#compute RSUM FREE reduce sum fx fy fz
#dump CONFIG all custom 10000 ${tag}.dmp id type x y z c_U[1] c_U[2] c_U[3] fx fy fz
variable a equal 0
variable i loop ${ng}
label loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
min_style sd
min_modify line backtrack
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable uz equal c_CM[3]
# variable F equal f_AtC[5]
# variable Fz equal f_AtC[7]
variable F equal c_RSUM[1]
variable Fz equal c_RSUM[3]
variable R equal $F-$C*$b
variable Rz equal ${Fz}-$C*$a
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal ${EI}*${eV2J}*${A2m}
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
next i
jump SELF loop_i

164
examples/USER/atc/elastic/in.electrostatic_bending_dos Normal file
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echo both
units metal
atom_style charge
dielectric 1.
boundary s s f
# read in CNT
read_data min_CNT_dos.data
set group all charge 0
lattice diamond 3.6
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
compute q all property/atom q
compute Q all reduce sum c_q
# PARAMETERS-----------------------------
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
variable Lx equal xhi-xlo
variable L equal zhi-zlo
variable zTip equal zhi-3.5
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${yhiFE}
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable Lfree equal zhi-${zloFE}
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
variable Vb equal 0.1
variable Vg equal 0.15
variable V0 equal 1. # 2.
print "bias voltage ${Vb}, gate voltage ${Vg}"
variable ng equal 3
variable n equal 100000
variable s equal 250
# END -----------------------------------
region TIP block INF INF INF INF ${zTip} INF units box
group TIP region TIP
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
group FIXED subtract all internal
fix FIX FIXED setforce 0 0 0
thermo 10
set group all image 0 0 0
compute CM TIP com
thermo_style custom step c_Q etotal c_CM[1] c_CM[3]
#minimize 0 0 1000 1000
#write_restart min_CNT_dos.rst
run 0
#EXIT
variable L equal c_CM[1]
variable Lx equal $L
variable dx equal c_CM[1]-${Lx}
variable L equal c_CM[3]
variable Lz equal $L
variable dz equal c_CM[3]-${Lz}
print "initial ${Lx} ${Lz} "
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep 0
thermo 100
# coupling ............................................................
fix AtC internal atc electrostatic CNT_electrostatic2.mat
fix_modify AtC omit atomic_charge
#fix_modify AtC internal_quadrature off ## NOTE active -> error
# note weights don't affect phi or f i.e. they divide out
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
fix_modify AtC source_integration atom
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum none # flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
# node sets ............................................................
variable t equal 1.1*$R
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box
# boundary conditions ..................................................
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix displacement y lbc 0.
fix_modify AtC fix displacement z lbc 0.
fix_modify AtC fix velocity x lbc 0.
fix_modify AtC fix velocity y lbc 0.
fix_modify AtC fix velocity z lbc 0.
# minimize .............................................................
compute FSUM all reduce sum fx fy fz
compute RSUM internal reduce sum fx fy fz
thermo $s
fix_modify AtC output electrostatic_bending_dosFE 100000000 full_text binary
fix_modify AtC output index step
# store original (reference) coordinates
fix X all store/state 0 x y z
# NOTE not recognized as vector by paraview - due to dump2ensight
variable uX atom x-f_X[1]
variable uY atom y-f_X[2]
variable uZ atom z-f_X[3]
#variable uX atom x-f_AtC[1]
#variable uY atom y-f_AtC[2]
#variable uZ atom z-f_AtC[3]
variable rho atom mass*f_AtC[4]
dump CONFIG all custom 100000 electrostatic_bending_dos.dmp id type x y z c_q v_uX v_uY v_uZ v_rho
reset_timestep 0
log electrostatic_bending_dos.log
thermo 10 # 1 # 10
min_modify line quadratic
variable a equal 0
variable i loop ${ng}
thermo_style custom step c_Q pe v_dx v_dz f_FIX[1] f_FIX[3]
label loop_i
variable b equal ($i-1)*${Vg}/${ng}/${Lz}
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
min_style cg
min_modify line quadratic
minimize 0 0 1000 1000
#min_style sd
#min_modify line backtrack
#minimize 0 0 1000 1000
fix_modify AtC output now
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable Q equal c_Q
variable ux equal ${dx}
variable uz equal ${dz}
variable Fx equal f_FIX[1]
variable Fz equal f_FIX[3]
variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
variable EI equal ${EI}*${eV2J}*${A2m}
print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
next i
jump SELF loop_i

42
examples/USER/atc/elastic/in.no_atoms Executable file
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# needs description
#AtC thermal Coupling
# DESCRIPTION: no atoms, FE region with full periodic boundary conditions.
units real
atom_style atomic
# create domain
lattice fcc 5.25623 origin 0.25 0.25 0.25
region feRegion block 0 100 0 10 0 10
boundary f p p
create_box 1 feRegion
atom_modify sort 0 1
mass 1 39.95 # need to keep this
# ID group atc PhysicsType ParameterFile
fix AtC all atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 25 1 1 feRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11
fix_modify AtC fix displacement x lbc 0.0
fix_modify AtC initial displacement x rbc1 0.00004
fix_modify AtC initial displacement x rbc2 0.00014
fix_modify AtC initial displacement x rbc3 0.00026
fix_modify AtC initial displacement x rbc4 0.00036
fix_modify AtC initial displacement x rbc5 0.0004
thermo_style custom step cpu
fix_modify AtC output no_atomsFE 500 text
timestep 20
thermo 100
run 3000

