31b31f0a6a
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10659 f3b2605a-c512-4ea7-a41b-209d697bcdaa
268 lines
11 KiB
Plaintext
268 lines
11 KiB
Plaintext
LAMMPS (24 Aug 2013)
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units metal
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# PARAMETERS-----------------------------
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variable s equal 1
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variable L equal 10
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variable e equal 4
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variable E equal 0.0001
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variable V equal $E*$L
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variable V equal 0.00010000000000000000479*$L
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variable V equal 0.00010000000000000000479*10
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# END -----------------------------------
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atom_style atomic
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lattice diamond 1.0
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Lattice spacing in x,y,z = 1 1 1
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boundary f p p
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region box block -$L $L 0 1 0 1
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region box block -10 $L 0 1 0 1
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region box block -10 10 0 1 0 1
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create_box 1 box
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Created orthogonal box = (-10 0 0) to (10 1 1)
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4 by 1 by 1 MPI processor grid
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group box region box
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0 atoms in group box
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atom_modify sort 0 1
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timestep 0.0
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mass * 12.01
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# coupling
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### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
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fix AtC box atc electrostatic-equilibrium CNT.mat
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ATC: constructing equilibrium electrostatic coupling with parameter file CNT.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: 7 materials defined from CNT.mat
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ATC: creating electrostatic extrinsic model
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: 7 materials defined from CNT.mat
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: computed mass density : 96.08
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ATC: 7 materials defined from CNT.mat
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fix_modify AtC internal_quadrature off
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#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
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fix_modify AtC atom_weight constant box 1.0
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fix_modify AtC omit atomic_charge
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fix_modify AtC mesh create $e 1 1 box f p p
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fix_modify AtC mesh create 4 1 1 box f p p
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ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements
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#fix_modify AtC control momentum flux
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fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
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ATC: created elementset all with 4 elements
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# bcs/ics conditions
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fix_modify AtC fix displacement x all 0.0
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fix_modify AtC fix displacement y all 0.0
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fix_modify AtC fix displacement z all 0.0
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fix_modify AtC fix velocity x all 0.0
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fix_modify AtC fix velocity y all 0.0
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fix_modify AtC fix velocity z all 0.0
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fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
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ATC: created nodeset lbc with 1 nodes
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fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
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ATC: created nodeset rbc with 1 nodes
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fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
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fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 $V
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fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
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ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)
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fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
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fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 $V
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fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
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ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)
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# run
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thermo_style custom step cpu etotal ke
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thermo $s
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thermo 1
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fix_modify AtC output electron_densityFE $s text
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fix_modify AtC output electron_densityFE 1 text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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fix_modify AtC output index step
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log electron_density.log
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# run default material
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print "default material - table linear"
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default material - table linear
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run $s
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run 1
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Setting up run ...
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
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ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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Memory usage per processor = 0.432442 Mbytes
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Step CPU TotEng KinEng
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0 0 0 -0
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1 0.001942873 0 -0
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Loop time of 0.00195646 on 4 procs for 1 steps with 0 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 1.72853e-06 (0.08835)
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Outpt time (%) = 0.000358939 (18.3463)
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Other time (%) = 0.0015958 (81.5653)
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Nlocal: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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# run CNT1 material
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print "CNT1 material - analytical linear"
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CNT1 material - analytical linear
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fix_modify AtC material all CNT1
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run $s
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run 1
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Setting up run ...
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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Memory usage per processor = 0.432442 Mbytes
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Step CPU TotEng KinEng
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1 0 0 -0
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2 0.001652956 0 -0
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Loop time of 0.00166643 on 4 procs for 1 steps with 0 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 7.15256e-07 (0.0429215)
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Outpt time (%) = 0.00018388 (11.0344)
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Other time (%) = 0.00148183 (88.9227)
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Nlocal: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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# run CNT2 material
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print "CNT2 material - analytical exponetial"
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CNT2 material - analytical exponetial
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fix_modify AtC material all CNT2
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run $s
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run 1
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Setting up run ...
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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Memory usage per processor = 0.432442 Mbytes
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Step CPU TotEng KinEng
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2 0 0 -0
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3 0.0015969276 0 -0
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Loop time of 0.00160939 on 4 procs for 1 steps with 0 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 2.02656e-06 (0.125921)
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Outpt time (%) = 0.000166118 (10.3218)
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Other time (%) = 0.00144124 (89.5522)
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Nlocal: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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# run CNT material
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print "CNT material - table DOS"
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CNT material - table DOS
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fix_modify AtC material all CNT
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#variable E equal 10*$E
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#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
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#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
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run $s
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run 1
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Setting up run ...
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt-exp] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
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ATC: WARNING: material: [cnt] cannot find body_force
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ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
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Memory usage per processor = 0.432442 Mbytes
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Step CPU TotEng KinEng
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3 0 0 -0
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4 0.0015408993 0 -0
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Loop time of 0.00155497 on 4 procs for 1 steps with 0 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 1.3113e-06 (0.08433)
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Outpt time (%) = 0.00017637 (11.3424)
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Other time (%) = 0.00137728 (88.5733)
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Nlocal: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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