I’m busy with a research project in materials science and I’m using LAMMPS for my simulations. My goal is to find the energy required for an atom to bind to the 111 surface of an fcc metal surface. I’ve successfully achieved this using periodic boundary conditions, but I need to obtain similar results using fixed boundary conditions as well.
During minimization, some degree of (expected) deformation occurs around the edges of the simulated particle. To avoid this I’m using the fix wall/region command to fix the x and y surfaces in place. This works really well until I create the atom on the z surface. The atom is created but remains in the same position even after the “run 1” and “minimize” command. Without the fix wall command, the atom successfully bonds to the surface after minimization. Why won’t my atom move to the surface when I use the fix wall command? My script is as follows.
--------------- INITIALIZATION ------------------
label loop2
variable CCT1 loop 0 20
variable CCT equal {CCT1}/20
variable Conc equal {CCT}*100
variable ao index 3.615 3.647 3.678 3.708 3.737 3.764 3.790 3.815 3.840 3.863 3.886 3.908 3.929 3.950 3.971 3.991 4.011 4.031 4.050 4.070 4.090
label loop1100 # loop_1_(100)
variable LP1100 loop 1 25
clear
units metal
dimension 3
boundary f f f
atom_style atomic
dump 1 all custom 1000 simbox.lammpstrj id type x y z
------------------ ATOM DEFINITION -------------------
lattice fcc ${ao} orient x 1 1 -2 orient y -1 1 0 orient z 1 1 1 # for (111) orientation
region box block -8 8 -8 8 -8 8 units lattice
create_box 2 box
region cube block -3.01 3.01 -3.51 3.51 -2.01 2.01 units lattice
region bound block -3.01 3.01 -3.51 3.51 INF INF units lattice
create_atoms 1 region cube
group Cu type 1
group Ag type 2
mass 1 63.546
mass 2 107.868
set group all type/fraction 2 ${CCT} 56584
------------------------ FORCE FIELDS -----------------------
pair_style eam/alloy
pair_coeff * * CuAg.eam.alloy Cu Ag
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#---------------------------Settings----------------------------
compute csym all centro/atom fcc
compute eng all pe/atom
compute eatoms all reduce sum c_eng
#----------------------Run Minimization-------------------------
#reset_timestep 0
thermo 1000
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
fix wall all wall/region bound lj93 1.0 1.0 2.5
min_style cg
minimize 1e-25 1e-25 5000 10000
run 1
variable N equal count(all)
variable No equal $N
variable Up equal “c_eatoms”
variable Uperfect equal ${Up}
#--------------------------------PYTHON------------------------------------------
python xcoordinate &
return v_xcor &
format f &
here “”"
def xcoordinate():
import random
return round(random.uniform(-2, 2), 2)
“”"
variable xcor python xcoordinate
print “-------------------------------x-coordinate = ${xcor}-----------------------”
python ycoordinate &
return v_ycor &
format f &
here “”"
def ycoordinate():
import random
return round(random.uniform(-2.5, 2.5), 2)
“”"
variable ycor python ycoordinate
print “-------------------------------y-coordinate = ${ycor}--------------------------”
#--------------------------Add 1 atom on surface-------------------------------------
create_atoms 1 single {xcor} {ycor} 2.5 units lattice
run 1
#------------------------Run Minimization---------------------------------------
min_style cg
minimize 1e-25 1e-25 5000 10000
run 1
variable Us equal “c_eatoms”
variable Usurface equal {Us}
variable Esurface equal {Usurface}-${Uperfect}
undump 1
######################################
SIMULATION DONE
#print “All done”
#print “Total number of atoms = {No}"
#print "Total Initial energy of atoms = {Uperfect}”
#print “Total Energy after adatom = {Usurface}"
#print "Surface energy = {Esurface}”
#print “{xcor} {ycor} {No} {Uperfect} {Usurface} {Esurface}” append SBEl_Cu_${Conc}Ag(111)Cu.txt screen no
#next LP1100
#jump SELF loop1100
#next CCT1
#next ao
#jump SELF loop2