Comments (3)
zahachtah
commented on September 21, 2024
Just had a thought, could one do it as a view of a SArray?
xpositions = rand(SVector{2,Float64},10)
alive=[2,5,6,7]
system = PeriodicSystem(
xpositions = view(xpositions,alive),
unitcell=[1.0,1.0],
cutoff = 0.1,
output = 0.0,
output_name = :organism
);
Now one could update the alive vector and this should make CellListMap.map_pairwise! skip pairwise calculations of any non-existing organisms....maybe....
(late now, will test tomorrow if you haven't commented yet :-) )
from celllistmap.jl.
lmiq
commented on September 21, 2024
That won't really bring you any benefit, because the coordinates are internally copied anyway to make them local to each computation.
The simplest approach is to simply put the live individuals at the beginning of the array and resize it. Partition the array in live/death is a relatively cheap operation (actually there is an internal function in CellListMap that can almost do that, here is a variation of it:
julia> function keep_alive!(alive, x::AbstractVector)
iswap = 1
@inbounds for i in eachindex(alive,x)
if alive[i]
if iswap != i
x[iswap], x[i] = x[i], x[iswap]
alive[iswap], alive[i] = alive[i], alive[iswap]
end
iswap += 1
end
end
return resize!(x,iswap - 1), resize!(alive,iswap - 1)
end
keep_alive! (generic function with 1 method)
julia> x = rand(SVector{2,Float64}, 100); alive = rand(Bool, 100);
julia> keep_alive!(alive, x)
(SVector{2, Float64}[[0.29119093606094626, 0.14799284331418305], [0.4972730380281174, 0.09269265678798855], [0.9159907295858599, 0.023425334184397073], [0.6070998442833461, 0.5991916701778053], [0.3160812299339907, 0.3164821161774142], [0.7439114803685659, 0.11559108939285456], [0.6670382934847978, 0.9839740944475307], [0.657358664500978, 0.32044636378412406], [0.6082878186504177, 0.50068291214486], [0.08662133450538845, 0.4684000312786505] … [0.3151220417919539, 0.4605952237829716], [0.2875938461476413, 0.5834502287377114], [0.030323370160795338, 0.6514632971028673], [0.11688254221953154, 0.6127507999882679], [0.44709649959706943, 0.41760496956657467], [0.7726898156341978, 0.6743612022838364], [0.189673060868509, 0.2515943452830405], [0.6597804541954473, 0.028298360650823362], [0.002315181581732384, 0.30165618551226736], [0.9019060110665619, 0.9487908898003208]], Bool[1, 1, 1, 1, 1, 1, 1, 1, 1, 1 … 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])Then, for example, let us say that you initialized the system with the original coordinates:
julia> x = rand(SVector{2,Float64}, 100); alive = rand(Bool, 100);
julia> sys = PeriodicSystem(xpositions=x,unitcell=[1,1],cutoff=0.05,output=0.0)
PeriodicSystem1{output} of dimension 2, composed of:
Box{OrthorhombicCell, 2}
unit cell matrix = [ 1.0, 0.0; 0.0, 1.0 ]
cutoff = 0.05
number of computing cells on each dimension = [22, 22]
computing cell sizes = [0.05, 0.05] (lcell: 1)
Total number of cells = 484
CellList{2, Float64}
100 real particles.
87 cells with real particles.
123 particles in computing box, including images.
Parallelization auxiliary data set for:
Number of batches for cell list construction: 1
Number of batches for function mapping: 1
Type of output variable (output): Float64Note that the system has 100 real particles.
If you now "kill" the individuals:
julia> keep_alive!(alive, x);The next time map_pairwise! is called the system will be updated for the new set of coordinates:
julia> PeriodicSystems.map_pairwise!((x,y,i,j,d2,out) -> out += d2, sys)
0.00416479370378711
julia> sys
PeriodicSystem1{output} of dimension 2, composed of:
Box{OrthorhombicCell, 2}
unit cell matrix = [ 1.0, 0.0; 0.0, 1.0 ]
cutoff = 0.05
number of computing cells on each dimension = [22, 22]
computing cell sizes = [0.05, 0.05] (lcell: 1)
Total number of cells = 484
CellList{2, Float64}
45 real particles.
41 cells with real particles.
55 particles in computing box, including images.
Parallelization auxiliary data set for:
Number of batches for cell list construction: 1
Number of batches for function mapping: 1
Type of output variable (output): Float64(note now that there are 45 real particles, the ones that were alive).
Note that that partition and resizing is cheap, and won't affect the overall performance of almost any simulation. Here with 10_000 particles:
julia> x = rand(SVector{2,Float64}, 10^4); alive = rand(Bool, 10^4);
julia> sys = PeriodicSystem(xpositions=x,unitcell=[1,1],cutoff=0.05,output=0.0);
julia> @btime PeriodicSystems.map_pairwise!((x,y,i,j,d2,out) -> out += d2, $sys)
1.049 ms (144 allocations: 14.78 KiB)
489.7633383677577
julia> @btime keep_alive!(alive, x) setup=(x = rand(SVector{2,Float64}, 10^4); alive = rand(Bool, 10^4)) evals=1;
46.064 μs (0 allocations: 0 bytes)
julia> keep_alive!(alive, x);
julia> @btime PeriodicSystems.map_pairwise!((x,y,i,j,d2,out) -> out += d2, $sys)
499.010 μs (144 allocations: 14.78 KiB)
119.80104258632134from celllistmap.jl.
zahachtah
commented on September 21, 2024
Great explanation,thank you very much. I think I can adapt this to birth events too. Enjoying the package, very efficient!
from celllistmap.jl.
Related Issues (20)
- Covert example to doc test HOT 1
- Better handling when `NaN` occurs in a position HOT 11
- 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
- Removing periodic boundary conditions HOT 2
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from celllistmap.jl.