LAMMPS (30 Aug 2013) units real atom_style full ########### BEGIN PARAMETERS #################################### variable a equal 5.719025032 variable i equal 1 variable s equal 100 variable n equal 1000 # 500 2000 variable dt equal 4.0 variable W equal 4 variable L equal 20 variable Ls equal 4 # surface variable h equal 10 variable phiInf equal -1. # 0. 10 -10.0 variable R equal 2*$a variable R equal 2*5.7190250320000002304 ############## END PARAMETERS ################################# dimension 3 boundary f p p pair_style lj/cut 13.0 lattice fcc $a lattice fcc 5.7190250320000002304 Lattice spacing in x,y,z = 5.71903 5.71903 5.71903 read_data interface.init Scanning data file ... Reading data file ... orthogonal box = (0 0 0) to (114.381 22.8761 22.8761) 4 by 1 by 1 MPI processor grid 544 atoms 544 velocities Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors atom_modify sort 0 1 mass * 39.948 pair_coeff * * 0.2381 3.405 dielectric 1.0 region BOX block 0 $L 0 $W 0 $W region BOX block 0 20 0 $W 0 $W region BOX block 0 20 0 4 0 $W region BOX block 0 20 0 4 0 4 group SOLID type 1 288 atoms in group SOLID group FLUID type 2 3 4 256 atoms in group FLUID group P type 3 66 atoms in group P group N type 4 76 atoms in group N set group SOLID charge 0 # use ATC to provide charge to the surface Setting atom values ... 288 settings made for charge # charged layer -- NOTE on an element boundary variable b equal ${Ls}-0.1 variable b equal 4-0.1 variable c equal ${Ls}+0.1 variable c equal 4+0.1 region LAYER block $b $c INF INF INF INF region LAYER block 3.8999999999999999112 $c INF INF INF INF region LAYER block 3.8999999999999999112 4.0999999999999996447 INF INF INF INF group LAYER region LAYER 32 atoms in group LAYER timestep ${dt} timestep 4 neigh_modify every $i check no neigh_modify every 1 check no fix WALLS all wall/reflect xlo EDGE xhi EDGE fix PP all atc field ATC: constructing shape function field estimate ATC: version 2.0 ATC: peratom PE compute created with ID: 3 fix_modify PP add_species IONS type 1 2 3 4 fix_modify PP fields add species_concentration mass_density charge_density # temperature fix_modify PP output volume_integral all mass_density fix_modify PP output volume_integral all charge_density fix_modify PP atom_element_map eulerian $s fix_modify PP atom_element_map eulerian 100 fix_modify PP mesh create $h 1 1 BOX f p p fix_modify PP mesh create 10 1 1 BOX f p p ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: 1 materials defined from Ar_electrostatic.mat ATC: creating fem_efield extrinsic model ATC: 1 materials defined from Ar_electrostatic.mat fix_modify ATC add_species P type 3 fix_modify ATC add_species N type 4 fix_modify ATC boundary SOLID #fix_modify ATC kernel cell $R $R $W fix_modify ATC atom_element_map eulerian $i fix_modify ATC atom_element_map eulerian 1 fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error) fix_modify ATC mass_matrix fe fix_modify ATC include atomic_charge # mesh : 2x2 tosses an atom to infinity and beyond #fix_modify ATC mesh create $h 4 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 #fix_modify ATC mesh create $h 1 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 # 0.0 1.0 0.2 1.0 0.207812 0.1 1.0 1.0 ### >>> node h vs list reepat and scale to box fix_modify ATC mesh create $h 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5 fix_modify ATC mesh create 10 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5 ATC: created structured mesh with 110 nodes, 44 unique nodes, and 40 elements fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF ATC: created nodeset lbc with 4 nodes fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF fix_modify ATC mesh create_nodeset rbc 20 $L -INF INF -INF INF fix_modify ATC mesh create_nodeset rbc 20 20 -INF INF -INF INF ATC: created nodeset rbc with 4 nodes fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4 fix_modify ATC mesh create_nodeset wall 0 4 0 4 0 4 ATC: created nodeset wall with 12 nodes fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4 fix_modify ATC mesh create_elementset wall 0 4 0 4 0 4 ATC: created elementset wall with 8 elements #fix_modify ATC mesh create_faceset lbc plane x 0 fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF fix_modify ATC mesh create_faceset surface -INF 4 -INF INF -INF INF ATC: created faceset surface with 4 faces fix_modify ATC mesh create_elementset fluidElts ${Ls} INF -INF INF -INF INF fix_modify ATC mesh create_elementset fluidElts 4 INF -INF INF -INF INF ATC: created elementset fluidElts with 32 elements fix_modify ATC internal_element_set fluidElts fix_modify ATC mesh output conducting_interfaceMESH full_text binary fix_modify ATC output volume_integral fluidElts mass_density fix_modify ATC output volume_integral fluidElts charge_density # ic/bcs #fix_modify ATC initial charge_density all 0. fix_modify ATC initial mass_density all 0. fix_modify ATC initial electric_potential all 0. # output thermo $s thermo 100 variable cFLUID equal count(FLUID) compute PAVE P reduce ave x compute PMIN P reduce min x compute PMAX P reduce max x compute NAVE N reduce ave x compute NMIN N reduce min x compute NMAX N reduce max x compute q all property/atom q compute Q all reduce sum c_q compute Qf FLUID reduce sum c_q compute m all property/atom mass compute M all reduce sum c_m compute Mf FLUID reduce sum c_m compute F FLUID reduce sum fx fy fz thermo_style custom step temp press etotal pe c_Q c_M c_Qf c_Mf c_PMIN c_PAVE c_PMAX c_NMIN c_NAVE c_NMAX c_F[1] c_F[2] c_F[3] compute T FLUID temp thermo_modify temp T WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438) thermo_modify flush yes log conducting_interface.log fix_modify ATC output conducting_interfaceFE $s full_text binary fix_modify ATC output conducting_interfaceFE 100 full_text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN species_concentration : species_concentrationP species_concentration : species_concentrationN fix_modify PP output conducting_interfacePP $s full_text binary fix_modify PP output conducting_interfacePP 100 full_text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_1 NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_2 NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_3 NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_4 species_concentration : species_concentrationIONS_1 species_concentration : species_concentrationIONS_2 species_concentration : species_concentrationIONS_3 species_concentration : species_concentrationIONS_4 dump X all custom $s conducting_interface.dmp id type x y z q vx vy vz fx fy fz dump X all custom 100 conducting_interface.dmp id type x y z q vx vy vz fx fy fz fix_modify ATC fix electric_potential rbc 0. # stage 1 : active source controlling far-field shielding fix_modify ATC control charge LAYER conductor ${phiInf} fix_modify ATC control charge LAYER conductor -1 ERROR: Illegal fix_modify command (../fix.cpp:104)