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Write Square_OneSpecies example; Fix plotter; Update docs
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| The documentation can be found in: docs/_build/html/index.html | ||
| Or can be accessed online at: https://ardis.readthedocs.io/en/latest |
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| Tutorial | ||
| ####################################### | ||
| Examples | ||
| ####################################### | ||
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| One species in a square | ||
| ========================= | ||
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| In this simulation, we use a single species (no reactions) placed in a square-shaped reactor. | ||
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| We place an initial concentration of the species in a corner of the reactor. | ||
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| .. image:: images/square_onespecies_t=0.png | ||
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| Here is what the siulation should output after a few iterations of diffusion. | ||
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| .. image:: images/square_onespecies_t=10.png |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,16 @@ | ||
| Tutorial | ||
| ####################################### | ||
| Examples | ||
| ####################################### | ||
|
|
||
|
|
||
| One species in a square | ||
| ========================= | ||
|
|
||
| In this simulation, we use a single species (no reactions) placed in a square-shaped reactor. | ||
|
|
||
| We place an initial concentration of the species in a corner of the reactor. | ||
|
|
||
| .. image:: images/square_onespecies_t=0.png | ||
|
|
||
| Here is what the siulation should output after a few iterations of diffusion. | ||
|
|
||
| .. image:: images/square_onespecies_t=10.png |
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| from ardis import * | ||
| import ardis.d_geometry as dg | ||
| import ardis.geometry as geo | ||
| import numpy as np | ||
| import os | ||
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| #Set paths and locations | ||
| matrixFolder = "data" | ||
| outputFolder = "output" | ||
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| dataName = "coarse_square" | ||
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| dampingPath = matrixFolder+"/"+dataName+"_damping.mtx" | ||
| stiffnessPath = matrixFolder+"/"+dataName+"_stiffness.mtx" | ||
| meshPath = matrixFolder + "/" + dataName + "_mesh.dat" | ||
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| #Load the mesh | ||
| Mesh = dg.read_mesh(meshPath) | ||
| #Copy the mesh to the GPU | ||
| d_Mesh = dg.d_mesh(Mesh.x, Mesh.y) | ||
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| #Load Damping and stiffness matrices | ||
| S = read_spmatrix(stiffnessPath, read_type.Symetric) | ||
| D = read_spmatrix(dampingPath, read_type.Symetric) | ||
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| #Copy the matrices to the GPU) | ||
| d_S = to_d_spmatrix(S, matrix_type.CSR) | ||
| d_D = to_d_spmatrix(D, matrix_type.CSR) | ||
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| #Create a simulation | ||
| n = len(Mesh.x) #Number of nodes | ||
| simu = simulation(n) | ||
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| #Set parameters | ||
| simu.drain = 0 | ||
| simu.epsilon = 1.e-3 | ||
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| #Load matrices into the simulation | ||
| simu.load_stiffness_matrix(d_S) | ||
| simu.load_dampness_matrix(d_D) | ||
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| #Create a species and set its concentration to zero | ||
| simu.add_species("A") | ||
| simu.set_species("A", np.zeros(n)) | ||
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| #Set the concentration of species A to 10 in the upper-left corner | ||
| upleftcorner = dg.rect_zone(dg.point2d(0, 7), dg.point2d(3, 10)) | ||
| dg.fill_zone(simu.get_species("A"), d_Mesh, upleftcorner, 10) | ||
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| #Plot the initial state of the simulation | ||
| fig = plot_state(simu.state, Mesh, title="square_onespecies", listSpecies=["A"], colors={"background": (0,0,0,0), "A": (0.8, 0.2, 0, 1)}) | ||
| plt.show() | ||
| fig.savefig(outputFolder +"/square_onespecies_t=0.png") | ||
| plt.close(fig) | ||
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| #Iterate diffusion | ||
| dt = 1 | ||
| for i in range(0, 10): | ||
| simu.iterate_diffusion(dt) | ||
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| #Plot the final state of the simulation | ||
| fig = plot_state(simu.state, Mesh, title="square_onespecies", listSpecies=["A"], colors={"background": (0,0,0,0), "A": (0.8, 0.2, 0, 1)}) | ||
| plt.show() | ||
| fig.savefig(outputFolder +"/square_onespecies_t=10.png") | ||
| plt.close(fig) | ||
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| print("Simulation completed!") | ||
| print("Figures saved in '" + outputFolder + "'") |
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