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AndrewSazonovAndrewSazonov
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Updates NCAF tutorial
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‎.github/workflows/building-deploying-docs.yml

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@@ -124,6 +124,7 @@ jobs:
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- name: Build site with MkDocs
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run: |
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export JUPYTER_PLATFORM_DIRS=1
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export PYTHONWARNINGS="ignore::RuntimeWarning"
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export PYTHONPATH=$(pwd)/src:$PYTHONPATH
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mkdocs build
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‎tutorials/cryst-struct_pd-neut-tof_NCAF-WISH.py

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@@ -5,7 +5,7 @@
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# structure using time-of-flight neutron powder diffraction data from WISH at
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# ISIS.
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#
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# Temporarily, only a single dataset from detector banks 5 & 6 is used here.
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# Two datasets from detector banks 5_6 and 4_7 are used for joint fitting.
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# %% [markdown]
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# ## Import Library
@@ -45,12 +45,24 @@
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# ### Set Atom Sites
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# %%
48-
model.atom_sites.add('Ca', 'Ca', 0.4661, 0.0, 0.25, wyckoff_letter="b", b_iso=0.9)
49-
model.atom_sites.add('Al', 'Al', 0.25171, 0.25171, 0.25171, wyckoff_letter="a", b_iso=0.66)
50-
model.atom_sites.add('Na', 'Na', 0.08481, 0.08481, 0.08481, wyckoff_letter="a", b_iso=1.9)
51-
model.atom_sites.add('F1', 'F', 0.1375, 0.3053, 0.1195, wyckoff_letter="c", b_iso=0.9)
52-
model.atom_sites.add('F2', 'F', 0.3626, 0.3634, 0.1867, wyckoff_letter="c", b_iso=1.28)
53-
model.atom_sites.add('F3', 'F', 0.4612, 0.4612, 0.4612, wyckoff_letter="a", b_iso=0.79)
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model.atom_sites.add('Ca', 'Ca',
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0.4665, 0.0, 0.25,
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wyckoff_letter="b", b_iso=0.92)
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model.atom_sites.add('Al', 'Al',
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0.2520, 0.2520, 0.2520,
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wyckoff_letter="a", b_iso=0.73)
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model.atom_sites.add('Na', 'Na',
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0.0852, 0.0852, 0.0852,
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wyckoff_letter="a", b_iso=2.08)
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model.atom_sites.add('F1', 'F',
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0.1376, 0.3055, 0.1196,
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wyckoff_letter="c", b_iso=0.90)
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model.atom_sites.add('F2', 'F',
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0.3623, 0.3631, 0.1870,
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wyckoff_letter="c", b_iso=1.37)
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model.atom_sites.add('F3', 'F',
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0.4611, 0.4611, 0.4611,
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wyckoff_letter="a", b_iso=0.88)
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# %% [markdown]
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# ## Define Experiment
@@ -61,50 +73,71 @@
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# ### Download Measured Data
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# %%
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download_from_repository('wish_ncaf.xye',
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download_from_repository('wish_ncaf_5_6.xye',
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branch='docs',
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destination='data')
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# %%
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download_from_repository('wish_ncaf_4_7.xye',
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branch='docs',
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destination='data')
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# %% [markdown]
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# ### Create Experiment
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# %%
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expt = Experiment('wish',
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beam_mode='time-of-flight',
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data_path='data/wish_ncaf.xye')
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expt1 = Experiment('wish_5_6',
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beam_mode='time-of-flight',
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data_path='data/wish_ncaf_5_6.xye')
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# %%
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expt2 = Experiment('wish_4_7',
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beam_mode='time-of-flight',
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data_path='data/wish_ncaf_4_7.xye')
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# %% [markdown]
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# ### Set Instrument
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# %%
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expt.instrument.setup_twotheta_bank = 152.827
81-
expt.instrument.calib_d_to_tof_offset = 0.0
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expt.instrument.calib_d_to_tof_linear = 20770
83-
expt.instrument.calib_d_to_tof_quad = -1.08308
102+
expt1.instrument.setup_twotheta_bank = 152.827
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expt1.instrument.calib_d_to_tof_offset = -13.0
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expt1.instrument.calib_d_to_tof_linear = 20752.1
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expt1.instrument.calib_d_to_tof_quad = -1.08308
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# %%
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expt2.instrument.setup_twotheta_bank = 121.660
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expt2.instrument.calib_d_to_tof_offset = -15.0
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expt2.instrument.calib_d_to_tof_linear = 18640.7
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expt2.instrument.calib_d_to_tof_quad = -0.47488
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# %% [markdown]
