LAMMPS (30 Aug 2013) units real atom_style full # charge ### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces ########### BEGIN PARAMETERS #################################### variable T equal 300 variable a equal 1.0 # 5.719025032 variable i equal 10 # thermo variable f equal 50 # neighbor & conc interval variable s equal 100 # 10 # 100 # output variable n equal 800 # 20 # 200 # 300 # duration variable x equal 4 # 40 # 2 # 4 # exchanges variable e equal 100. # 1. # 100. # 10. # energy variable h equal 5 # nelems variable dt equal 4. #1. # 0 # 4.0 ############## END PARAMETERS ################################# dimension 3 boundary p p p pair_style lj/cut/coul/cut 13.0 lattice sc $a lattice sc 1 Lattice spacing in x,y,z = 1 1 1 read_data concentration_init.data Scanning data file ... Reading data file ... orthogonal box = (0 0 0) to (114.381 22.8761 22.8761) 4 by 1 by 1 MPI processor grid 544 atoms 544 velocities Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors atom_modify sort 0 1 mass * 39.948 pair_coeff * * 0.2381 3.405 pair_coeff 1 * 0.4 3.405 dielectric 80.0 variable xlo equal xlo variable xhi equal xhi variable xmid equal 0.5*(${xhi}+${xlo}) variable xmid equal 0.5*(114.38050064000000816+${xlo}) variable xmid equal 0.5*(114.38050064000000816+0) print "reservior x ${xmid}:${xhi}" reservior x 57.190250320000004081:114.38050064000000816 variable ylo equal ylo variable yhi equal yhi variable zlo equal zlo variable zhi equal zhi region BOX block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region BOX block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region BOX block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box region BOX block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box region BOX block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region FLUID block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region FLUID block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box region FLUID block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box region FLUID block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box region R block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region R block 57.190250320000004081 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box region R block 57.190250320000004081 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box region R block 57.190250320000004081 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box group SOLID type 1 288 atoms in group SOLID variable xdof equal 3*count(SOLID) compute_modify thermo_temp extra ${xdof} compute_modify thermo_temp extra 864 #set group SOLID charge 0 group NEUTRAL type 2 114 atoms in group NEUTRAL group FLUID type 2 3 4 256 atoms in group FLUID group NION type 3 66 atoms in group NION group PION type 4 76 atoms in group PION #group tPION type 5 # not dynamic #group tNION type 6 # not dynamic #variable typeP atom type[]==5 set group PION charge 1 Setting atom values ... 76 settings made for charge set group NION charge -1 Setting atom values ... 66 settings made for charge variable O equal count(NEUTRAL) variable S equal count(SOLID) variable F equal count(FLUID) variable P equal count(PION) variable N equal count(NION) variable Pr equal count(PION,R) variable Nr equal count(NION,R) #variable tP equal count(tPION) #variable tN equal count(tNION) variable V equal vol variable cO equal v_O/v_V variable cS equal v_S/v_V variable cN equal v_N/v_V variable cP equal v_P/v_V compute q all property/atom q compute m all property/atom mass compute Q all reduce sum c_q compute M all reduce sum c_m compute Qf FLUID reduce sum c_q compute Mf FLUID reduce sum c_m compute PMIN PION reduce min x compute PMAX PION reduce max x compute NMIN NION reduce min x compute NMAX NION reduce max x timestep ${dt} timestep 4 #neighbor 13 bin neigh_modify every $i check no neigh_modify every 10 check no # coulombic interactions 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: 13 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 parallel_consistency off fix_modify ATC extrinsic short_range off #fix_modify ATC boundary SOLID fix_modify ATC atom_element_map eulerian $i fix_modify ATC atom_element_map eulerian 10 fix_modify ATC internal_quadrature off fix_modify ATC consistent_fe_initialization on fix_modify ATC filter type exponential fix_modify ATC filter scale $i fix_modify ATC filter scale 10 fix_modify ATC filter equilibrate # mesh print "x = ${xlo}:${xhi}" x = 0:114.38050064000000816 fix_modify ATC mesh create $h 1 1 BOX p p p # f p p ExtrinsicModelElectrostatic::correct_electrostatic_forces iterates through ghosts fix_modify ATC mesh create 5 1 1 BOX p p p ATC: created uniform mesh with 24 nodes, 5 unique nodes, and 5 elements fix_modify ATC mesh create_nodeset LBC ${xlo} ${xlo} -INF INF -INF INF fix_modify ATC mesh create_nodeset LBC 0 ${xlo} -INF INF -INF INF fix_modify ATC mesh create_nodeset LBC 0 0 -INF INF -INF INF ATC: created nodeset LBC with 1 nodes fix_modify ATC mesh create_elementset FLUID FLUID ATC: created elementset FLUID with 5 elements fix_modify ATC mesh create_elementset R R ATC: created elementset R with 2 elements fix_modify ATC mesh create_elementset BOX BOX ATC: created elementset BOX with 5 elements ## NOTE tag instead of type, what about transition tyme fix_modify ATC mass_matrix fe fix_modify ATC internal_element_set FLUID fix_modify ATC include atomic_charge fix_modify ATC add_species N type 3 fix_modify ATC add_species P type 4 fix_modify ATC add_species Nt type 5 fix_modify ATC add_species Pt type 6 ## CC fix_modify ATC control concentration N R 0.001 Nt # deletions R ERROR: Illegal fix_modify command (../fix.cpp:104)