Merge branch 'master' into gpu-constraints

Author: ejmeitz

Project.toml

@@ -4,6 +4,7 @@ authors = ["Joe G Greener <jgreener@hotmail.co.uk>"]
 version = "0.22.3"
 
 [deps]
+AcceleratedKernels = "6a4ca0a5-0e36-4168-a932-d9be78d558f1"
 Atomix = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 AtomsCalculators = "a3e0e189-c65a-42c1-833c-339540406eb1"
@@ -15,6 +16,7 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
@@ -25,12 +27,12 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SimpleCrystals = "64031d72-e220-11ed-1a7e-43a2532b2fa8"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
-UnsafeAtomicsLLVM = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
 
 [weakdeps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -48,6 +50,7 @@ MollyKernelDensityExt = "KernelDensity"
 MollyPythonCallExt = "PythonCall"
 
 [compat]
+AcceleratedKernels = "0.4.3"
 Atomix = "0.1, 1.0"
 AtomsBase = "0.5"
 AtomsCalculators = "0.2"
@@ -57,11 +60,12 @@ CellListMap = "0.8.11, 0.9"
 Chemfiles = "0.10.3"
 Colors = "0.11, 0.12, 0.13"
 Combinatorics = "1"
-DataStructures = "0.18"
+DataStructures = "0.18, 0.19"
 Distances = "0.10"
 Distributions = "0.23, 0.24, 0.25"
 Enzyme = "0.13.20"
 EzXML = "1"
+FFTW = "1"
 GLMakie = "0.8, 0.9, 0.10, 0.11, 0.12, 0.13"
 GPUArrays = "11"
 Graphs = "1.8"
@@ -75,10 +79,10 @@ Random = "1.9"
 Reexport = "1"
 SimpleCrystals = "0.4"
 SparseArrays = "1.9"
+SpecialFunctions = "2"
 StaticArrays = "1.8.2"
 Statistics = "1.9"
 StructArrays = "0.7.1"
 Unitful = "1"
 UnitfulAtomic = "1"
-UnsafeAtomicsLLVM = "0.1, 0.2"
 julia = "1.10"

README.md

@@ -104,6 +104,7 @@ using Molly
 sys = System(
     joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmx_coords.gro"),
     joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmx_top_ff.top");
+    nonbonded_method="pme",
     loggers=(
         temp=TemperatureLogger(10),
         writer=TrajectoryWriter(10, "traj_5XER_1ps.pdb"),

benchmark/benchmarks.jl

@@ -82,7 +82,6 @@ function test_sim(nl::Bool, parallel::Bool, f32::Bool, ::Type{AT}) where AT
         if Molly.uses_gpu_neighbor_finder(AT)
             neighbor_finder = GPUNeighborFinder(
                 eligible=AT(trues(n_atoms, n_atoms)),
-                n_steps_reorder=10,
                 dist_cutoff=cutoff.dist_cutoff,
             )
         else
@@ -113,7 +112,7 @@ function test_sim(nl::Bool, parallel::Bool, f32::Bool, ::Type{AT}) where AT
         neighbor_finder=neighbor_finder,
     )
 
-    n_threads = parallel ? Threads.nthreads() : 1
+    n_threads = (parallel ? Threads.nthreads() : 1)
     simulate!(sys, simulator, n_steps; n_threads=n_threads)
     return sys.coords
 end

benchmark/protein.jl

@@ -32,6 +32,7 @@ function setup_system(::Type{AT}, f32::Bool, units::Bool) where AT
         array_type=AT,
         dist_cutoff=(units ? dist_cutoff * u"nm" : dist_cutoff),
         dist_neighbors=(units ? dist_neighbors * u"nm" : dist_neighbors),
+        nonbonded_method="cutoff",
     )
 
     dt = T(0.0005)

data/openmm_6mrr/coordinates_100steps.txt

@@ -0,0 +1 @@
+42575.40185442937

data/openmm_6mrr/energy_all_cut.txt

@@ -0,0 +1 @@
+31811.9317595554

data/openmm_6mrr/energy_all_only.txt

@@ -0,0 +1 @@
+31811.9317595554