ScatterSim:Examples:002Lattice - Revision history

JulienLhermitte at 16:01, 30 March 2017

2017-03-30T16:01:48Z

JulienLhermitte at 16:06, 29 March 2017

2017-03-29T16:06:10Z

JulienLhermitte at 16:05, 29 March 2017

2017-03-29T16:05:15Z

JulienLhermitte at 16:04, 29 March 2017

2017-03-29T16:04:55Z

JulienLhermitte at 16:03, 29 March 2017

2017-03-29T16:03:09Z

KevinYager at 21:19, 28 March 2017

2017-03-28T21:19:36Z

JulienLhermitte: Created page with "
2017-03-28T20:39:21Z

Created page with "<source lang="python> # The next step is creating a lattice from ScatterSim.NanoObjects import SphereNanoObject, PolydisperseNanoObject # We'll import a few lattices, cubic, ..."

New page
<source lang="python>
# The next step is creating a lattice

from ScatterSim.NanoObjects import SphereNanoObject, PolydisperseNanoObject
# We'll import a few lattices, cubic, FCC, BCC and Diamond
from ScatterSim.LatticeObjects import SimpleCubic, FCCLattice, BCCLattice, DiamondTwoParticleLattice
# import the peak shape for the peaks, tunable
from ScatterSim.PeakShape import PeakShape

import numpy as np
import matplotlib.pyplot as plt

</source>

TBA

@@ Line 11: / Line 11: @@
 import matplotlib.pyplot as plt
 # Let's use our polydisperse sphere nanoobject since it's more realistic
 # In general though, you'll want to start with simpler objects to reduce computation time

@@ Line 34: / Line 34: @@
 # We'll deal with simple lattices, so all unit vectors are aligned with x, y and z axes, and same length
 lattice_spacing = 10. # 10 times radius (1 nm)
-lat_sc = SimpleCubic([polysphere], lattice_spacing_a=lattice_spacing)
+sigma_D = .06 # add a Debye-Waller factor
-lat_fcc = FCCLattice([polysphere], lattice_spacing_a=lattice_spacing)
+lat_sc = SimpleCubic([polysphere], lattice_spacing_a=lattice_spacing, sigma_D=sigma_D)
-lat_bcc = BCCLattice([polysphere], lattice_spacing_a=lattice_spacing)
+lat_fcc = FCCLattice([polysphere], lattice_spacing_a=lattice_spacing, sigma_D=sigma_D)
-lat_diamond = DiamondTwoParticleLattice([polysphere], lattice_spacing_a=lattice_spacing)
+lat_bcc = BCCLattice([polysphere], lattice_spacing_a=lattice_spacing, sigma_D=sigma_D)
 q = np.linspace(.4, 4, 1000)

@@ Line 90: / Line 90: @@
 </source>
-[[File:ScatterSimExamples-001-fig2.png]]
+[[File:ScatterSimExamples-002-fig1.png]]
 <source lang='python'>
 # Same, but loglog plot (sometimes easier to see)
@@ Line 109: / Line 109: @@
 </source>
-[[File:ScatterSimExamples-001-fig2.png]]
+[[File:ScatterSimExamples-002-fig2.png]]

@@ Line 89: / Line 89: @@
 plt.plot(q, Sq_diamond)
+</source>
 # Same, but loglog plot (sometimes easier to see)
@@ Line 105: / Line 107: @@
 plt.title("Diamond Structure Factor")
 plt.loglog(q, Sq_diamond)

← Older revision		Revision as of 16:03, 29 March 2017
Line 14:		Line 14:

