Comments (2)
I see, you are right, I have now implemented periodic boundary conditions and it works as expected.
Maybe I had the wrong impression of having to specify a unit cell in the neighborlist
function, as per the documentation, but I understand now that this is not enforced by the cells themsleves, it is a matter of how the coordinates are propagated.
Thanks for the clarification.
from celllistmap.jl.
But does the system has periodic boundary conditions or not? CellListMap does not modify the original coordinates provided, so if you propagate your coordinates in you simulation without wrapping them manually, they will "appear" as not having periodic boundary conditions and the MSD will be the one expected. This is what one normally expects: the system does have PBCs, but the coordinates can be saved without wrapping, thus facilitating the computation of these quantities. Is this the case?
from celllistmap.jl.
Related Issues (20)
- simplify output conversion for numpy arrays
- dealing with highly non-homogeneous systems HOT 6
- Error when creating PeriodicSystem with empty positions HOT 1
- Suggestion: Is it possible to output the coordinates and size of cells so one can visualize them? HOT 2
- Suggestion: In a transient simulation, based on the first time step, can I define a "box of interest"? HOT 2
- update!() fails with disperse coordinate points HOT 6
- Does the 'update_lists = false' option only apply to periodic systems? HOT 5
- Is it possible to store some historical information of pairs? HOT 26
- Neighborlists contain repeated elements HOT 4
- Make the high-level interface more flexible HOT 3
- InPlaceNeighborList() result is incorrect HOT 10
- Setting `nbatches` doesn't work HOT 1
- `limits(x, y)` requires arrays of the same type for no reason HOT 1
- Update previous cells instead of re-initializing all cells HOT 11
- CellListMap hangs HOT 9
- ReverseDiff gradients HOT 14
- CellListMap allocating too much memory HOT 13
- Difference from brute force HOT 6
- Computing virial and pressure HOT 6
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from celllistmap.jl.