How to add

Hi All,

I have a question to make sure if my model is correct. I am modelling water evaporation. I want to define a zone on top of my box with p p f boundary conditions. I have defined a region on top of the simulation box called Eva, where all the atoms will be deleted if they reach into this region.
I have defined a reflecting wall on top of the box by fix wall/reflect. My question is can I define a reflecting wall on top of the simulation box, while I want to define the deleted zone there?

Thanks,
Atefeh

variable Ts equal 300.0

variable Ts_end equal 380.0

variable dt equal 0.001

variable Tdamp equal 100000dt #10dt

----------------- Initialize Simulation ---------------------

units metal

dimension 3

boundary p p f

processors * * 1

atom_style full

read_data data.data

pair_style hybrid eam/alloy lj/class2/coul/long 10.0 morse 9.8

pair_modify mix sixthpower

kspace_style pppm 0.00001

kspace_modify slab 5

kspace_modify order 7

pair_coeff * * eam/alloy Pt.lammps.eam_alloy.txt NULL NULL Pt

pair_coeff 1 1 lj/class2/coul/long 0.00055966 1.098 #H1-H1

pair_coeff 2 2 lj/class2/coul/long 0.01187722 3.608 #O1-O1

pair_coeff 1 3 morse 0.059 1.61 3.054

pair_coeff 2 3 morse 0.1084 2.411 2.416

bond_style class2

bond_coeff 1 0.970 24.43149365 -61.94706171 82.50182428 #H1-O1

angle_style class2

angle_coeff 1 103.700 2.161747342 -0.503133971 -0.346988942 # H1-O1-H1

angle_coeff 1 bb -0.412054554 0 0

angle_coeff 1 ba 0.969402954 0.969402954 0 0

group solid type 3

group water type 1 2

region fixed block EDGE EDGE EDGE EDGE EDGE 1 units box

region phan block EDGE EDGE EDGE EDGE 1 13.59 units box

region Eve block EDGE EDGE EDGE EDGE 200 EDGE units box

group fixed region fixed # fixed atoms at the bottom

group phan region phan # phantom atoms that control temperature

group surf subtract solid fixed # surface atoms, wall atoms excluding fixed atoms

#group free subtract surf phan # free atoms, thermal conduction layer

neighbor 0.3 bin

neigh_modify delay 0 every 1 check yes exclude group fixed fixed

---------- Run Minimization ---------------------

fix freeze fixed setforce 0 0 0

velocity phan set 0 0 0

fix top_wall all wall/reflect zhi EDGE units box

fix loadbalance all balance 100000 1.0 shift xy 10 1.1 weight time 0.8 out balance.output

thermo 1000

thermo_style custom step temp press etotal density

min_style cg

minimize 1e-6 1e-8 5000 10000

write_data data.system_min

reset_timestep 0

---------- Run Equilibration ---------------------

velocity all create ${Ts} 13425 mom yes rot yes dist gaussian

velocity fixed set 0.0 0.0 0.0 sum no units box

velocity phan set 0.0 0.0 0.0 sum no units box

fix 1 all nvt temp 300 300 ${Tdamp}

#fix 1 water nve

#fix 2 water temp/berendsen {Ts} {Ts} ${Tdamp}

#fix 3 phan nve

#fix 4 phan temp/berendsen {Ts} {Ts} ${Tdamp}

thermo 1000

thermo_style custom step temp press etotal density

dump 1 all xyz 1000 dumpnew.xyz

timestep ${dt}

run 15000

#write_data data.system_equil

#write_restart restart.equil

reset_timestep 0

----------------- Main NEMD simulation: Temperature ramp in the phantom layers -----------------

unfix 1

#unfix 2

#unfix 4

fix 5 all nve

fix tempramp phan nvt temp {Ts_end} {Ts_end} ${Tdamp}

fix 6 water evaporate 10 30 Eve 38277 molecule yes

thermo 100

thermo_style custom step temp press etotal density

----------------- Main NEMD simulation: run -----------------

dump 2 all xyz 100 dumpnew2.xyz

dump mydump2 all custom 100 run.*.lammpstrj id type x y z vx vy vz

dump_modify mydump2 sort id

restart 3400 restart.*.run

run 3400

Capture.PNG

capture2.PNG

Hi Atefeh

Would you please let me know why you want to delete those molecules???

Alireza Shadloo Jahromi

Ph.D. Candidate in Mechanical Engineering

Shiraz University of Technology.