fix dir error

yjchoi1 · Oct 20, 2023 · 5adca9e · 5adca9e
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diff --git a/docs/LICENSE b/docs/LICENSE
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+MIT License
+
+Copyright (c) 2021 docsifyjs
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,289 @@
+# CB-geo MPM Input File Generator for Granular Flow Simulation  
+Generate mpm inputs for random colliding cubes in 2d or 3d box domain for [CB-geo MPM solver](https://www.cb-geo.com/research/mpm/).
+
+# Input
+Input files can be randomly generated. Random genernation parameters is included in the `examples/inputs.json`.
+
+```json
+{
+  "ndims": 3,  
+  "save_path": "examples/sand3d/", 
+  "simulation_case": "sand3d",
+  "data_id_range": [
+    0,
+    3
+  ],
+  "k0": null,
+  "wall_friction": 0.385,
+  "gen_cube_randomly": {
+    "generate": false,
+    "sim_inputs": {
+      "mesh": {
+        "simulation_domain": [
+          [
+            0.0,
+            1.0
+          ],
+          [
+            0.0,
+            1.0
+          ],
+          [
+            0.0,
+            1.0
+          ]
+        ],
+        "ncells_per_dim": [
+          20,
+          20,
+          20
+        ],
+        "outer_cell_thickness": 0.0125
+      },
+      "particle": {
+        "nparticle_perdim_percell": 2,
+        "particle_randomness": 0.8,
+        "num_particle_groups": 2,
+        "material_id": [
+          0,
+          0
+        ],
+        "particle_gen_candidate_area": [
+          [
+            0.0,
+            1.0
+          ],
+          [
+            0.0,
+            1.0
+          ],
+          [
+            0.0,
+            1.0
+          ]
+        ],
+        "particle_length": [
+          0.30,
+          0.30,
+          0.30
+        ],
+        "range_randomness": 0.1,
+        "vel_bound": [
+          [
+            -1.5,
+            1.5
+          ],
+          [
+            -1.5,
+            1.5
+          ],
+          [
+            -1.5,
+            1.5
+          ]
+        ]
+      }
+    }
+  },
+  "gen_cube_from_data": {
+    "generate": true,
+    "metadata_path": "examples/sand3d/metadata-sand3d.json"
+  },
+  "mpm_inputs": {
+    "materials": [
+      {
+        "id": 0,
+        "density": 1800,
+        "youngs_modulus": 2000000.0,
+        "poisson_ratio": 0.3,
+        "friction": 42.0,
+        "dilation": 0.0,
+        "cohesion": 100,
+        "tension_cutoff": 50,
+        "softening": false,
+        "peak_pdstrain": 0.0,
+        "residual_friction": 42.0,
+        "residual_dilation": 0.0,
+        "residual_cohesion": 0.0,
+        "residual_pdstrain": 0.0
+      }
+    ],
+    "analysis": {
+      "mpm_scheme": "usf",
+      "locate_particles": false,
+      "dt": 1e-06,
+      "damping": {
+        "type": "Cundall",
+        "damping_factor": 0.05
+      },
+      "resume": {
+        "resume": false,
+        "step": 0
+      },
+      "velocity_update": false,
+      "nsteps": 100000
+    },
+    "analysis_resume": {
+      "mpm_scheme": "usf",
+      "locate_particles": false,
+      "dt": 1e-06,
+      "damping": {
+        "type": "Cundall",
+        "damping_factor": 0.05
+      },
+      "resume": {
+        "resume": true,
+        "step": 0
+      },
+      "velocity_update": false,
+      "nsteps": 100000
+    },
+    "post_processing": {
+      "path": "results/",
+      "output_steps": 2500,
+      "vtk": ["displacements"]
+    }
+  }
+}
+```
+### General inputs
+* `ndims`: # dimensionality of the simulation.
+* `save_path`: path to save outputs of the code.
+* `simulation_case`: user defined name of simulation case. This is used for 
+identifying the higher level output cases. 
+* `data_id_range`: id range of the outputs that will be saved under. 
+the name `{simulation_case}-{id}`. It follows Python range convention.
+* `k0`: used for generating k0 stress.
+* `wall_friction`: friction of the simulation boundaries.
