def btAddMatClick(master=None):
global w, root, material
dial = GenerateMaterialDialog(root)
if dial.result is None:
return
name, conc = dial.result
if name == 'alloyAuAg':
try:
mat = AlloyAuAg(conc)
except Exception as err:
tkMessageBox.showerror('Error', err)
return
else:
try: # try create material
mat = Material(name)
except Exception as err:
tkMessageBox.showerror('Error', err)
return
key = gen_mat_key(True)
add_material(key, mat)
update_materials_tree()
from mstm_studio.nearfield import NearField from mstm_studio.mstm_spectrum import ExplicitSpheres from mstm_studio.alloy_AuAg import AlloyAuAg mat = AlloyAuAg(x_Au=0.0) # silver material nf = NearField(wavelength=385) # near the resonance nf.environment_material = 1.5 # glass matrix nf.set_plane(plane='xz', hmin=-10, hmax=20, vmin=-15, vmax=15, step=0.25) spheres = ExplicitSpheres(2, [0, 0, 0, 5, 0, 0, 11, 3], mat_filename=2 * [mat]) nf.set_spheres(spheres) nf.simulate() nf.plot()
from mstm_studio.alloy_AuAg import AlloyAuAg
au1ag2 = AlloyAuAg(x_Au=1. / 3)
fig, axs = au1ag2.plot()
fig.savefig('mat_au1ag2.png', bbox_inches='tight')
def _eps(self, omega, x_au):
drude, cp1, cp2 = self._drude(omega, x_au)
kk = drude + cp1 + cp2
eps1 = kk.real
eps2 = kk.imag
return eps1, eps2
def get_n(self, wls):
omega = h * c / wls
eps1, eps2 = self._eps(omega, self.x_Au)
n = (eps1 + 1j * eps2)**0.5
return n.real
def get_k(self, wls):
omega = h * c / wls
eps1, eps2 = self._eps(omega, self.x_Au)
n = (eps1 + 1j * eps2)**0.5
return n.imag
if __name__ == '__main__':
print('Alloy material test')
from mstm_studio.alloy_AuAg import AlloyAuAg
mat = AlloyAuAg(0.5)
print(mat)
# mat.plot()
print('n, k = ', mat.get_n(800), mat.get_k(800))
input('Press enter')
mat.plot()
self._M = np.zeros(shape=(len(self.wavelengths),
len(self.diameters)))
self.number_of_params = 2 # else will get error on a check
for i, diameter in enumerate(self.diameters):
self._M[:, i] = super(
MieLognormSpheres,
self).calculate(values=[1.0, diameter / 2.0])
self.number_of_params = 3 # ugly, but everything has a price
print('Building cache... done')
dD = np.ediff1d(self.diameters, to_begin=1e-3)
distrib = self.lognorm(self.diameters, values[1], values[2])
result = np.dot(self._M, distrib * dD)
return values[0] * result
if __name__ == '__main__':
# tests come here
# ~ cb = ConstantBackground(name='const', wavelengths=[300,400,500,600,700,800])
# ~ print(cb.calculate([3]))
# ~ cb.plot([3])
# ~ mie = MieSingleSphere(name='mie', wavelengths=np.linspace(300,800,50))
# ~ mie = MieLognormSpheres(name='mie', wavelengths=np.linspace(300,800,50))
from mstm_studio.contributions import MieLognormSpheresCached
from mstm_studio.alloy_AuAg import AlloyAuAg
mie = MieLognormSpheresCached(name='mie',
wavelengths=np.linspace(300, 800, 50))
mie.set_material(AlloyAuAg(x_Au=1), 1.66)
mie.plot([1, 1.5, 0.5]) # scale mu sigma
print('See you!')
