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lammps/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen
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schrodinger-poisson2d_convective.screen
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LAMMPS (27 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: version 2.0
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)
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