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lammps/examples/USER/atc/elastic/in.cnt_electrostatic2
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in.cnt_electrostatic2
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# needs description
# E = - grad \phi
# f = q E
# NOTE tangent is constant for LAGRANGIAN but not exact...
# NOTE try one atom and one free node
# issue is one of magnitude of E since
# tangent = perm BB - dn/dphi NN
# CHECK CONDITIONING?
echo both
units metal
atom_style atomic
lattice diamond 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.data
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*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${xhiFE}
variable zhiFE equal zhi
variable zloFE equal zlo+10
print "Length $L [${zloFE}, ${zhiFE}]"
variable E equal 0.01 # 1.0 10.0 0.01
variable V equal $E*${zloFE}
variable V equal 2
print "Electric field $E ref.voltage $V"
variable s equal 20
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
#neighbor 5. bin
#neigh_modify every 10 delay 0 check no
timestep 0.0005
# coupling
fix AtC internal atc electrostatic-equilibrium 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 10
fix_modify AtC atom_weight constant internal $w
fix_modify AtC source_integration atom
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC mesh create 5 1 12 feRegion f p f
fix_modify AtC control momentum flux
#fix_modify AtC extrinsic poisson_solver max_iterations 5
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
#variable a equal -$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 rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
# 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 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
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output cnt_electrostatic2FE $s full_text # binary
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
log cnt_electrostatic2.log
#run $s
run 100
# NOTE try fix charge on tip
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