#!/usr/bin/python
# -*- coding: utf-8 -*-
from mstm_studio.contributions import MieLognormSpheres
from mstm_studio.alloy_AuAg import AlloyAuAg
import numpy as np
mie = MieLognormSpheres(name='mie', wavelengths=np.linspace(300, 800, 51))
mie.set_material(AlloyAuAg(x_Au=1), 1.5) # golden sphere in glass
values = [1, 1.5, 0.5] # scale, mu, sigma
fig, _ = mie.plot(values)
fig.savefig('mie_contrib.png', bbox_inches='tight')
mie.MAX_DIAMETER_TO_PLOT = 20 # 100 nm is by default
fig, _ = mie.plot_distrib(values)
fig.savefig('mie_distrib.png', bbox_inches='tight')
from mstm_studio.alloy_AuAg import AlloyAuAg
from mstm_studio.contrib_spheroid import SpheroidSP
import numpy as np
wls = np.linspace(300, 800, 51) # range for calculation, in nm
SIZE = 20 # nm, particle diameter
ASPECT = 1.5 # a / c = horiz. axis / rot. axis
sph = SpheroidSP(wavelengths=wls) # create object
sph.set_material(AlloyAuAg(x_Au=1), 1.5) # particle and matrix refr. ind.
fig, axs = sph.plot_shape([1, SIZE, ASPECT])
fig.savefig('spheroid_shape.png', bbox_inches='tight')
ext_sph = sph.calculate([1, SIZE, ASPECT])
fig, axs = sph.plot([1, SIZE, ASPECT]) # scale, diameter, aspect
fig.savefig('spheroid_ext.png', bbox_inches='tight')
#!/usr/bin/python
# -*- coding: utf-8 -*-
from mstm_studio.alloy_AuAg import AlloyAuAg
from mstm_studio.contributions import LinearBackground, MieLognormSpheresCached
from mstm_studio.mstm_spectrum import ExplicitSpheres, Profiler
from mstm_studio.fit_spheres_optic import Fitter, FixConstraint, ConcentricConstraint
fitter = Fitter(
exp_filename='experiment.dat') # load experiment from tabbed file
fitter.set_extra_contributions(
[LinearBackground(fitter.wls)], # wavelengths from experiment
[0.02, 0.0001]) # initial values for a, b
spheres = ExplicitSpheres(2, [0, 0, 0, 10, 0, 0, 0, 12],
mat_filename=[AlloyAuAg(1.),
AlloyAuAg(0.)])
fitter.set_spheres(spheres) # core-shell Au@Ag particle
fitter.set_matrix(1.5) # in glass
fitter.add_constraint(ConcentricConstraint(0, 1)) # 0 -> 1
fitter.add_constraint(FixConstraint('x00'))
fitter.add_constraint(FixConstraint('y00'))
fitter.add_constraint(FixConstraint('z00'))
# run fit (takes ~200 seconds on 2GHz CPU)
with Profiler():
fitter.run()
fitter.report_result()
# plot results
return s
if __name__ == '__main__':
fitter = Fitter('../example/experiment.dat')
# test Mie fit
from mstm_studio.contributions import LinearBackground, MieSingleSphere, MieLognormSpheresCached
from mstm_studio.alloy_AuAg import AlloyAuAg
fitter.set_extra_contributions([
LinearBackground(fitter.wls, 'lin bkg'),
MieLognormSpheresCached(fitter.wls, 'LN Mie')
], [0.02, -0.001, 0.1, 1.5, 0.5])
#~ MieSingleSphere(fitter.wls, 'Mie')],
#~ [0.02, -0.001,
#~ 0.1, 10])
fitter.extra_contributions[1].set_material(AlloyAuAg(1.), 1.66)
fitter.extra_contributions[1].plot([0.1, 1.5, 0.5])
fitter.extra_contributions[1].plot_distrib([0.1, 1.5, 0.5])
#~ fitter.extra_contributions[1].plot([0.1, 10])
fitter.set_spheres(None) # no spheres, no mstm runs
fitter.report_freedom()
input('Press enter to run peak fitting')
fitter.run()
fitter.report_result()
input('Press enter to continue')
# test peak fit
from contributions import LinearBackground, LorentzPeak
fitter.set_extra_contributions([
LinearBackground(fitter.wls, 'lin bkg'),
LorentzPeak(fitter.wls, 'lorentz peak')
], [0.02, -0.001, 100, 550, 50])
from mstm_studio.mstm_spectrum import LogNormalSpheres
from mstm_studio.alloy_AuAg import AlloyAuAg
spheres = LogNormalSpheres(9, 10.0, 0.2, 5., AlloyAuAg(1.))
