LAMMPS (24 Aug 2013) units metal # PARAMETERS----------------------------- variable s equal 1 variable L equal 10 variable e equal 4 variable E equal 0.0001 variable V equal $E*$L variable V equal 0.00010000000000000000479*$L variable V equal 0.00010000000000000000479*10 # END ----------------------------------- atom_style atomic lattice diamond 1.0 Lattice spacing in x,y,z = 1 1 1 boundary f p p region box block -$L $L 0 1 0 1 region box block -10 $L 0 1 0 1 region box block -10 10 0 1 0 1 create_box 1 box Created orthogonal box = (-10 0 0) to (10 1 1) 4 by 1 by 1 MPI processor grid group box region box 0 atoms in group box atom_modify sort 0 1 timestep 0.0 mass * 12.01 # coupling ### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null fix AtC box atc electrostatic-equilibrium CNT.mat ATC: constructing equilibrium electrostatic coupling with parameter file CNT.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: 7 materials defined from CNT.mat ATC: creating electrostatic extrinsic model ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: 7 materials defined from CNT.mat ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: computed mass density : 96.08 ATC: 7 materials defined from CNT.mat fix_modify AtC internal_quadrature off #fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group fix_modify AtC atom_weight constant box 1.0 fix_modify AtC omit atomic_charge fix_modify AtC mesh create $e 1 1 box f p p fix_modify AtC mesh create 4 1 1 box f p p ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements #fix_modify AtC control momentum flux fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF ATC: created elementset all with 4 elements # bcs/ics conditions fix_modify AtC fix displacement x all 0.0 fix_modify AtC fix displacement y all 0.0 fix_modify AtC fix displacement z all 0.0 fix_modify AtC fix velocity x all 0.0 fix_modify AtC fix velocity y all 0.0 fix_modify AtC fix velocity z all 0.0 fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF ATC: created nodeset lbc with 1 nodes fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF ATC: created nodeset rbc with 1 nodes 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 0.00010000000000000000479 0 0 $V fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208 ATC: created function : 0.001 + 0.0001(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 rbc linear 0 0 0 0.00010000000000000000479 0 0 $V fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208 ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0) # run thermo_style custom step cpu etotal ke thermo $s thermo 1 fix_modify AtC output electron_densityFE $s text fix_modify AtC output electron_densityFE 1 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify AtC output index step log electron_density.log # run default material print "default material - table linear" default material - table linear run $s run 1 Setting up run ... ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null 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 ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 0.432442 Mbytes Step CPU TotEng KinEng 0 0 0 -0 1 0.001942873 0 -0 Loop time of 0.00195646 on 4 procs for 1 steps with 0 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 1.72853e-06 (0.08835) Outpt time (%) = 0.000358939 (18.3463) Other time (%) = 0.0015958 (81.5653) Nlocal: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Neighbor list builds = 0 Dangerous builds = 0 # run CNT1 material print "CNT1 material - analytical linear" CNT1 material - analytical linear fix_modify AtC material all CNT1 run $s run 1 Setting up run ... ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 0.432442 Mbytes Step CPU TotEng KinEng 1 0 0 -0 2 0.001652956 0 -0 Loop time of 0.00166643 on 4 procs for 1 steps with 0 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 7.15256e-07 (0.0429215) Outpt time (%) = 0.00018388 (11.0344) Other time (%) = 0.00148183 (88.9227) Nlocal: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Neighbor list builds = 0 Dangerous builds = 0 # run CNT2 material print "CNT2 material - analytical exponetial" CNT2 material - analytical exponetial fix_modify AtC material all CNT2 run $s run 1 Setting up run ... ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 0.432442 Mbytes Step CPU TotEng KinEng 2 0 0 -0 3 0.0015969276 0 -0 Loop time of 0.00160939 on 4 procs for 1 steps with 0 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 2.02656e-06 (0.125921) Outpt time (%) = 0.000166118 (10.3218) Other time (%) = 0.00144124 (89.5522) Nlocal: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Neighbor list builds = 0 Dangerous builds = 0 # run CNT material print "CNT material - table DOS" CNT material - table DOS fix_modify AtC material all CNT #variable E equal 10*$E #fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V #fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V run $s run 1 Setting up run ... ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt-exp] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [cnt] cannot find body_force ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 0.432442 Mbytes Step CPU TotEng KinEng 3 0 0 -0 4 0.0015408993 0 -0 Loop time of 0.00155497 on 4 procs for 1 steps with 0 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 1.3113e-06 (0.08433) Outpt time (%) = 0.00017637 (11.3424) Other time (%) = 0.00137728 (88.5733) Nlocal: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Neighbor list builds = 0 Dangerous builds = 0