# [lammps-users] Silicon

Hi LAmmps users,
As I am building silicon using diamond lattice in lammps, but when I am visualizing dump file in ovito with polyhedral template matching. I did not get the percentage of cubic diamond it shows zero there. Here is my input file

units metal
dimension 3
boundary p p p
atom_style atomic
#atom_modify map array

# ---------- Create Atoms ---------------------

##ATOM DEFINITION
variable latparam equal 5.43
lattice diamond \${latparam} orient x 1 1 -2 orient y 1 1 1 orient z 1 -1 0
region whole block 0 1 0 1 0 1 units lattice
create_box 1 whole
mass 1 28.0855
create_atoms 1 region whole
replicate 1 1 1

##---------- Define Interatomic Potential ---------------------
pair_style tersoff
pair_coeff * * Si.tersoff Si
neighbor 2.0 bin
neigh_modify delay 10 check yes

# ---------- Define Settings ---------------------

compute eng all pe/atom
compute eatoms all reduce sum c_eng

# ---------- Run Minimization ---------------------

reset_timestep 0
fix 1 all box/relax iso 0.0 vmax 0.001
thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
dump 2 all custom 10 ./dumpid.lammpstrj id type x y z
dump 1 all custom 10 ./dump/*.custom_silicon_tensile id type x y z
dump_modify 1 sort id
min_style cg
minimize 1e-25 1e-25 5000 10000

undump 2

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};”

#dump 2 all custom 10 ./dumpid.lammpstrj id type x y z
#dump 2 all atom 10 eqlb.lammpstrj id type x y z
write_restart silicon.equil
write_data silicon.dat

print “All done!”

Hi LAmmps users,
As I am building silicon using diamond lattice in lammps, but when I am visualizing dump file in ovito with polyhedral template matching. I did not get the percentage of cubic diamond it shows zero there. Here is my input file

LAMMPS will create the atoms as you request it (and not as you mean it). keep in mind that you will not automatically get a rotated crystal with correct replication by simply changing the lattice orientation, and that could also confuse the analysis in ovito. please see the documentation of the lattice command for explanations of what it does exactly.

you should be able to tell if it is correct by simply comparing a visualization of a replicated system (not just the principal cell).
there are plenty of previous discussions on how to define and choose the cell dimensions for rotated lattices in the mailing list archives. I suggest you have a look.

axel.

Thanks, I’ll check it out.