while spheres.check_overlap():
print('spheres are overlapping, regenerating...')
spheres = LogNormalSpheres(9, 10.0, 0.2, 5., AlloyAuAg(1.))
print(spheres.a)
# ~ Box size estimated as: 77.0 nm
# ~ Desired number of particles: 9
# ~ Number of particles in a box: 8
# ~ Resulted number of particles: 8
# ~ spheres are overlapping, regenerating...
# ~ Box size estimated as: 77.0 nm
# ~ Desired number of particles: 9
# ~ Number of particles in a box: 8
# ~ Resulted number of particles: 8
# ~ [ 9.307773 8.61185299 9.92867988 8.84140858 9.87175352 8.71090184
# ~ 9.71505038 12.40459688]
#!/usr/bin/python
# -*- coding: utf-8 -*-
from mstm_studio.alloy_AuAg import AlloyAuAg
from mstm_studio.contributions import LinearBackground, MieLognormSpheresCached
from mstm_studio.fit_spheres_optic import Fitter
fitter = Fitter(
exp_filename='experiment.dat') # load experiment from tabbed file
fitter.set_extra_contributions(
[
LinearBackground(fitter.wls), # wavelengths from experiment
MieLognormSpheresCached(fitter.wls, 'LN Mie')
], # cached version for faster fittting
[0.02, 0.0001, 0.1, 2.0, 0.4]) # initial values for a, b, C, mu, sigma
fitter.extra_contributions[1].set_material(AlloyAuAg(1.),
1.5) # gold particles in glass
fitter.set_spheres(None) # no spheres - no slow MSTM runs
# run fit (takes ~20 seconds on 2GHz CPU)
fitter.run()
fitter.report_result()
# plot results
import matplotlib.pyplot as plt
plt.plot(fitter.wls, fitter.exp, 'ro', label='exp.')
plt.plot(fitter.wls, fitter.calc, 'b-', label='fit')
plt.xlabel('Wavelength, nm')
plt.ylabel('Exctinction, a.u.')
plt.legend()
plt.savefig('fit_by_Mie.png', bbox_inches='tight')
print(s)
return s
if __name__ == '__main__':
fitter = Fitter('../example/experiment.dat')
# test Mie fit
from mstm_studio.contributions import LinearBackground, MieSingleSphere, MieLognormSpheresCached
from mstm_studio.alloy_AuAg import AlloyAuAg
fitter.set_extra_contributions([LinearBackground(fitter.wls, 'lin bkg'),
MieLognormSpheresCached(fitter.wls, 'LN Mie')],
[0.02, -0.001,
0.1, 1.5, 0.5])
#~ MieSingleSphere(fitter.wls, 'Mie')],
#~ [0.02, -0.001,
#~ 0.1, 10])
fitter.extra_contributions[1].set_material(AlloyAuAg(1.), 1.66)
fitter.extra_contributions[1].plot([0.1, 1.5, 0.5])
fitter.extra_contributions[1].plot_distrib([0.1, 1.5, 0.5])
#~ fitter.extra_contributions[1].plot([0.1, 10])
fitter.set_spheres(None) # no spheres, no mstm runs
fitter.report_freedom()
input('Press enter to run peak fitting')
fitter.run()
fitter.report_result()
contribs = fitter.get_extra_contributions()
print(contribs)
input('Press enter to continue')
# test peak fit
from contributions import LinearBackground, LorentzPeak
fitter.set_extra_contributions([LinearBackground(fitter.wls, 'lin bkg'),
LorentzPeak(fitter.wls, 'lorentz peak')],