Merge branch 'main' of https://github.com/PeriHub/PeriLab.jl

src/IO/mesh_data.jl

@@ -365,12 +365,12 @@ function get_bond_geometry(datamanager::Module)
     undeformed_bond = datamanager.create_constant_bond_field("Bond Geometry", Float64, dof)
     undeformed_bond_length =
         datamanager.create_constant_bond_field("Bond Length", Float64, 1)
-    Geometry.bond_geometry(
+    Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector{Int64}(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
     return datamanager
 end

src/Models/Pre_calculation/bond_deformation.jl

@@ -80,7 +80,13 @@ function compute(
     deformed_coor = datamanager.get_field("Deformed Coordinates", "NP1")
     deformed_bond = datamanager.get_field("Deformed Bond Geometry", "NP1")
     deformed_bond_length = datamanager.get_field("Deformed Bond Length", "NP1")
-    Geometry.bond_geometry(nodes, nlist, deformed_coor, deformed_bond, deformed_bond_length)
+    Geometry.bond_geometry!(
+        deformed_bond,
+        deformed_bond_length,
+        nodes,
+        nlist,
+        deformed_coor,
+    )
     return datamanager
 end
 

src/Support/geometry.jl

@@ -10,13 +10,13 @@ using StaticArrays
 using Rotations
 include("helpers.jl")
 using .Helpers: invert, smat, mat_mul_transpose_mat!
-export bond_geometry
+export bond_geometry!
 export compute_shape_tensors!
 export compute_deformation_gradients!
 
 
 """
-     bond_geometry(nodes::Union{SubArray,Vector{Int64}}, nlist, coor, undeformed_bond, undeformed_bond_length)
+     bond_geometry!(nodes::Union{SubArray,Vector{Int64}}, nlist, coor, undeformed_bond, undeformed_bond_length)
 
 Calculate bond geometries between nodes based on their coordinates.
 
@@ -46,12 +46,12 @@ Calculate bond geometries between nodes based on their coordinates.
  undeformed_bond(nodes, dof, nlist, coor, undeformed_bond)
 """
 
-function bond_geometry(
+function 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}},
-    undeformed_bond::Vector{Vector{Vector{Float64}}},
-    undeformed_bond_length::Vector{Vector{Float64}},
 )
 
     for iID in nodes
@@ -141,7 +141,7 @@ function compute_shape_tensors!(
             volume,
             omega[iID],
             bond_damage[iID],
-            mapreduce(permutedims, vcat, undeformed_bond[iID]),
+            undeformed_bond[iID],
             nlist,
             iID,
         )
@@ -180,8 +180,8 @@ 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 +271,8 @@ function compute_deformation_gradients!(
         compute_deformation_gradient!(
             temp,
             bond_damage[iID],
-            mapreduce(permutedims, vcat, deformed_bond[iID]),
-            mapreduce(permutedims, vcat, undeformed_bond[iID]),
+            deformed_bond[iID],
+            undeformed_bond[iID],
             volume,
             omega[iID],
             nlist,
@@ -300,8 +300,8 @@ 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/Core/Solver/ut_Verlet.jl

@@ -76,12 +76,12 @@ volume = [0.5, 0.5, 0.5, 0.5, 0.5]
 density = [1e-6, 1e-6, 3e-6, 3e-6, 1e-6]
 horizon = [3.1, 3.1, 3.1, 3.1, 3.1]
 
-PeriLab.IO.Geometry.bond_geometry(
+PeriLab.IO.Geometry.bond_geometry!(
+    undeformed_bond,
+    undeformed_bond_length,
     Vector(1:nnodes),
     nlist,
     coor,
-    undeformed_bond,
-    undeformed_bond_length,
 )
 
 blocks = [1, 1, 2, 2, 1]

test/unit_tests/IO/ut_mesh_data.jl

@@ -529,12 +529,12 @@ end
         test_data_manager.create_constant_bond_field("Bond Geometry", Float64, dof)
     undeformed_bond_length =
         test_data_manager.create_constant_bond_field("Bond Length", Float64, 1)
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
 
     @test undeformed_bond[1][1][1] == 1

test/unit_tests/Support/ut_geometry.jl

@@ -142,12 +142,12 @@ end
     @test undeformed_bond[1][2][2] == 0
     @test undeformed_bond_length[1][2] == 1
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
 
     @test undeformed_bond[1][1][1] == 0.5
@@ -174,12 +174,12 @@ end
     @test undeformed_bond[4][1][1] == 0.5
     @test undeformed_bond[4][1][2] == -0.5
     @test undeformed_bond_length[4][1] / sqrt(1.25) - 1 < 1e-8
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
     # test if a sum exists or not
     @test undeformed_bond[1][1][1] == 0.5
@@ -216,12 +216,12 @@ end
         end
     end
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
 end
 
@@ -305,12 +305,12 @@ end
     coor[4, 1] = 1
     coor[4, 2] = 0.5
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        undeformed_bond,
+        undeformed_bond_length,
         Vector(1:nnodes),
         nlist,
         coor,
-        undeformed_bond,
-        undeformed_bond_length,
     )
     PeriLab.IO.Geometry.compute_shape_tensors!(
         shape_tensor,
@@ -348,12 +348,12 @@ end
     deformed_coor[2, 1] = 0.25
     deformed_coor[4, 1] = 0.25
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        deformed_bond,
+        deformed_bond_length,
         Vector(1:nnodes),
         nlist,
         deformed_coor,
-        deformed_bond,
-        deformed_bond_length,
     )
     PeriLab.IO.Geometry.compute_deformation_gradients!(
         deformation_gradient,
@@ -382,12 +382,12 @@ end
     deformed_coor[3, 2] = 1.5
     deformed_coor[4, 2] = 1.5
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        deformed_bond,
+        deformed_bond_length,
         Vector(1:nnodes),
         nlist,
         deformed_coor,
-        deformed_bond,
-        deformed_bond_length,
     )
     PeriLab.IO.Geometry.compute_deformation_gradients!(
         deformation_gradient,
@@ -420,12 +420,12 @@ end
     deformed_coor[4, 1] = 1.5
     deformed_coor[4, 2] = 0.5
 
-    PeriLab.IO.Geometry.bond_geometry(
+    PeriLab.IO.Geometry.bond_geometry!(
+        deformed_bond,
+        deformed_bond_length,
         Vector(1:nnodes),
         nlist,
         deformed_coor,
-        deformed_bond,
-        deformed_bond_length,
     )
     PeriLab.IO.Geometry.compute_deformation_gradients!(
         deformation_gradient,