add the description of the parameters to README.md

README.md

@@ -25,14 +25,47 @@ and consists in a phase-field model for tumor angiogenesis. The model is based o
 ### Parameters
 
 We provide typical parameters for simulations in [`input_file`](https://github.com/phydev/angio/blob/master/input_file). 
+See the description of each paramter in the table bellow and the mapping with experimental data in [Supplementary material](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-018-27034-8/MediaObjects/41598_2018_27034_MOESM1_ESM.pdf).
+
+
+| Reference value | Variable               | Description                            |
+|-----------------|-----------------------|----------------------------------------|
+| 4.00 | cell_radius | Radius of individual cells |
+| 100.0 | diffusion_const | Diffusion constant for VEGF |
+| 1.00 | interface_width | Width of the phase-field interface |
+| 0.30 | vegf_p | VEGF concentration for maximum proliferation |
+| 0.09 | vegf_c | VEGF concentration for branching |
+| 20.0 | diff_oxy_length | Diffusion length for oxygen |
+| 6.25 | vegf_rate | Rate of VEGF uptake by cells |
+| 1.00 | vegf_source_conc | Concentration of VEGF at source |
+| 1.00 | prolif_rate | Rate of proliferation of endothelial cells |
+| 5.00 | vessel_radius | Initial radius of blood vessels |
+| 150000 | total_time_step | Total time steps for simulation |
+| 0.0010 | dt | Time step size |
+| 800.00 | chi_chemiotactic_resp | Chemotactic response of endothelial cells |
+| 100, 100, 50,  1, 1, 1 | Lx_Ly_Lz_dx_dy_dz | Simulation domain size and grid spacing |
+| -754333222 | random_seed | Seed for random number generation - must be negative |
+| 20 | number_of_boundary_points | Number of boundary points to keep track |
+| 10000 | source_max | Maximum number of VEGF source points |
+| 0.01 | vegf_grad_min | Threshold for VEGF gradient |
+| 0.03 | vegf_max | Maximum VEGF concentration |
+| 2.00 | depletion_weight | Energy cost to avoid overlap between vessels and hypoxic cells |
+| 2000 | output_period | Time period between outputting results |
+| 40000 | extra_steps | Additional time steps for simulation |
+| 4000 | max_number_of_tip_cells | Maximum number of tip cells allowed |
+| T | thinning_FT | Flag for using thinning algorithm |
+| F | periodic_FT | Flag for using periodic boundary conditions |
+| F | flow_FT | Flag for computing the blood flow |
+
+
 
 Beware that the input file `inp001` is solely used to run the docker image with Github actions. The parameters were changed to produce a short simulation with small grid, few iterations, and no sources of VEGF. Please do __not__ base future studies on this file. 
 
 ### Postprocessing tools
 
 In the folder `tools` we have scripts to postprocess the data generated with the simulations. The documentation for each script is found [here](https://github.com/phydev/angio/blob/master/tools/about.md).
 
-### Publications:
+### Publications
 
 M. Moreira-Soares, R. Coimbra, L. Rebelo, J. Carvalho & R. D. M. Travasso. [Angiogenic Factors produced by Hypoxic Cells are a leading driver of Anastomoses in Sprouting Angiogenesis–a computational study](https://www.nature.com/articles/s41598-018-27034-8). Scientific Reports 8, 8726 (2018)