hey all,

suppose i’ve got some xyz file of a crystal lattice, how can I know the exact (lo,hi) values of the simulation box to put in the data file

besides the obvious way which is looking manualy for the smallest and biggest coordinates in the xyz file ?

is there any smarter way to determine the simulation box values for a given crystal lattice xyz file ?

for example, if my crystal isn’t located at the origin, then its lattice vectors which are known to me from crystallographic info aren’t the xhi y hi zhi values (but some displacement of them)… is there a quick and efficient way of determining the xlo xhi ylo yhi zlo zhi correct values in this case ?

does the simulation box size matter in case of a p p p boundary conditions ?

thanks alot,

hey all,

suppose i've got some xyz file of a crystal lattice, how can I know the

exact (lo,hi) values of the simulation box to put in the data file

besides the obvious way which is looking manualy for the smallest and

biggest coordinates in the xyz file ?

have you tried looking up the lattice constant somewhere?

is it a cubic system?

is there any smarter way to determine the simulation box values for a given

crystal lattice xyz file ?

for example, if my crystal isn't located at the origin, then its lattice

vectors which are known to me from crystallographic info aren't the xhi y hi

zhi values (but some displacement of them)..... is there a quick and

efficient way of determining the xlo xhi ylo yhi zlo zhi correct values in

this case ?

you could have VMD create the data file for you. VMD doesn't store the

simulation cell origin internally, so when you write out a data file with

topo writelammpsdata data.myfile full

it will derive a box center from the geometric center of the total set of atoms

in the system and then apply the box dimensions and finally generate

image indicators as needed.

does the simulation box size matter in case of a p p p boundary conditions ?

yes, depends a bit on your system. if you would have a significantly wrong

box, you might have overlapping atoms or a "crack" that would either deform

the system or implode and thus create some sound wave.

axel.