Dear Users
I have some problem to use replicate for creation of big simulation box.
ERROR: Replicate did not assign all atoms correctly (replicate.cpp:369)"
Please let me know is there any technical difference between use ‘replicate 4 2 4’ command and ‘region 0 4 0 2 0 4 units lattice’ command to create simulation box.
Thanks
Dear Users
I have some problem to use replicate for creation of big simulation box.
ERROR: Replicate did not assign all atoms correctly (replicate.cpp:369)"
Please let me know is there any technical difference between use
'replicate 4 2 4' command and 'region 0 4 0 2 0 4 units lattice' command to
create simulation box.
yes, there certainly is.
Dear Axel
Thanks for your reply. I created a unit cell by “lattice custom” and “create_atoms & basis”.
1- what is the difference between create final simulation box with region directly and use replicate the unit cell " region sim_box 0 1 0 1 0 1".Because in some situations the results are the same.
2- The boundary of my simulation box is P P S, and when I replicate the unit cell I find the “ERROR: Replicate did not assign all atoms correctly (replicate.cpp:369)”. why this Error occurs and any suggestion to solve it?
Mohammad
Dear Axel
Thanks for your reply. I created a unit cell by "lattice custom" and
"create_atoms & basis".
1- what is the difference between create final simulation box with region
directly and use replicate the unit cell " region sim_box 0 1 0 1 0
1".Because in some situations the results are the same.
getting the same result doesn't mean it was achieved in the same way. atom
positions are a state function, they contain no information whatsorever how
they happened to be. nevertheless there is a fundamental difference between
first creating a small box and then replicating or immediately creating a
large box. this should be obvious to anybody even without knowing how it is
implemented.
2- The boundary of my simulation box is P P S, and when I replicate the
unit cell I find the "ERROR: Replicate did not assign all atoms
correctly (replicate.cpp:369)". why this Error occurs and any suggestion to
solve it?
i suspected something like that. if you set shrinkwrap boundaries but fill
them with a system that doesn't conform to it (i.e. the S dimension would
need to shrink a lot in the first step), you have a mistake in your input.
this will also fail in regular simulations without replicate with a lost
atom error. the error message you see is equivalent to having lost atoms.
this is a common question that has been answered many, many times. fix your
input or use "m" boundary conditions.
axel.
Dear Axel
I used “m” boundary instead of “s”, in the Al2O3 crystal,(attached pic) and the simulation run without error. but the atoms shrinked, but the region don’t shrink with atoms.
1- is it correct that the region have distant from the end of atoms?
2- I need to calculate the stress-strain of the Al2O3 crystal, then I need to have the length of “Lz” in each step during loading. how I can do that if the Lz is constant.
Hadi
