Hello everyone,
I’m trying to model srd particles in a no-slip cylinder, and am having trouble creating the wall.
I’ve defined variables for xlo/xhi and ylo/yhi as follows:
variable xlength equal 10
variable ylength equal 10
variable zlength equal 10
variable x0 equal v_xlength/2
variable y0 equal v_ylength/2
variable radius equal 4.5
variable WallSRDxlo equal v_x0-sqrt(v_radiusv_radius-(y-v_y0)(y-v_y0))
variable WallSRDxhi equal v_x0+sqrt(v_radiusv_radius-(y-v_y0)(y-v_y0))
variable WallSRDylo equal v_y0-sqrt(v_radiusv_radius-(x-v_x0)(x-v_x0))
variable WallSRDyhi equal v_y0+sqrt(v_radiusv_radius-(x-v_x0)(x-v_x0))
I then set the wall fix:
fix 4 all wall/srd xlo WallSRDxlo xhi WallSRDxhi ylo WallSRDylo yhi WallSRDyhi
Which doesn’t complain. However, when I then run the simulation all the atoms escape and are lost, whereas I’d like them to stay within the cylinder. I initially create the atoms inside a cylinder of radius 4 inside the wall.
I get the feeling that you can’t define xlo etc using atom-vector positions, if that’s the case is there a way to do this? I’d use something like wall/region, but I don’t think that works with srd particles.
Full code here: http://pastebin.com/AA6pCY5i
Many thanks,
Sam Brown
Hello everyone,
I'm trying to model srd particles in a no-slip cylinder, and am having
trouble creating the wall.
I've defined variables for xlo/xhi and ylo/yhi as follows:
variable xlength equal 10
variable ylength equal 10
variable zlength equal 10
variable x0 equal v_xlength/2
variable y0 equal v_ylength/2
variable radius equal 4.5
variable WallSRDxlo equal v_x0-sqrt(v_radius*v_radius-(y-v_y0)*(y-v_y0))
variable WallSRDxhi equal v_x0+sqrt(v_radius*v_radius-(y-v_y0)*(y-v_y0))
variable WallSRDylo equal v_y0-sqrt(v_radius*v_radius-(x-v_x0)*(x-v_x0))
variable WallSRDyhi equal v_y0+sqrt(v_radius*v_radius-(x-v_x0)*(x-v_x0))
I then set the wall fix:
fix 4 all wall/srd xlo WallSRDxlo xhi WallSRDxhi ylo WallSRDylo yhi
WallSRDyhi
Which doesn't complain. However, when I then run the simulation all the
atoms escape and are lost, whereas I'd like them to stay within the
cylinder. I initially create the atoms inside a cylinder of radius 4 inside
the wall.
I get the feeling that you can't define xlo etc using atom-vector positions,
if that's the case is there a way to do this? I'd use something like
wall/region, but I don't think that works with srd particles.
sam,
have you read the documentation for fix wall/srd?
it doesn't say anything that it allows to build any
shaped container, but it provides simply a _flat_
wall or "face". so your entire "vector math" is completely
bogus (also you are using properties that are only
available to atom style variables in an equal style
variable).
you can use variables only to determine the wall/face
location. also, you are not referencing the variables
correctly. the documentation even gives examples
with variables (prefixing them with v_ ). so in your
case, you simply provide strings which have a
"numerical value" of 0. no surprise that particles
go everywhere.
if you use any of the other wall options, they won't
be using srd, but simply add a force to the center
of the particles.
axel.