hello
i have built titanium alpha structure in 11-20 orientation using Atomistix ToolKit than i saved the file in lammps format
when i equilibrate the structure i found that some atoms are missing from the top
can any one help to resolve this problem
PS:i joint picture of stucture generated and equilibrated and the input i used in a simulation.
Best Regards
Ahmed
in.alpha_300_11-20 (950 Bytes)
hello
i have built titanium alpha structure in 11-20 orientation using Atomistix
ToolKit than i saved the file in lammps format
when i equilibrate the structure i found that some atoms are missing from
the top
look at the bottom, they'll be added there. after all, you're running
with periodic boundaries.
axel.
thank you axel for your responce.
now my question how i can equilibrate this structure with out having the problem above again
ps: i will use this equilibrated structure as a substrate to deposit the atoms
Best Regards
Ahmed
hello
i have built titanium alpha structure in 11-20 orientation using Atomistix
ToolKit than i saved the file in lammps format
when i equilibrate the structure i found that some atoms are missing from
the top
look at the bottom, they’ll be added there. after all, you’re running
with periodic boundaries.
axel.
thank you axel for your responce.
now my question how i can equilibrate this structure with out having the
problem above again
ps: i will use this equilibrated structure as a substrate to deposit the
atoms
simply adjust your simulation cell accordingly; either through
changing dimensions or boundary conditions or both.
however your real problem is not the atoms going across periodic
boundaries, but the fact that you obviously don't have any significant
training in MD and haven't even spent sufficient time reading up on
how to set up simulations for the kind of system you are after.
otherwise you would not have asked a question with such an obvious
answer. there is more to running a successful simulation than to stick
some atom coordinates into a simulation software and let them wiggle
around. thus my recommendation is: find yourself a competent person
that can serve as your instructor/trainer. you won't be able to pick
up what you need to know from posting to a mailing list.
axel.