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Commit c1ea8c32 authored by Lars Hubatsch's avatar Lars Hubatsch
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Unifying sweep for distance from coverslip. New default for phi_tot_out.

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@Ternary_model/plot_sim.m
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View file @ c1ea8c32
......@@ -30,7 +30,7 @@ elseif strcmp(mode, 'plot')
ax = gca;
ax.FontSize = 26;
xlabel('x [\mum]'); ylabel('volume fraction');
plot(T.x, T.sol(1:nth:si(1), :), 'LineWidth', 1, 'Color', color);
plot(T.x, T.sol([1, 2:nth:si(1)], :), 'LineWidth', 1, 'Color', color);
% plot(T.x, T.sol(nth, :), 'LineWidth', 1, 'Color', color);
plot(T.x, Ternary_model.phi_tot(T.x, T.a, T.b, T.e, T.u0),...
'LineWidth', 1, 'LineStyle', '--', 'Color', [0.97, 0.55, 0.03]);
......
Half_Frap_Phi_u.ipynb
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View file @ c1ea8c32
%% Cell type:markdown id: tags:
### FRAP geometries
%% Cell type:code id: tags:
``` python
from fem_sol import frap_solver
import matplotlib.pyplot as plt
import numpy as np
```
%% Cell type:code id: tags:
``` python
font = {'family' : 'normal',
'weight' : 'normal',
'size' : 12}
import matplotlib
matplotlib.rc('font', **font)
def make_graph_pretty(xlab, ylab, loc=0, markerfirst=True, handlelength=None):
color1 = 'black'#'darkorange'
color2 = (0, 0, 0)
color2 = (1, 1, 1)
ax = plt.gca()
ax.tick_params(axis='x', colors=color1, which='both')
ax.tick_params(axis='y', colors=color1, which='both')
plt.xlabel(xlab, color=color1)
plt.ylabel(ylab, color=color1)
ax.spines['left'].set_color(color1)
ax.spines['bottom'].set_color(color1)
# Hide the right and top spines
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.set_facecolor(color2)
plt.gcf().subplots_adjust(bottom=0.17, left=0.15)
plt.legend(frameon=False, loc=loc, labelspacing=0.1,
markerfirst=markerfirst, handlelength=handlelength)
```
%% Cell type:code id: tags:
``` python
m = ['Meshes/multi_drop_gauss.xml', 'Meshes/multi_drop_gauss_med.xml',
'Meshes/multi_drop_gauss_far.xml']
point_lists = [[[4, 4.5, 0.5], [4, 3.5, 0.5], [3.5, 4, 0.5], [4.5, 4, 0.5]],
[[4, 5, 0.5], [4, 3, 0.5], [3, 4, 0.5], [5, 4, 0.5]],
[[4, 5.5, 0.5], [4, 2.5, 0.5], [2.5, 4, 0.5], [5.5, 4, 0.5]]]
f_i = []
for j in range(len(m)):
f = frap_solver([4, 4, 0.5], m[j], name=str(j), point_list=point_lists[j],
T=3)
T=50, phi_tot_int=0.99, phi_tot_ext=0.01)
f.solve_frap()
f_i.append(f)
```
%% Cell type:code id: tags:
``` python
for i in range(len(cs[0])):
plt.plot([np.mean(x[1:49])/0.8 for x in cs[0][0:i]], label='dist=0.5')
plt.plot([np.mean(x[1:49])/0.8 for x in cs[1][0:i]], label='dist=1')
plt.plot([np.mean(x[1:49])/0.8 for x in cs[2][0:i]], label='dist=1.5')
plt.plot(range(0, 100), np.ones(100), linestyle='--', color='k')
plt.ylim((0, 1.1))
plt.xlim((0, 100))
make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)
# plt.savefig('img_'+str(i)+'.png', dpi=300)
plt.show()
```
%% Cell type:code id: tags:
``` python
f_0 = frap_solver([4, 4, 0.5], 'Meshes/single_drop_coverslip.xml',
name='FRAP_coverslip', T=300, phi_tot_ext=0.001)
name='FRAP_coverslip', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_0.solve_frap()
f_1 = frap_solver([4, 4, 1.5], 'Meshes/single_drop_1_5.xml',
name='FRAP_symmetric', T=300, phi_tot_ext=0.001)
name='FRAP_symmetric', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_1.solve_frap()
f_2 = frap_solver([4, 4, 4], 'Meshes/single_drop_symmetric.xml',
name='FRAP_symmetric', T=300, phi_tot_ext=0.001)
name='FRAP_symmetric', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_2.solve_frap()
```
%% Cell type:code id: tags:
``` python
f_3 = frap_solver([4, 4, 0.5], 'Meshes/single_drop_coverslip.xml',
name='FRAP_symmetric', T=100, phi_tot_ext=0.01)
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_3.solve_frap()
f_4 = frap_solver([4, 4, 1.5], 'Meshes/single_drop_1_5.xml',
name='FRAP_symmetric', T=100, phi_tot_ext=0.01)
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_4.solve_frap()
f_5 = frap_solver([4, 4, 4], 'Meshes/single_drop_symmetric.xml',
name='FRAP_symmetric', T=100, phi_tot_ext=0.01)
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_5.solve_frap()
```
%% Cell type:code id: tags:
``` python
plt.plot([np.mean(x[1:49])/0.99 for x in f_0.cs], label='dist=0.5')
plt.plot([np.mean(x[1:49])/0.99 for x in f_1.cs], label='dist=1.5')
plt.plot([np.mean(x[1:49])/0.99 for x in f_2.cs], label='dist=4')
plt.plot([np.mean(x[1:49])/0.99 for x in f_3.cs], label='dist=0.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.99 for x in f_4.cs], label='dist=1.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.99 for x in f_5.cs], label='dist=4, G_out=10')
plt.plot(range(0, 300), np.ones(300), linestyle='--', color='k')
plt.plot([np.mean(x[1:49])/0.9 for x in f_3.cs], label='dist=0.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.9 for x in f_4.cs], label='dist=1.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.9 for x in f_5.cs], label='dist=4, G_out=10')
plt.plot(range(0, 50), np.ones(50), linestyle='--', color='k')
plt.ylim((0, 1.1))
plt.xlim((0, 300))
plt.xlim((0, 50))
make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)
```
%% Cell type:code id: tags:
``` python
plt.plot(np.transpose(f_3.cs))
```
%% Cell type:code id: tags:
``` python
```
......
fem_sol.py
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View file @ c1ea8c32
......@@ -28,7 +28,7 @@ def point_expr(p_c, p_list, phi_tot_int, phi_tot_ext, phi_init,
class frap_solver:
def __init__(self, cent_poin, mesh, tol=1E-14, dt=0.1, G_in=1,
G_out=1, name='FRAP', phi_tot_int=0.99, phi_tot_ext=0.001,
G_out=1, name='FRAP', phi_tot_int=0.99, phi_tot_ext=0.01,
phi_tot_initial=0, point_list=[], rad_drop=0.25, T=100):
'''
Initialise solver
......
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