5302074b3f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
193 lines
9.8 KiB
Plaintext
193 lines
9.8 KiB
Plaintext
LAMMPS (30 Aug 2013)
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#variable iter equal 2 # need two for potential to affect density
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variable iter equal 1 # NOTE <<<<
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variable r equal 1
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variable nx equal 30 # 30 # 40 10
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variable mx equal 4 # 4 2
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#variable ny equal ${nx}
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variable ny equal 30 # 40
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variable my equal 12 # 6
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variable nz equal 1
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variable hx equal 1.0
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variable hy equal ${hx}*${nx}/${ny}
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variable hy equal 1*${nx}/${ny}
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variable hy equal 1*30/${ny}
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variable hy equal 1*30/30
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variable l equal -${hx}*${nx}
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variable l equal -1*${nx}
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variable l equal -1*30
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variable u equal ${hx}*${nx}
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variable u equal 1*${nx}
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variable u equal 1*30
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variable w equal ${hy}*${my}
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variable w equal 1*${my}
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variable w equal 1*12
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variable q equal ${hx}*${mx}
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variable q equal 1*${mx}
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variable q equal 1*4
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variable y equal ${nx}+1-${mx}
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variable y equal 30+1-${mx}
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variable y equal 30+1-4
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variable T equal 300
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variable E equal 0.1
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variable S equal 1
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variable n0 equal 0.01
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variable V equal 5.
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variable tol equal 0.01
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#################################################
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atom_style atomic
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timestep 0.001
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boundary f f f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
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region BOX block ${l} ${u} ${l} ${u} 0 1
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region BOX block -30 ${u} ${l} ${u} 0 1
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region BOX block -30 30 ${l} ${u} 0 1
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region BOX block -30 30 -30 ${u} 0 1
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region BOX block -30 30 -30 30 0 1
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create_box 1 BOX
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Created orthogonal box = (-47.622 -47.622 0) to (47.622 47.622 1.5874)
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2 by 2 by 1 MPI processor grid
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mass * 12.01
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atom_modify sort 0 1
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# ID group atc PhysicsType ParameterFile
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fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
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Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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ATC: creating drift_diffusion extrinsic model
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
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fix_modify AtC mesh create 30 ${ny} ${nz} BOX f f p
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fix_modify AtC mesh create 30 30 ${nz} BOX f f p
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fix_modify AtC mesh create 30 30 1 BOX f f p
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ATC: created uniform mesh with 1922 nodes, 961 unique nodes, and 900 elements
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# surfaces & regions
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variable a equal $l-${tol}
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variable a equal -30-${tol}
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variable a equal -30-0.010000000000000000208
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variable b equal $l+$q+${tol}
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variable b equal -30+$q+${tol}
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variable b equal -30+4+${tol}
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variable b equal -30+4+0.010000000000000000208
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variable c equal -$w-${tol}
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variable c equal -12-${tol}
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variable c equal -12-0.010000000000000000208
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variable d equal $w+${tol}
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variable d equal 12+${tol}
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variable d equal 12+0.010000000000000000208
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variable e equal $l+$q-${tol}
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variable e equal -30+$q-${tol}
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variable e equal -30+4-${tol}
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variable e equal -30+4-0.010000000000000000208
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fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
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fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 $b -INF INF
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fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 -25.989999999999998437 -INF INF
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ATC: created nodeset bot with 93 nodes
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fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 -25.989999999999998437 -INF INF -INF INF
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ATC: created nodeset lbc with 93 nodes
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variable a equal $u-$q-${tol}
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variable a equal 30-$q-${tol}
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variable a equal 30-4-${tol}
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variable a equal 30-4-0.010000000000000000208
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variable b equal $u+${tol}
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variable b equal 30+${tol}
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variable b equal 30+0.010000000000000000208
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variable e equal $u-$q+${tol}
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variable e equal 30-$q+${tol}
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variable e equal 30-4+${tol}
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variable e equal 30-4+0.010000000000000000208
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fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
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fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 $b -INF INF
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fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 30.010000000000001563 -INF INF
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ATC: created nodeset top with 93 nodes
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fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 30.010000000000001563 -INF INF -INF INF
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ATC: created nodeset rbc with 93 nodes
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variable a equal -$w-${tol}
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variable a equal -12-${tol}
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variable a equal -12-0.010000000000000000208
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variable b equal $w+${tol}
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variable b equal 12+${tol}
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variable b equal 12+0.010000000000000000208
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variable c equal $l+$q-${tol}
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variable c equal -30+$q-${tol}
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variable c equal -30+4-${tol}
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variable c equal -30+4-0.010000000000000000208
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variable d equal $u-$q+${tol}
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variable d equal 30-$q+${tol}
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variable d equal 30-4+${tol}
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variable d equal 30-4+0.010000000000000000208
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fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -26.010000000000001563 $d $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF
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fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
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ATC: created elementset wire with 312 elements
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fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -26.010000000000001563 $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF
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fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
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ATC: created nodeset wire with 351 nodes
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variable e equal $c+2*${tol}
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variable e equal -26.010000000000001563+2*${tol}
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variable e equal -26.010000000000001563+2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 $e $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 12.009999999999999787 -INF INF
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ATC: created nodeset lwire with 13 nodes
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variable e equal $d-2*${tol}
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variable e equal 26.010000000000001563-2*${tol}
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variable e equal 26.010000000000001563-2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF
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ATC: created nodeset rwire with 13 nodes
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variable e equal $a+2*${tol}
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variable e equal -12.009999999999999787+2*${tol}
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variable e equal -12.009999999999999787+2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 $d $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 -11.990000000000000213 -INF INF
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ATC: created nodeset bwire with 27 nodes
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variable e equal $b-2*${tol}
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variable e equal 12.009999999999999787-2*${tol}
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variable e equal 12.009999999999999787-2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -26.010000000000001563 $d $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 $b -INF INF
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fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 12.009999999999999787 -INF INF
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ATC: created nodeset twire with 27 nodes
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# new material
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fix_modify AtC material wire Si
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# simplify
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fix_modify AtC extrinsic one_dimensional x wire $y
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fix_modify AtC extrinsic one_dimensional x wire 27
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ERROR: Illegal fix_modify command (../fix.cpp:104)
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