+
+### Inputs for randomly generating the mass cubes
+* `generate`: options whether you do random gen or not
+Mesh-related inputs
+* `simulation_domain`: simulation domain, 
+e.g., [[x_min, x_max], [y_min, y_max], [z_min, z_max]]
+* `ncells_per_dim`: number of cells to generate per each dimension
+* `outer_cell_thickness`: thickness of the outermost cells added on the perimeter of simulation domain
+Material point-related inputs
+* `nparticle_perdim_percell`: number of particles per dimension in a cell. For example,
+if it is 2 in three-dimensional space, $2^3=8$ material points is generated in a cell.
+* `num_particle_groups`: the number of particles groups (mass cubes) to randomly generate
+* `material_id`: material id associated with each particle group.
+* `particle_gen_candidate_area`: particle gen candidate area, 
+e.g., [[x_min, x_max], [y_min, y_max], [z_min, z_max]]
+* `particle_length`: length of cube for each dim.
+* `range_randomness`: magnitude of randomness for varying particle length
+* `vel_bound`:  random initial velocity range [lower_bound, upper_bound] for each dim.
+
+### Inputs for manually generating the random mass cubes from user-defined input file
+If you want to generate the mass cubes from user defined data, `gen_cube_from_data` in
+the input json file can be used. Set `generate` option `true` and specify your input
+file (metadata) path to `metadata_path`.
+
+This input can be passed with `.json` file. An example is shown below.
+Need to remove the comments for actual input.
+
+```json
+{
+  "simulation0": {
+    "name": "sand3d0",
+    "ncells_per_dim": [
+      20,
+      20,
+      20
+    ],
+    "outer_cell_thickness": 0.0125,
+    "simulation_domain": [
+      [
+        0.0,
+        1.0
+      ],
+      [
+        0.0,
+        1.0
+      ],
+      [
+        0.0,
+        1.0
+      ]
+    ],
+    "nparticle_perdim_percell": 2,
+    "particle_randomness": 0.8,
+    "k0": null,
+    "wall_friction": 0.385,
+    "particle": {
+      "group0": {
+        "particle_geometry": [
+          [
+            0.02376750633275534,
+            0.3139062907954934
+          ],
+          [
+            0.24805536783250387,
+            0.538194152295242
+          ],
+          [
+            0.05619339296677366,
+            0.3463321774295118
+          ]
+        ],
+        "particle_vel": [
+          0.6298567178815921,
+          0.4818766015726872,
+          -0.23723459156915316
+        ],
+        "material_id": 0
+      },
+      "group1": {
+        "particle_geometry": [
+          [
+            0.5944128202556003,
+            0.8760021779497826
+          ],
+          [
+            0.49658469579313413,
+            0.7781740534873165
+          ],
+          [
+            0.40501560151497407,
+            0.6866049592091565
+          ]
+        ],
+        "particle_vel": [
+          -1.3890943817767503,
+          -0.8816225625110533,
+          1.2106387664782687
+        ],
+        "material_id": 0
+      }
+    }
+  },
+  "simulation1": {
+    ...
+  },
+  "simulation2": {
+    ...
+  },
+  ...
+}
+
+```
+
+### Inputs for [CB-geo MPM solver](https://www.cb-geo.com/research/mpm/).
+Inputs for CB-geo MPM solver is required. This follows the same input format 
+described in [CB-geo MPM docs](https://mpm.cb-geo.com/#/user/preprocess/input), so 
+refer to their docs for more information. 
+
+
+# Generate input
+```shell
+python3 gen.py --input_path="examples/sand3d/inputs.json"
+```
+
+# Run MPM
+* Install MPM solver based on [CB-geo MPM docs](https://mpm.cb-geo.com/#/user/compile/compile).
+* Following script can be used to impose initial velocity and resume from this state
+automatically. 
+```shell
+timeout 30s mpm -i mpm_input.json -f "${MPM_DIR}"
+mpm -i mpm_input_resume.json -f "${MPM_DIR}"
+```
diff --git a/docs/_sidebar.md b/docs/_sidebar.md
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+- [Read Me](README)
+- [Inputs](inputs.md)
diff --git a/docs/index.html b/docs/index.html
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diff --git a/docs/inputs.md b/docs/inputs.md
@@ -0,0 +1,3 @@
+# Inputs
+
+Inputs