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Some fixes for comments during JOSS reviews #39

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Feb 7, 2025
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Some fixes for comments during JOSS reviews #39

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630b701
JOSS review: clean-up, remove unused files
prashjha Feb 6, 2025
ad056cf
JOSS review: clean-up, update example files from test/test_data/peridem
prashjha Feb 6, 2025
6d94357
JOSS review: finalize examples
prashjha Feb 7, 2025
182f6e4
update README file
prashjha Feb 7, 2025
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49 changes: 28 additions & 21 deletions README.md
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Expand Up @@ -47,32 +47,32 @@ We have created channels on various platforms:
- [PeriDEM on slack](peridem.slack.com)
* Send us an email if interested in joining the workspace.

## [Documentation](https://prashjha.github.io/PeriDEM/)
## Documentation
[Doxygen generated documentation](https://prashjha.github.io/PeriDEM/) details functions and objects in the library.

## Tutorial
We explain the setting-up of simulations in further details in [tutorial](./tutorial/README.md).
We consider `two-particle` test setup with non-circular particles and `compressive-test` to
discuss the various aspects of simulations.

## [Examples](./examples/README.md)
## Examples
We next highlight some key examples. Further details are available in [examples/README.md](./examples/README.md).

### Two-particle tests

| <img src="./assets/two_particle_circ_no_damp.gif" width="200"> | <img src="./assets/two_particle_circ_damp.gif" width="200"> |
|:--------------------------------------------------------------------------:|:--------------------------------------------------------------------:|
| [Circular without damping](./examples/PeriDEM/two_particles/circ_no_damp/) | [Circular with damping](./examples/PeriDEM/two_particles/circ_damp/) |
| <img src="./assets/two_particle_circ_no_damp.gif" width="200"> | <img src="./assets/two_particle_circ_damp.gif" width="200"> |
|:-------------------------------------------------------------------------:|:--------------------------------------------------------------------:|
| Circular without damping | Circular with damping |

| <img src="./assets/two_particle_circ_diff_material.gif" width="200"> | <img src="./assets/two_particle_circ_damp_diff_radius.gif" width="200"> | <img src="./assets/two_particle_circ_diff_radius_diff_material.gif" width="200"> |
|:---------------------------------------------------------------------------:|:---------------------------------------------------------------------------:|:-------------------------------------------------------------------------------------------------------:|
| [Different materials](./examples/PeriDEM/two_particles/circ_diff_material/) | [Different radius](./examples/PeriDEM/two_particles/circ_damp_diff_radius/) | [Different radius different material](./examples/PeriDEM/two_particles/circ_diff_radius_diff_material/) |
| <img src="./assets/two_particle_circ_diff_material.gif" width="200"> | <img src="./assets/two_particle_circ_damp_diff_radius.gif" width="200"> | <img src="./assets/two_particle_circ_diff_radius_diff_material.gif" width="200"> |
|:--------------------------------------------------------------------------:|:---------------------------------------------------------------------------:|:------------------------------------------------------------------------------------------------------:|
| Different materials | Different radius | Different radius different material |

### Two-particle with wall test

| <img src="./assets/two_particle_wall_concave_diff_material_diff_size.gif" width="400"> |
|:-------------------------------------------------------------------------------------------:|
| [Concave particles](./examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size/) |
| <img src="./assets/two_particle_wall_concave_diff_material_diff_size.gif" width="400"> |
|:------------------------------------------------------------------------------------------:|
| Concave particles |

### Compressive tests
Setup for this test consists of 502 circular and hexagonal-shaped particles of varying
Expand Down Expand Up @@ -224,7 +224,7 @@ Above gives the basic idea of simulation steps. For more thorough understanding
the implementation, interested readers can look at
[demModel.cpp](.n/src/model/dem/demModel.cpp).

## [Installation](./tools/README.md)
## Installation

### Dependencies
Core dependencies are:
Expand Down Expand Up @@ -302,42 +302,49 @@ with paths are correctly provided in `input.yaml`, we will run the problem (usin
Some examples are listed below.

### Two-particle with wall
Navigate to the example directory [examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size/inp](./examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size/inp)
Navigate to the example directory [examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size/inp](.examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size/inp)
and run the example as follows
```sh
# manually
examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size/inp
mkdir ../out # <-- make directory for simulation output. In .yaml, we specify output path as './out'
<peridem build path>bin/PeriDEM -i input_0.yaml -nThreads 2

# or call run.sh script
cd examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size
./run.sh 4 # with 4 threads
```

You may also use the included [problem_setup.py](./examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size/inp/problem_setup.py)
You may also use the included [problem_setup.py](./examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size/inp/problem_setup.py)
to modify simulation parameters and run the simulation using
[run.sh](./examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size/run.sh)
(in directory [examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size](./examples/PeriDEM/two_particles_wall/concave_diff_material_diff_size)).
`run.sh` shows how different input files are created for the simulation.
[run.sh](./examples/PeriDEM/two_particles/twop_wall_concave_diff_material_diff_size/run.sh).

