add doc

models/README.md

@@ -2,7 +2,7 @@
 
 The model requires several mesh files (the file format can be [.ply](https://en.wikipedia.org/wiki/PLY_(file_format)) or [.off](https://en.wikipedia.org/wiki/OFF_(file_format))):
 * **mandible**:   
-    * Thi is the closed surface mesh of the mandible. 
+    * This is the closed surface mesh of the mandible. 
     * the boundary conditions will be applied in the global cartesian reference frame. Thus, this mesh should be aligned with its principal axes (see [MeshLab](https://www.meshlab.net/): Filters / Normals, Curvatures and Orientation / Transform: Align To Principal Axis)
     * A gmsh file (.msh) of the volume mesh can also be given
     * If this mesh is given as a surface mesh file, it will be meshed with gmsh. Try to mesh it manually in gmsh first because it sometimes fail.
@@ -54,3 +54,33 @@ For each muscle, the "method" can be 'U', 'T' or 'T+N' referring to (see [Grosse
 * **T**: Tangential-Traction Model: Same as 'U' but the traction on the faces which do not have a direct line of sight to the focal point are projected onto the face and become tangential.
 * **T+N**: Tangential-Plus-Normal-Traction Model: Same as 'T' but a normal pressure component is added to the faces which do not have a direct line of sight to the focal point. This normal component depends on the local curvature and the distance to the muscle fiber origin.
 
+# List of folders
+
+* CLIpro: (V.Gaudichon) Clidastes propython FHSM17576
+* contact: files used to create a meshed cylindrical surface so that we could model a bite onto a meshed surface (UNFINISHED). T
+* cylinder: files used as a demontrator of boneload (see also view_cylinder_T.py and also view_cylinder_TN.py)
+* Dolico_bon: (V.Gaudichon) Dolicorhyncops_bonneri_KUVP40001
+* Dolico_osb: (V.Gaudichon)
+* dolicorhynchops: first meshes sent by V.Gaudichon at the beginning of his master thesis
+* PLTtymFrankencarpus: first meshes sent by V.Gaudichon at the beginning of his master thesis
+* TYLber: (V.Gaudichon) Tylosaurus bernardi
+* TYLnep: (V.Gaudichon) TYLnep_FHSM2209
+
+# run simulations on warson
+
+List the files you want to run in a file named `simus.txt`. For example:
+```
+ls *750k* > simus.txt
+```
+Edit `run_sim.py` and check Metafor executable path. Then, run the `run_sim.py` script through `at` (check `.forward` to get an e-mail notification at the end of the calculations):
+```
+echo ./run_sim.py | at now -m
+```
+Copy `zip_all_folders.sh` and `send_tbz2_to_dox.sh` to `workspace`.
+```
+cp *.sh workspace
+cd workspace
+./zip_all_folders.sh       # <= create a .tbz2 archive for each simulation
+./send_tbz2_to_dox.sh      # <= send the tbz2 files to DoX
+```
+