From e16ae36b357ed91d49918f4f8437c9796cef49eb Mon Sep 17 00:00:00 2001
From: Leandro Martinez <leandro@iqm.unicamp.br>
Date: Fri, 25 Nov 2022 11:26:47 -0300
Subject: [PATCH] implements preserve_lists option

---
 Project.toml                    |  2 +-
 docs/src/PeriodicSystems.md     | 10 ++++++++--
 src/PeriodicSystems.jl          |  9 +++++++--
 test/BasicForPeriodicSystems.jl |  4 ++++
 4 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/Project.toml b/Project.toml
index a1ad0ba1..ec628122 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "CellListMap"
 uuid = "69e1c6dd-3888-40e6-b3c8-31ac5f578864"
 authors = ["Leandro Martinez <lmartine@unicamp.br> and contributors"]
-version = "0.8.7-DEV"
+version = "0.8.7"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
diff --git a/docs/src/PeriodicSystems.md b/docs/src/PeriodicSystems.md
index 1eb7a825..be1e1656 100644
--- a/docs/src/PeriodicSystems.md
+++ b/docs/src/PeriodicSystems.md
@@ -15,8 +15,6 @@ using CellListMap.PeriodicSystems
         - [Two sets of particles](@ref)
         - [Particle simulation](@ref)
 
-
-
 ## The mapped function
 
 The function to be mapped for every pair of particles within the cutoff follows the same interface as the standard interface. It must be of the form
@@ -51,6 +49,14 @@ const masses = # ... some masses
 u = map_pairwise((x,y,i,j,d2,u) -> energy(d2,u,masses), system)
 ```
 
+To compute a different property from the same coordinates and cell lists, use `preserve_lists=true`, for example,
+```julia
+u = map_pairwise((x,y,i,j,d2,u) -> u += sqrt(d2), system; preserve_lists = true)
+```
+in which case we are computing the sum of distances from the same cell lists used to compute the energy in the previous example
+(requires version 0.8.7). Specifically, this will skip the updatding of the cell lists, thus be careful to not use this
+option if the cutoff, unitcell, or any other property of the system changed. 
+
 ## Potential energy example
 
 !!! note
diff --git a/src/PeriodicSystems.jl b/src/PeriodicSystems.jl
index b6e3ab5e..63c9e0e4 100644
--- a/src/PeriodicSystems.jl
+++ b/src/PeriodicSystems.jl
@@ -822,7 +822,7 @@ end
 """
 
 ```
-map_pairwise!(f::Function, system; show_progress = true)
+map_pairwise!(f::Function, system; show_progress = true, preserve_lists = false)
 ```
 
 Function that maps the `f` function into all pairs of particles of
@@ -848,6 +848,10 @@ Thread-safety is taken care automatically in parallel executions.
 `map_pairwise` is an alias to `map_pairwise!` for syntax consistency
 when the `output` variable is immutable.
 
+If `preserve_lists` is `true`, the cell lists will not be recomputed,
+this may be useful for computing a different function from the same
+coordinates.
+
 # Example
 
 In this example we compute the sum of `1/(1+d)` where `d` is the
@@ -869,10 +873,11 @@ julia> map_pairwise((x,y,i,j,d2,output) -> output += 1 / (1 + sqrt(d2)), sys)
 function map_pairwise!(
     f::F,
     sys::AbstractPeriodicSystem;
+    preserve_lists::Bool=false,
     show_progress::Bool=false
 ) where {F<:Function}
     sys.output = _reset_all_output!(sys.output, sys._output_threaded)
-    UpdatePeriodicSystem!(sys)
+    preserve_lists || UpdatePeriodicSystem!(sys)
     sys.output = CellListMap.map_pairwise!(
         f, sys.output, sys._box, sys._cell_list;
         output_threaded=sys._output_threaded,
diff --git a/test/BasicForPeriodicSystems.jl b/test/BasicForPeriodicSystems.jl
index d22b0140..0c38cb56 100644
--- a/test/BasicForPeriodicSystems.jl
+++ b/test/BasicForPeriodicSystems.jl
@@ -250,6 +250,10 @@ end
     naive = CellListMap.map_pairwise!((x, y, i, j, d2, u) -> potential(i, j, d2, u, mass), 0.0, box, cl)
     system = PeriodicSystem(xpositions=x, cutoff=cutoff, unitcell=sides, output=0.0)
     @test PeriodicSystems.map_pairwise!((x, y, i, j, d2, u) -> potential(i, j, d2, u, mass), system) ≈ naive
+
+    # Check the functionality of computing a different function from the same coordinates (new_coordinates=false)
+    naive = CellListMap.map_pairwise!((x, y, i, j, d2, u) -> u += d2, 0.0, box, cl)
+    @test PeriodicSystems.map_pairwise!((x, y, i, j, d2, u) -> u += d2, system; preserve_lists = true) ≈ naive
     
     # Function to be evalulated for each pair: gravitational force
     function calc_forces!(x, y, i, j, d2, mass, forces)