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