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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
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