I have fixed the bottom few layers, set the z BC non periodic, used tersoff potential, minimized energy. I even tried to relax the atoms in x and y directions using fix box/relax command.
But I don’t see why am I not getting 1x2 reconstruction of Si 001. There is something very basic I am missing. I am a beginner in MD simulations. Can anyone help me with that?
---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p s
atom_style atomic
atom_modify map array
---------- Create Atoms ---------------------
diamond lattice, lattice constant 5.5 AA
lattice diamond 5.5
region box block 0 5 0 5 0 10 units lattice
region boxfix block 0 5 0 5 0 2 units lattice
create_box 1 box
lattice diamond 5.5 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
mass 1 28.0855
create_atoms 1 box
#replicate 2 2 2
group fixed region boxfix
---------- Define Interatomic Potential ---------------------
pair_style tersoff
pair_coeff * * Si.tersoff Si
neighbor 4.0 bin
neigh_modify delay 10 check yes
#------------ dump xyz file with atoms and bonds --------
read with JMol
dump 1 all xyz 10000 sisurf.xyz
dump_modify 1 element Si
---------- Define Settings ---------------------
compute eng all pe/atom
compute eatoms all reduce sum c_eng
---------- Run Minimization ---------------------
reset_timestep 0
#fix 1 all box/relax x 0.0 y 0.0 vmax 0.001
fix 1 fixed setforce 0.0 0.0 0.0
thermo 10
thermo_style custom step pe lx ly lz c_eatoms
min_style cg
minimize 1e-25 1e-25 5000 10000
variable natoms equal “count(all)”
variable teng equal “c_eatoms”
variable length equal “lx”
variable ecoh equal “v_teng/v_natoms”
print “Total energy (eV) = {teng};"
print "Number of atoms = {natoms};”
print “Lattice constant (Angstoms) = {length};"
print "Cohesive energy (eV) = {ecoh};”
print “All done!”