	TBA		TBA
		+	<source lang="python">
		+	# Let's use our polydisperse sphere nanoobject since it's more realistic
		+	# In general though, you'll want to start with simpler objects to reduce computation time
		+	# but this one should be okay...
		+	pargs_polysphere = dict(radius= 1, sigma_R=.04)
		+
		+	polysphere = PolydisperseNanoObject(SphereNanoObject, pargs_polysphere, argname='radius', argstdname='sigma_R')
		+
		+	# The peak shape
		+	# delta is sigma of a Gaussian, and nu is FWHM of a Lorentzian
		+	# Generally, you'll want to keep one zero and vary the other (to get a Gaussian or Lorentzian)
		+	# but when finalizing a fit, you may want to play with intermediate values
		+	peak = PeakShape(delta=0.03, nu=0.01)
		+
		+	# now define your lattices
		+	# lattices, to first order are just defined by 6 parameters:
		+	# lattice_spacing_a, lattice_spacing_b and lattice_spacing_c (the unit vector spacings)
		+	# alpha, beta, gamma (the angles the unit vectors make with the axes)
		+	# We'll deal with simple lattices, so all unit vectors are aligned with x, y and z axes, and same length
		+	lattice_spacing = 10. # 10 times radius (1 nm)
		+	lat_sc = SimpleCubic([polysphere], lattice_spacing_a=lattice_spacing)
		+	lat_fcc = FCCLattice([polysphere], lattice_spacing_a=lattice_spacing)
		+	lat_bcc = BCCLattice([polysphere], lattice_spacing_a=lattice_spacing)
		+	lat_diamond = DiamondTwoParticleLattice([polysphere], lattice_spacing_a=lattice_spacing)
		+
		+	q = np.linspace(.4, 4, 1000)
		+	# Now compute the intensity, it will take some time...
		+	Z0_sc = lat_sc.intensity(q, peak)
		+	Pq_sc = lat_sc.form_factor_squared_isotropic(q)
		+
		+	c_sc = .1
		+
		+	# note Gq is same for all three here (just depends on sigma_D, it's an exponential decay...)
		+	Gq_sc = lat_sc.G_q(q)
		+
		+	Sq_sc = c_scZ0_sc/Pq_scGq_sc + (1-Gq_sc)
		+
		+	print("Finished calculating Simple Cubic")
		+
		+	Z0_fcc = lat_fcc.intensity(q, peak)
		+	Pq_fcc = lat_fcc.form_factor_squared_isotropic(q)
		+	Gq_fcc = lat_fcc.G_q(q)
		+
		+	Sq_fcc = c_scZ0_fcc/Pq_fccGq_fcc + (1-Gq_fcc)
		+
		+	print("Finished calculating Face Centered Cubic")
		+
		+	Z0_bcc = lat_bcc.intensity(q, peak)
		+	Pq_bcc = lat_bcc.form_factor_squared_isotropic(q)
		+	Gq_bcc = lat_bcc.G_q(q)
		+
		+	Sq_bcc = c_scZ0_bcc/Pq_bccGq_bcc + (1-Gq_bcc)
		+
		+	print("Finished calculating Body Centered Cubic")
		+	Z0_diamond = lat_diamond.intensity(q, peak)
		+	Pq_diamond = lat_diamond.form_factor_squared_isotropic(q)
		+	Gq_diamond = lat_diamond.G_q(q)
		+
		+	Sq_diamond = c_scZ0_diamond/Pq_diamondGq_diamond + (1-Gq_diamond)
		+
		+	print("Finished calculating Diamond")
		+	plt.figure(0, figsize=(10,8));plt.clf()
		+	plt.subplot(2,2,1)
		+	plt.title("Simple Cubic Structure Factor")
		+	plt.plot(q, Sq_sc)
		+	plt.subplot(2,2,2)
		+	plt.title("Face Centered Cubic Structure Factor")
		+	plt.plot(q, Sq_fcc)
		+	plt.subplot(2,2,3)
		+	plt.title("Body Centered Cubic Structure Factor")
		+	plt.plot(q, Sq_bcc)
		+	plt.subplot(2,2,4)
		+	plt.title("Diamond Structure Factor")
		+	plt.plot(q, Sq_diamond)
		+
		+
		+	# Same, but loglog plot (sometimes easier to see)
		+
		+	plt.figure(1, figsize=(10,8));plt.clf()
		+	plt.subplot(2,2,1)
		+	plt.title("Simple Cubic Structure Factor")
		+	plt.loglog(q, Sq_sc)
		+	plt.subplot(2,2,2)
		+	plt.title("Face Centered Cubic Structure Factor")
		+	plt.loglog(q, Sq_fcc)
		+	plt.subplot(2,2,3)
		+	plt.title("Body Centered Cubic Structure Factor")
		+	plt.loglog(q, Sq_bcc)
		+	plt.subplot(2,2,4)
		+	plt.title("Diamond Structure Factor")
		+	plt.loglog(q, Sq_diamond)

← Older revision		Revision as of 21:19, 28 March 2017
Line 1:		Line 1:
−	<source lang="python>	+	<source lang="python">
	# The next step is creating a lattice		# The next step is creating a lattice