LAMMPS (30 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: 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_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)