43
examples/USER/atc/elastic/in.no_atoms_cb Executable file
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# needs description
#AtC thermal Coupling
# DESCRIPTION: no atoms, FE region with full periodic boundary conditions.
units real
atom_style atomic
# create domain
lattice fcc 5.25623 origin 0.25 0.25 0.25
region feRegion block 0 100 0 10 0 10
boundary f p p
create_box 1 feRegion
atom_modify sort 0 1
mass 1 39.95 # need to keep this
# ID group atc PhysicsType ParameterFile
fix AtC all atc elastic Ar_CauchyBorn.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 25 1 1 feRegion f p p
fix_modify AtC mesh quadrature face
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11
fix_modify AtC fix displacement x lbc 0.0
fix_modify AtC initial displacement x rbc1 0.0004
fix_modify AtC initial displacement x rbc2 0.0014
fix_modify AtC initial displacement x rbc3 0.0026
fix_modify AtC initial displacement x rbc4 0.0036
fix_modify AtC initial displacement x rbc5 0.004
thermo_style custom step cpu
fix_modify AtC output no_atoms_cbFE 500 text
timestep 20
thermo 100
run 3000

42
examples/USER/atc/elastic/in.no_atoms_cb_linear Executable file
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# needs description
#AtC thermal Coupling
# DESCRIPTION: no atoms, FE region with full periodic boundary conditions.
units real
atom_style atomic
# create domain
lattice fcc 5.25623 origin 0.25 0.25 0.25
region feRegion block 0 100 0 10 0 10
boundary f p p
create_box 1 feRegion
atom_modify sort 0 1
mass 1 39.95 # need to keep this
# ID group atc PhysicsType ParameterFile
fix AtC all atc elastic Ar_CauchyBornLinear.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 25 1 1 feRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11
fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11
fix_modify AtC fix displacement x lbc 0.0
fix_modify AtC initial displacement x rbc1 0.00004
fix_modify AtC initial displacement x rbc2 0.00014
fix_modify AtC initial displacement x rbc3 0.00026
fix_modify AtC initial displacement x rbc4 0.00036
fix_modify AtC initial displacement x rbc5 0.0004
thermo_style custom step cpu
fix_modify AtC output no_atoms_cb_linearFE 500 text
timestep 20
thermo 100
run 3000

74
examples/USER/atc/elastic/no_atoms.screen Normal file
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LAMMPS (14 Aug 2013)
Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
Created orthogonal box = (0 0 0) to (525.623 52.5623 52.5623)
4 by 1 by 1 MPI processor grid
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.10041
ATC: computed mass density : 1.10041
ATC: computed mass density : 1.10041
ATC: 3 materials defined from Ar_elastic.mat
ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements
ATC: created nodeset lbc with 1 nodes
ATC: created nodeset rbc1 with 1 nodes
ATC: created nodeset rbc2 with 1 nodes
ATC: created nodeset rbc3 with 1 nodes
ATC: created nodeset rbc4 with 1 nodes
ATC: created nodeset rbc5 with 1 nodes
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
Setting up run ...
Memory usage per processor = 0.432442 Mbytes
Step CPU
0 0
100 0.28801608
200 0.60494804
300 1.9659522
400 5.8900452
500 8.2498631
600 8.6479681
700 10.04323
800 10.456577
900 10.742816
1000 11.104007
1100 11.349205
1200 11.689583
1300 11.902604
1400 12.098199
1500 12.934268
1600 19.349941
1700 22.496211
1800 23.167077
1900 24.027154
2000 24.235364
2100 24.432181
2200 24.628729
2300 25.034703
2400 28.890065
2500 31.916798
2600 33.219873
2700 34.139887
2800 34.52512
2900 34.766055
3000 35.032684
Loop time of 35.0327 on 4 procs for 3000 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0106689 (0.030454)
Outpt time (%) = 0.0495699 (0.141496)
Other time (%) = 34.9725 (99.828)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

77
examples/USER/atc/elastic/no_atoms_cb.screen Normal file
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LAMMPS (14 Aug 2013)
Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
Created orthogonal box = (0 0 0) to (525.623 52.5623 52.5623)
4 by 1 by 1 MPI processor grid
ATC: constructing elastic coupling with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.10041
ATC: 1 materials defined from Ar_CauchyBorn.mat
using face quad!
using face quad!
using face quad!
ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements
using face quad!
ATC: created nodeset lbc with 1 nodes
ATC: created nodeset rbc1 with 1 nodes
ATC: created nodeset rbc2 with 1 nodes
ATC: created nodeset rbc3 with 1 nodes
ATC: created nodeset rbc4 with 1 nodes
ATC: created nodeset rbc5 with 1 nodes
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
Setting up run ...
ATC: CB stiffness: 7.56711 Einstein freq: 0.355647
Memory usage per processor = 0.432442 Mbytes
Step CPU
0 0
100 5.373224
200 13.156875
300 17.393315
400 23.759932
500 28.611823
600 36.396029
700 40.553676
800 47.000228
900 51.579739
1000 57.538064
1100 64.053463
1200 71.077067
1300 76.430127
1400 84.956777
1500 88.559395
1600 90.649106
1700 93.449754
1800 95.849976
1900 98.488277
2000 100.78877
2100 102.80799
2200 104.88818
2300 106.89208
2400 108.89542
2500 110.89934
2600 114.3289
2700 116.6514
2800 118.66646
2900 120.66124
3000 122.65321
Loop time of 122.653 on 4 procs for 3000 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0159223 (0.0129816)
Outpt time (%) = 0.0753418 (0.0614267)
Other time (%) = 122.562 (99.9256)
Nlocal: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

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