LAMMPS (30 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)