improved speed

src/Models/Material/Material_Models/Ordinary/PD_Solid_Elastic.jl

@@ -142,7 +142,7 @@ function compute_model(
 
     # optimizing, because if no damage it has not to be updated
     # TBD update_list should be used here as in shape_tensor.jl
-    @timeit to "Weighted Volume" weighted_volume = compute_weighted_volume(
+    @timeit to "Weighted Volume" compute_weighted_volume(
         weighted_volume,
         nodes,
         nlist,
@@ -151,7 +151,7 @@ function compute_model(
         omega,
         volume,
     )
-    @timeit to "Dilatation" theta = compute_dilatation(
+    @timeit to "Dilatation" compute_dilatation(
         nodes,
         nneighbors,
         nlist,
@@ -161,6 +161,7 @@ function compute_model(
         volume,
         weighted_volume,
         omega,
+        theta,
     )
     @timeit to "elastic" bond_force_deviatoric_part, bond_force_isotropic_part = elastic(
         nodes,

src/Support/geometry.jl

@@ -16,16 +16,21 @@ export compute_deformation_gradients!
 
 
 """
-     bond_geometry!(nodes::Union{SubArray,Vector{Int64}}, nlist, coor, undeformed_bond, undeformed_bond_length)
+     bond_geometry(undeformed_bond::Vector{Vector{Vector{Float64}}},
+    undeformed_bond_length::Vector{Vector{Float64}},
+    nodes::Union{SubArray,Vector{Int64}},
+    nlist::Vector{Vector{Int64}},
+    coor::Union{SubArray,Matrix{Float64},Matrix{Int64}},
 
 Calculate bond geometries between nodes based on their coordinates.
 
 # Arguments
+ - `undeformed_bond`: A preallocated array or data structure to store bond geometries.
+ - `undeformed_bond_length`: A preallocated array or data structure to store bond distances.
  - `nodes::Union{SubArray,Vector{Int64}}`: A vector of integers representing node IDs.
  - `nlist`: A data structure (e.g., a list or array) representing neighboring node IDs for each node.
  - `coor`: A matrix representing the coordinates of each node.
- - `undeformed_bond`: A preallocated array or data structure to store bond geometries.
- - `undeformed_bond_length`: A preallocated array or data structure to store bond distances.
+
 
 # Output
  - `undeformed_bond`: An updated `undeformed_bond` array with calculated bond geometries.
@@ -141,7 +146,7 @@ function compute_shape_tensors!(
             volume,
             omega[iID],
             bond_damage[iID],
-            undeformed_bond[iID],
+            mapreduce(permutedims, vcat, undeformed_bond[iID]),
             nlist,
             iID,
         )
@@ -180,8 +185,8 @@ function compute_shape_tensor!(
         Cmn = zero(eltype(shape_tensor))
         @inbounds @fastmath for k ∈ axes(undeformed_bond, 1)
             Cmn +=
-                undeformed_bond[k][m] *
-                undeformed_bond[k][n] *
+                undeformed_bond[k, m] *
+                undeformed_bond[k, n] *
                 volume[nlist[iID][k]] *
                 omega[k] *
                 bond_damage[k]
@@ -271,8 +276,8 @@ function compute_deformation_gradients!(
         compute_deformation_gradient!(
             temp,
             bond_damage[iID],
-            deformed_bond[iID],
-            undeformed_bond[iID],
+            mapreduce(permutedims, vcat, deformed_bond[iID]),
+            mapreduce(permutedims, vcat, undeformed_bond[iID]),
             volume,
             omega[iID],
             nlist,
@@ -300,8 +305,8 @@ function compute_deformation_gradient!(
         Cmn = zero(eltype(deformation_gradient))
         @inbounds @fastmath for k ∈ axes(undeformed_bond, 1)
             Cmn +=
-                deformed_bond[k][m] *
-                undeformed_bond[k][n] *
+                deformed_bond[k, m] *
+                undeformed_bond[k, n] *
                 volume[nlist[iID][k]] *
                 omega[k] *
                 bond_damage[k]

test/unit_tests/Models/Material/Material_Models/Ordinary/ut_ordinary.jl

@@ -84,7 +84,7 @@ using .Ordinary
         0.8615883,
     ]
     vec = Vector{Int64}(1:nnodes)
-    weighted_volume = Ordinary.compute_weighted_volume(
+    Ordinary.compute_weighted_volume(
         weighted_volume,
         vec,
         nlist,
@@ -97,16 +97,7 @@ using .Ordinary
     for iID = 1:nnodes
         @test weighted_volume[iID] / weightedTest[iID] - 1 < 1e-6
     end
-    weighted_volume = Ordinary.compute_weighted_volume(
-        weighted_volume,
-        Int64[],
-        nlist,
-        undeformed_bond_length,
-        bond_damage,
-        omega,
-        volume,
-    )
-    @test weighted_volume == []
+
 end
 
 nnodes = 2
@@ -125,6 +116,7 @@ bond_damage[2][1] = 1
 
 volume = ones(Float64, 2)
 weighted_volume = ones(Float64, 2)
+theta = zeros(Float64, 2)
 omega = [ones(Float64, 2), ones(Float64, 2)]
 
 nlist = [Vector{Int64}(undef, 1), Vector{Int64}(undef, 1)]
@@ -133,7 +125,7 @@ nlist[2][1] = 2
 @testset "compute_dilatation" begin
     vec = Vector{Int64}(1:nnodes)
     theta = zeros(Float64, 2)
-    theta = Ordinary.compute_dilatation(
+    Ordinary.compute_dilatation(
         vec,
         nneighbors,
         nlist,
@@ -143,11 +135,12 @@ nlist[2][1] = 2
         volume,
         weighted_volume,
         omega,
+        theta,
     )
     @test theta[1] == 3.0
     @test theta[2] == 3.0
     weighted_volume[1] = 0
-    theta = Ordinary.compute_dilatation(
+    Ordinary.compute_dilatation(
         vec,
         nneighbors,
         nlist,
@@ -157,21 +150,11 @@ nlist[2][1] = 2
         volume,
         weighted_volume,
         omega,
+        theta,
     )
     @test theta[1] == 0.0
     @test theta[2] == 3.0
-    theta = Ordinary.compute_dilatation(
-        Int64[],
-        nneighbors,
-        nlist,
-        undeformed_bond_length,
-        deformed_bond_length,
-        bond_damage,
-        volume,
-        weighted_volume,
-        omega,
-    )
-    @test theta == []
+
 end
 
 @testset "calculate_symmetry_params" begin