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lammps/examples/USER/atc/fluids/in.concentration
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in.concentration
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echo both
units real
atom_style full # charge
### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces
########### BEGIN PARAMETERS ####################################
variable T equal 300
variable a equal 1.0 # 5.719025032
variable i equal 10 # thermo
variable f equal 50 # neighbor & conc interval
variable s equal 100 # 10 # 100 # output
variable n equal 800 # 20 # 200 # 300 # duration
variable x equal 4 # 40 # 2 # 4 # exchanges
variable e equal 100. # 1. # 100. # 10. # energy
variable h equal 5 # nelems
variable dt equal 4. #1. # 0 # 4.0
############## END PARAMETERS #################################
dimension 3
boundary p p p
pair_style lj/cut/coul/cut 13.0
lattice sc $a
read_data concentration_init.data
atom_modify sort 0 1
mass * 39.948
pair_coeff * * 0.2381 3.405
pair_coeff 1 * 0.4 3.405
dielectric 80.0
variable xlo equal xlo
variable xhi equal xhi
variable xmid equal 0.5*(${xhi}+${xlo})
print "reservior x ${xmid}:${xhi}"
variable ylo equal ylo
variable yhi equal yhi
variable zlo equal zlo
variable zhi equal zhi
region BOX block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
region R block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
group SOLID type 1
variable xdof equal 3*count(SOLID)
compute_modify thermo_temp extra ${xdof}
#set group SOLID charge 0
group NEUTRAL type 2
group FLUID type 2 3 4
group NION type 3
group PION type 4
#group tPION type 5 # not dynamic
#group tNION type 6 # not dynamic
#variable typeP atom type[]==5
set group PION charge 1
set group NION charge -1
variable O equal count(NEUTRAL)
variable S equal count(SOLID)
variable F equal count(FLUID)
variable P equal count(PION)
variable N equal count(NION)
variable Pr equal count(PION,R)
variable Nr equal count(NION,R)
#variable tP equal count(tPION)
#variable tN equal count(tNION)
variable V equal vol
variable cO equal v_O/v_V
variable cS equal v_S/v_V
variable cN equal v_N/v_V
variable cP equal v_P/v_V
compute q all property/atom q
compute m all property/atom mass
compute Q all reduce sum c_q
compute M all reduce sum c_m
compute Qf FLUID reduce sum c_q
compute Mf FLUID reduce sum c_m
compute PMIN PION reduce min x
compute PMAX PION reduce max x
compute NMIN NION reduce min x
compute NMAX NION reduce max x
timestep ${dt}
#neighbor 13 bin
neigh_modify every $i check no
# coulombic interactions
fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat
#fix_modify ATC parallel_consistency off
fix_modify ATC extrinsic short_range off
#fix_modify ATC boundary SOLID
fix_modify ATC atom_element_map eulerian $i
fix_modify ATC internal_quadrature off
fix_modify ATC consistent_fe_initialization on
fix_modify ATC filter type exponential
fix_modify ATC filter scale $i
fix_modify ATC filter equilibrate
# mesh
print "x = ${xlo}:${xhi}"
fix_modify ATC mesh create $h 1 1 BOX p p p # f p p ExtrinsicModelElectrostatic::correct_electrostatic_forces iterates through ghosts
fix_modify ATC mesh create_nodeset LBC ${xlo} ${xlo} -INF INF -INF INF
fix_modify ATC mesh create_elementset FLUID FLUID
fix_modify ATC mesh create_elementset R R
fix_modify ATC mesh create_elementset BOX BOX
## NOTE tag instead of type, what about transition tyme
fix_modify ATC mass_matrix fe
fix_modify ATC include atomic_charge
fix_modify ATC add_species N type 3
fix_modify ATC add_species P type 4
fix_modify ATC add_species Nt type 5
fix_modify ATC add_species Pt type 6
## CC
fix_modify ATC control concentration N R 0.001 Nt # deletions R
fix_modify ATC control concentration N frequency $f
fix_modify ATC control concentration N max_energy $e
fix_modify ATC control concentration N max_attempts 100
fix_modify ATC control concentration N max_exchanges $x
#-
fix_modify ATC control concentration P R 0.002 Pt # addtions R
fix_modify ATC control concentration P frequency $f
fix_modify ATC control concentration P max_energy $e
fix_modify ATC control concentration P max_attempts 100
fix_modify ATC control concentration P max_exchanges $x
fix_modify ATC output volume_integral all mass_density
fix_modify ATC output volume_integral all charge_density
# data reduction
fix PP all atc field
#fix_modify PP add_species ions type 3 4
#fix_modify PP add_species IONS type 3 4 1 2
fix_modify PP add_species n type 3
fix_modify PP add_species p type 4
fix_modify PP add_species s type 1
fix_modify PP add_species o type 2
fix_modify PP fields add species_concentration mass_density charge_density temperature
fix_modify PP fields add charge_flux species_flux
fix_modify PP output volume_integral all mass_density
fix_modify PP output volume_integral all charge_density
fix_modify PP mesh create $h 1 1 BOX f p p
fix_modify PP atom_element_map eulerian $i
# output
thermo $i
variable dN equal f_ATC[1]
variable dP equal f_ATC[2]
variable Nc equal f_ATC[3]
variable Pc equal f_ATC[4]
variable Nt equal f_ATC[5]
variable Pt equal f_ATC[6]
#
variable Nu equal f_ATC[7]
variable Pu equal f_ATC[8]
variable Ng equal f_ATC[9]
variable Pg equal f_ATC[10]
thermo_style custom step temp etotal &
atoms v_F v_P v_N v_dP v_dN v_Pc v_Nc v_Pr v_Nr v_Pt v_Nt &
c_PMIN c_NMIN c_PMAX c_NMAX c_Q c_M c_Qf c_Mf v_Pu v_Nu v_Pg v_Ng
# NOTE this doesn't seem to work
#thermo_modify format 4 %5d format 5 %5d format 6 %5d format 7 %5d format 8 %5d
#thermo_modify format 4 %5d
#thermo_modify format 5 %5d
#thermo_modify format 6 %5d
#thermo_modify format 7 %5d
#thermo_modify format 8 %5d
#thermo_modify format 9 %5d
#thermo_modify format 10 %5d
#thermo_modify format 11 %5d
log concentration.log
fix_modify ATC output concentrationFE $s text binary
fix_modify PP output concentrationPP $s text
dump D all custom $s concentration.dmp id type x y z q vx vy vz fx fy fz
#fix_modify ATC fix temperature all $T
fix_modify ATC fix electric_potential LBC 0.
thermo_modify lost ignore # HACK, look at fix_gcmc or ask Paul C.
run $n
#print "average concentration S:${cS} O:${sO} N:${cN} P:${cP}"
print "average_concentration_S: ${cS}"
print "average_concentration_O: ${cO}"
print "average_concentration_N: ${cN}"
print "average_concentration_P: ${cP}"
print "volume: $V"
#write_restart concentration.rst
#shell "restart2data concentration.rst concentration.data"
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