Merge pull request #33 from prashjha/main

Update joss branch

README.md

@@ -19,6 +19,8 @@
   - [Running simulations](#Running-simulations)
     * [Two-particle with wall](#Two-particle-with-wall)
     * [Compressive test](#Compressive-test)
+    * [Attrition tests](#Attrition-tests)
+    * [Single particle deformation](#Single-particle-deformation)
   - [Visualizing results](#Visualizing-results)
   - [Developers](#Developers)
 
@@ -88,7 +90,7 @@ yielding of the system. For more details, we refer to
 |              Compressive test simulation              | 
 
 
-### Attrition tests - Particles in a rotating container
+### Attrition tests
 We consider mix of different particles in a rotating container. Particles considered include circular, triangular, hexagonal, and drum shaped. Particles come in large and small shapes (their sizes are purturbed randomly). In order to to introduce diversity of material properties, we considered large particles to be tougher compared to the smaller ones. Setup files are in [examples/PeriDEM/attrition_tests](./examples/PeriDEM/attrition_tests)
 
 |                                         <img src="./assets/attrition_test_sim1.gif" width="250">                                         |                                                                              <img src="./assets/attrition_test_sim2.gif" width="250">                                                                               | 
@@ -99,6 +101,9 @@ Complex container geometries can be considered as well. For example, the image b
 
 <img src="./examples/PeriDEM/attrition_tests/sim4_multi_particle_circ_tri_drum_hex_with_rotating_rectangle_container_with_protrusion_and_opening_within_bigger_rectangle_container/init_view.png" width="600">
 
+### Single particle deformation
+We can use `PeriDEM` executable or `Peridynamics` executable in `apps` directory to simulate the deformation of single particle/structure using peridynamics. See [examples/README.md](./examples/README.md) and [examples/Peridynamics](./examples/Peridynamics) folder. 
+
 ## Brief implementation details
 The main implementation of the model is carried out in the model directory [dem](./src/model/dem). 
 The model is implemented in class [DEMModel](./src/model/dem/demModel.cpp). 
@@ -362,4 +367,4 @@ You can also cite the PeriDEM using zenodo doi:
 
 ## Developers
   - [Prashant K. Jha](https://prashjha.github.io/) 
-    (pjha.sci@gmail.com, prashant.jha@austin.utexas.edu, prashant.jha@port.ac.uk)
+    (pjha.sci@gmail.com, prashant.jha@sdsmt.edu)

apps/peridynamics/main.cpp

@@ -43,7 +43,7 @@
 #include <taskflow/taskflow/algorithm/for_each.hpp>
 
 /*!
- * @brief Namespace to define peridynamics apps that is meant to simulate single particle deformation.
+ * @brief Namespace to define peridynamics app for single particle deformation.
  */
 namespace peridynamics {
 

examples/Peridynamics/circle/input_0.yaml

@@ -0,0 +1,82 @@
+Model:
+  Dimension: 2
+  Discretization_Type:
+    Spatial: finite_difference
+    Time: central_difference
+  Final_Time: 1.000000e-02
+  Time_Steps: 20000
+  Particle_Sim_Type: Single_Particle
+# Zone block is optional
+# For Single_Particle simulation, zone = 1 is fixed
+Zone:
+  Zones: 1
+# Particle block is not needed if mesh file is provided but if we are creating mesh
+# using in-built function, we need geometry information within this block
+Particle:
+  # optional
+  Test_Name: test_peridynamics
+  Zone_1:
+    Type: circle
+    Parameters: [3.000000e-03, 0.000000e+00, 0.000000e+00, 0.000000e+00]
+Mesh:
+  Zone_1:
+    File: mesh_cir_1_0.msh
+Material:
+  Zone_1:
+    Type: PDState
+    Horizon: 6.000000e-04
+    Density: 1.200000e+03
+    Compute_From_Classical: true
+    K: 2.160000e+05
+    G: 1.296000e+05
+    Gc: 5.000000e+02
+    Influence_Function:
+      Type: 1
+Displacement_BC:
+  Sets: 2
+  Set_1:
+    Region:
+      Geometry:
+        Type: rectangle
+        Parameters: [-0.001, -0.001, 0, -0.0005, -0.0005, 0]
+    Direction: [1,2]
+    Time_Function:
+      Type: constant
+      Parameters:
+        - 0.0
+    Spatial_Function:
+      Type: constant
+    Zero_Displacement: true
+  Set_2:
+    Region:
+      Geometry:
+        Type: rectangle
+        Parameters: [0.0005, 0.0005, 0, 0.001, 0.001, 0]
+    Direction: [1,2]
+    Time_Function:
+      Type: linear
+      Parameters:
+        - 0.005
+    Spatial_Function:
+      Type: constant
+Output:
+  Path: ./out/
+  Tags:
+    - Displacement
+    - Velocity
+    - Force
+    - Force_Density
+    - Damage_Z
+    - Damage
+    - Nodal_Volume
+    - Zone_ID
+    - Particle_ID
+    - Fixity
+    - Force_Fixity
+    - Theta
+  Output_Interval: 1000
+  Compress_Type: zlib
+  Perform_FE_Out: true
+  Perform_Out: true
+  Debug: 3
+  Tag_PP: 0