LAMMPS (30 Aug 2013) units metal atom_style atomic lattice diamond 3.6 Lattice spacing in x,y,z = 3.6 3.6 3.6 boundary f f f #region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box #region box block 0 10 0 10 0 10 #create_box 1 box #group box region box #atom_modify sort 0 1 pair_style tersoff read_data tube_8_4.init Reading data file ... orthogonal box = (-4.34588 -4.34588 0) to (4.34588 4.34588 104.296) 1 by 1 by 4 MPI processor grid 1008 atoms 1008 velocities pair_coeff * * ../../../../potentials/SiC.tersoff C mass * 12.01 # PARAMETERS----------------------------- variable L equal zhi-zlo variable R equal 12.1/2 variable xhiFE equal 5.0*$R variable xhiFE equal 5.0*6.0499999999999998224 variable xloFE equal -${xhiFE} variable xloFE equal -30.25 variable yhiFE equal $R variable yhiFE equal 6.0499999999999998224 variable yloFE equal -${xhiFE} variable yloFE equal -30.25 variable zhiFE equal zhi variable zloFE equal zlo+10 print "Length $L [${zloFE}, ${zhiFE}]" Length 104.29551668000000575 [10, 104.29551668000000575] variable E equal 0.01 # 1.0 10.0 0.01 variable V equal $E*${zloFE} variable V equal 0.010000000000000000208*${zloFE} variable V equal 0.010000000000000000208*10 variable V equal 2 print "Electric field $E ref.voltage $V" Electric field 0.010000000000000000208 ref.voltage 2 variable s equal 20 # END ----------------------------------- # all atoms simulation region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box region feRegion block -30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box group internal region feRegion 908 atoms in group internal variable nAll equal count(all) variable nGhost equal count(all)-count(internal) print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" >>> number of stationary ghosts: 100 of 1008 #neighbor 5. bin #neigh_modify every 10 delay 0 check no timestep 0.0005 # coupling fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat ATC: constructing equilibrium electrostatic coupling with parameter file CNT_electrostatic2.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: computed mass density : 2.05933 ATC: 1 materials defined from CNT_electrostatic2.mat ATC: creating electrostatic extrinsic model ATC: computed mass density : 2.05933 ATC: 1 materials defined from CNT_electrostatic2.mat ATC: computed mass density : 2.05933 ATC: 1 materials defined from CNT_electrostatic2.mat fix_modify AtC omit atomic_charge #fix_modify AtC internal_quadrature off <<<< ??? variable alat equal 1.42 variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0 variable w equal 1.4199999999999999289*${alat}*3.*sqrt(3.)/4.0 variable w equal 1.4199999999999999289*1.4199999999999999289*3.*sqrt(3.)/4.0 #variable w equal 10 fix_modify AtC atom_weight constant internal $w fix_modify AtC atom_weight constant internal 2.6193804362864128166 fix_modify AtC source_integration atom fix_modify AtC atom_element_map eulerian 1 fix_modify AtC mesh create 5 1 12 feRegion f p f ATC: created uniform mesh with 156 nodes, 78 unique nodes, and 60 elements fix_modify AtC control momentum flux #fix_modify AtC extrinsic poisson_solver max_iterations 5 # initial conditions fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement y all 0.0 fix_modify AtC initial displacement z all 0.0 fix_modify AtC initial velocity x all 0.0 fix_modify AtC initial velocity y all 0.0 fix_modify AtC initial velocity z all 0.0 #variable a equal -$R-0.1 #variable b equal $R+0.1 #fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 30.25 ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 ${xhiFE} ${zloFE} ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 ${zloFE} ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 ${zloFE} units box fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 10 units box ATC: created nodeset lbc with 6 nodes fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 30.25 ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 ${xhiFE} ${zhiFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 ${zhiFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 ${zhiFE} units box fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 104.29551668000000575 units box ATC: created nodeset rbc with 6 nodes fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 -30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box ATC: created nodeset bot with 13 nodes fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box ATC: created nodeset top with 13 nodes # boundary conditions fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement y lbc 0. fix_modify AtC fix displacement z lbc 0. fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity y lbc 0. fix_modify AtC fix velocity z lbc 0. fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 $V fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 2 ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0) #fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V ##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 $V fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 2 ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0) # run thermo_style custom step cpu etotal ke thermo $s thermo 20 fix_modify AtC output cnt_electrostatic2FE $s full_text # binary fix_modify AtC output cnt_electrostatic2FE 20 full_text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify AtC output index step # NOTE not recognized as vector by paraview variable uX atom x-f_AtC[1] variable uY atom y-f_AtC[2] variable uZ atom z-f_AtC[3] variable rho atom mass*f_AtC[4] dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho dump CONFIG all custom 20 cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho log cnt_electrostatic2.log #run $s run 100 Setting up run ... ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero Memory usage per processor = 53.9593 Mbytes Step CPU TotEng KinEng 0 0 -7315.3918 4.2386027e-06 20 0.92063498 -7315.3918 0.0003453277 40 1.51669 -7315.3918 0.0012274403 60 2.113302 -7315.3918 0.0026370119 80 2.7108579 -7315.3918 0.004552872 100 3.3048739 -7315.3918 0.0069472253 Loop time of 3.3049 on 4 procs for 100 steps with 1008 atoms Pair time (%) = 0.198261 (5.99899) Neigh time (%) = 0 (0) Comm time (%) = 0.0253496 (0.76703) Outpt time (%) = 0.0820183 (2.48171) Other time (%) = 2.99928 (90.7523) Nlocal: 252 ave 256 max 248 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 59 ave 80 max 40 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 4456 ave 4608 max 4304 min Histogram: 1 0 0 0 1 1 0 0 0 1 Total # of neighbors = 17824 Ave neighs/atom = 17.6825 Neighbor list builds = 0 Dangerous builds = 0 # NOTE try fix charge on tip