Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/USER/atc/elastic/in.cnt_fixed_charge
666de878addcefficient_neuronet

Last Change
Raw File

in.cnt_fixed_charge
View Options

echo both
units metal
atom_style charge
dielectric 1.
variable type string "_charge"
boundary s s f
# read in CNT
read_data cnt_9_0_100${type}.data
lattice diamond 3.6 # NOTE ???
pair_style airebo 3.0
pair_coeff * * ./CH.airebo C
mass * 12.01
# PARAMETERS-----------------------------
variable dt equal 0.0005
variable L equal zhi-zlo
variable zhi equal zhi
variable zTip equal ${zhi}-2.0
variable zFree equal zhi
variable R equal 12.1/2
variable xhiFE equal 5.0*$R
variable xloFE equal -${xhiFE}
variable yhiFE equal $R
variable yloFE equal -${yhiFE}
variable zloFE equal zlo+10 # create fixed ghosts
variable zhiFE equal zhi+(zhi-${zloFE})/12*2
variable Lfree equal zhi-${zloFE}
variable nx equal 10 # 5
variable nz equal 14 # 12
print "Length $L [${zloFE}, ${zhiFE}] ${zTip}"
#variable E equal 0.1 # bias 1.0
variable Vb equal 0.0 # bias
variable Vg equal 0.5 # gate/modulation
print "bias voltage ${Vb}, gate voltage ${Vg}"
variable n equal 100000
variable s equal 250
# END -----------------------------------
# all atoms simulation
region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
group internal region feRegion
group fixed subtract all internal
fix FIX fixed setforce 0 0 0
thermo 100
#minimize 0 0 1000 1000
#write_restart cnt_in_box0.rst
region TIP block INF INF INF INF ${zTip} INF units box
group TIP region TIP
variable nAll equal count(all)
variable nGhost equal count(all)-count(internal)
variable nTip equal count(TIP)
print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
print ">>> number of tip atoms : ${nTip}"
neighbor 5. bin
neigh_modify every 10 delay 0 check no
timestep ${dt}
variable tag string "cnt_fixed_charge"
# set charge on tip
variable C equal -0.1 # -0.01 -0.0001102
print "charge $C [e]"
variable c equal $C/${nTip}
set group TIP charge $c
# coupling
fix AtC internal atc electrostatic CNT_id.mat
fix_modify AtC include atomic_charge
fix_modify AtC internal_quadrature off
# note weights don't affect phi or f
fix_modify AtC atom_weight constant internal 1.0
fix_modify AtC extrinsic short_range off
#fix_modify AtC atom_element_map eulerian 1
fix_modify AtC control momentum flux
fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC initial electric_potential all 0.0
# node sets
variable t equal 1.1*$R
fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box
fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box
fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box
fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box
fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF 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.
# ground
fix_modify AtC fix electric_potential lbc 0
# bias
fix_modify AtC fix electric_potential rbc ${Vb}
# gate
fix_modify AtC fix electric_potential bot ${Vg}
# run
compute CM TIP com
compute q all property/atom q
compute Q all reduce sum c_q
compute FSUM all reduce sum fx fy fz
thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] &
c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1]
thermo $s
log ${tag}.log
#run $n
#run $n
thermo 10
timestep 0.0
min_modify line quadratic
minimize 0 0 1000 1000
# u = F L^3 / 3 EI --> EI = F L^3 / 3 u
variable u equal c_CM[1]
variable F equal f_AtC[5]
# [eV/A * A^2] --> [N m]
variable eV2J equal 1.60217646e-19
variable A2m equal 1.e-10
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal ${EI}*${eV2J}*${A2m}
print "flexural rigidity ${EI} [Nm^2] NOTE z force"
# flexural rigidity 6.716732985e-25 [Nm^2]
fix_modify AtC output ${tag}FE 1 full_text
fix_modify AtC output index step
run 1
c4science · Help