> :exclamation: You may need to modify the path of `PeriDEM` executable in `run.sh` file.

> In all `problem_setup.py` files in the example and test directory, the main function is `create_input_file()`.
> Here we set all model parameters, create `.yaml` input file, and `.geo` files for meshing.

### Compressive test
Navigate to the example directory [examples/PeriDEM/compressive_test/n500_circ_hex/run1/inp](./examples/PeriDEM/compressive_test/n500_circ_hex/run1/inp)
Navigate to the example directory [examples/PeriDEM/compressive_test/compression_large_set/inp](./examples/PeriDEM/compressive_test/compression_large_set/inp)
and run the example as follows (note that this is a computationally expensive example)
```sh
cd examples/PeriDEM/compressive_test/compression_large_set/inp
mkdir ../out
<peridem build path>bin/PeriDEM -i input_0.yaml -nThreads 12

# or you can use the run.sh script in the path examples/PeriDEM/compressive_test/compression_large_set/
```

As before:
- you can modify [problem_setup.py](./examples/PeriDEM/compressive_test/n500_circ_hex/run1/inp/problem_setup.py), see `create_input_file()` method, to change the simulation settings
- run the simulation using [run.sh](./examples/PeriDEM/compressive_test/n500_circ_hex/run1/run.sh).
- you can modify [problem_setup.py](./examples/PeriDEM/compressive_test/compression_large_set/inp/problem_setup.py), see `create_input_file()` method, to change the simulation settings
- run the simulation using [run.sh](./examples/PeriDEM/compressive_test/compression_large_set//run.sh).

## Visualizing results
Simulation files `output_*.vtu` can be loaded in either [ParaView](https://www.paraview.org/)
or [VisIt](https://wci.llnl.gov/simulation/computer-codes/visit).

By default, in all tests and examples, we only output the particle mesh, i.e.,
pair of nodal coordinate and nodal volume, and not the finite element mesh
a pair of nodal coordinate and nodal volume, and not the finite element mesh
(it can be enabled by setting `Perform_FE_Out: true` within `Output` block in the input `yaml` file).
After loading the file in ParaView, the first thing to do is to change the plot
type from **`Surface`** to **`Point Gaussian`**. Next, a couple of things to do are:
Expand Down
47 changes: 47 additions & 0 deletions examples/PeriDEM/README.md
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@@ -0,0 +1,47 @@
# PeriDEM Examples

Many of the test files are copied from `PeriDEM/test/test_data/peridem`.

## single_particle

### single_particle_circle
Shows the capability of PeriDEM to handle single particle deformation

### single_particle_rectangle_inbuilt_mesh
Shows the capability of PeriDEM to handle single particle deformation

## two_particles
### twop_circ
Generic test where top circle either free falls or falls with specified initial velocity

### twop_concave_and_hex
Same as `twop_circ` but with non-standard particles

### twop_wall_concave_diff_material_diff_size
Same as `twop_circ` but now with multiple material properties and wall

## compressive_test

### compression_small_set
Compression of 15 particles in a container.

### compression_large_set
Compression of 352 particles in a container. Particles are assigned positions randomly, and the cohort consists of circle, hexagon, triangle, and drum-shaped particles.

## attrition_tests
### attrition_mix_particles_small_set
Set of 12 particles (circle, hexagon, triangle, and drum shaped) in rotating cylinder with portrusion.

### attrition_mix_particles_large_set
Set of 12 particles (circle, hexagon, triangle, and drum shaped) in rotating cylinder with portrusion.

### sim* tests
There are different versions of `particles in a rotating container` tests. We play with number of particles, geometry of rotating container, and rotation speed, etc.

| <img src="./attrition_tests/sim1_multi_particle_circ_tri_drum_with_rotating_cylinder_with_protrusion/init_view.png" width="400"> |
|:-------------------------------------------------------------------------------------------:|
| [particles in rotating cylinder]](./attrition_tests/sim1_multi_particle_circ_tri_drum_with_rotating_cylinder_with_protrusion/) |

| <img src="./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="400"> |
|:-------------------------------------------------------------------------------------------:|
| [particles in rotating rectangle]](./attrition_tests/sim4_multi_particle_circ_tri_drum_hex_with_rotating_rectangle_container_with_protrusion_and_opening_within_bigger_rectangle_container/) |
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