dear sir, i have created a cylindrical nanorod using the following commands
region domain cylinder x 40 40 42 -10 110 units box
region rod cylinder x 40 40 40 0 100 units box
create_box 2 domain
create_atoms 1 region rod
my problem is that when i increase the temperature of the rod it takes the shape of rectangular rod (according to the dimensions of orthognal box)
my question is that how can i creat a cylindrical box so that the shape of my nanorod does not change?
any help and suggestions is highly appereciated in advance.
thanks and regards
imran
Hi,
Maybe the rectangular shape is more stable at that given temperature … Perhaps a phase change from cylindrical to rectangular shape ? . I had same issues when trying to increase the temperature in Icosahedral nano particles… it shape was very temperature sensible and also dependable of the system size … But most of the potentials i used in my simulations where developed for Bulk materials and validation for nano particles is yet to be determined
dear sir, i have created a cylindrical nanorod using the following commands
region domain cylinder x 40 40 42 -10 110 units box
region rod cylinder x 40 40 40 0 100 units box
create_box 2 domain
create_atoms 1 region rod
my problem is that when i increase the temperature of the rod it takes the
shape of rectangular rod (according to the dimensions of orthognal box)
my question is that how can i creat a cylindrical box so that the shape of
my nanorod does not change?
there is quite a bit of important information missing here, but my guess
is that you have periodic boundaries and that the system doesn't turn into
a orthogonal rod, but into a bulk system when your nanostructure is melting
(and expanding). putting a confinement on your nanosystem is not going to
make your simulation more meaningful. if anything, it more likely would
qualify you for a job at pixar rather than having a publication in a
respectable journal.
LAMMPS simulation boxes are always parallelepipeds and usually orthogonal.
if you don't want atoms to join with their periodic images, you should
configure shrinkwrap boundaries.
furthermore, you need to investigate, whether the melting of your structure
is physical (and result of the choice of potential) or whether it is due to
bad simulation parameters (many times this is the case).
you *could* add a cylindrical confinement potential via fix wall/region,
but as mentioned above that does not solve your real problem, only mask it
and tour your simulation from science to animation.
axel.
Dear Sir,
thanks for your reply sir , but it make my argument (that we use a cylinderical nanorod for the simulation process) wrong. that new shape mantain even if i reduce the temperature . is it correct to delete the additional atoms to make the cylindrical rod again?
thanks and regards
imran
Hell nooo ! . Removing the atoms is a bad idea … As Axel said: “if anything, it more likely would qualify you for a job at pixar” i am just guessing here, but more probable the potential your using is for Bulk system and therefore your nanorod will tend to become a “Bulk” or at least the Bulk will tend to be the most favorable Phase …. Why would the bulk become a nanorod if you reduce the temperature once it become a bulk at the firs place ? … IF Bulk becomes nanorod , then why not start with a BULK then Quenching it And volla you make Nanorods (more likely not to happen ….)
Oscar Guerrero