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# ### Set Peak Profile
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# %%
89-
expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
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expt.peak.broad_gauss_sigma_0 = 0.0
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expt.peak.broad_gauss_sigma_1 = 0.0
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expt.peak.broad_gauss_sigma_2 = 5.0
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expt.peak.broad_mix_beta_0 = 0.01
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expt.peak.broad_mix_beta_1 = 0.01
95-
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# %% [markdown]
97-
# ### Set Peak Asymmetry
117+
expt1.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
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expt1.peak.broad_gauss_sigma_0 = 0.0
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expt1.peak.broad_gauss_sigma_1 = 0.0
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expt1.peak.broad_gauss_sigma_2 = 15.0
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expt1.peak.broad_mix_beta_0 = 0.01
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expt1.peak.broad_mix_beta_1 = 0.01
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expt1.peak.asym_alpha_0 = -0.01
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expt1.peak.asym_alpha_1 = 0.10
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# %%
100-
expt.peak.asym_alpha_0 = 0.0
101-
expt.peak.asym_alpha_1 = 0.1
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expt2.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
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expt2.peak.broad_gauss_sigma_0 = 0.0
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expt2.peak.broad_gauss_sigma_1 = 30.0
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expt2.peak.broad_gauss_sigma_2 = 20.0
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expt2.peak.broad_mix_beta_0 = 0.01
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expt2.peak.broad_mix_beta_1 = 0.01
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expt2.peak.asym_alpha_0 = -0.01
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expt2.peak.asym_alpha_1 = 0.10
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# %% [markdown]
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# ### Set Background
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# %%
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expt.background_type = 'line-segment'
140+
expt1.background_type = 'line-segment'
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for x, y in [
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(9162, 465),
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(11136, 593),
@@ -135,13 +168,49 @@
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(91958, 268),
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(102712, 262)
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]:
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expt.background.add(x, y)
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expt1.background.add(x, y)
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# %%
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expt2.background_type = 'line-segment'
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for x, y in [
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(9090, 488),
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(10672, 566),
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(12287, 494),
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(14037, 559),
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(15451, 529),
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(16764, 445),
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(18076, 460),
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(19456, 413),
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(20466, 511),
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(21880, 396),
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(23798, 391),
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(25447, 385),
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(28073, 349),
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(30058, 332),
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(32583, 309),
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(34804, 355),
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(37160, 318),
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(40324, 290),
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(46895, 260),
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(50631, 256),
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(54602, 246),
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(58439, 264),
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(66520, 250),
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(75002, 258),
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(83649, 257),
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(92770, 255),
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(101524, 260)
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]:
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expt2.background.add(x, y)
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# %% [markdown]
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# ### Set Linked Phases
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# %%
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expt.linked_phases.add('ncaf', scale=0.5)
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expt1.linked_phases.add('ncaf', scale=1.0)
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# %%
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expt2.linked_phases.add('ncaf', scale=2.0)
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# %% [markdown]
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# ## Define Project
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170239
# ### Add Experiment
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# %%
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project.experiments.add(expt)
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project.experiments.add(expt1)
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project.experiments.add(expt2)
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# %% [markdown]
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# ## Analysis
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project.analysis.current_minimizer = 'lmfit (leastsq)'
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# %% [markdown]
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# ### Plot Measured vs Calculated
194-
195-
# %%
196-
project.plot_meas_vs_calc(expt_name='wish',
197-
show_residual=True)
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# ### Set Fit Mode
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# %%
200-
project.plot_meas_vs_calc(expt_name='wish',
201-
x_min=37000, x_max=40000,
202-
show_residual=True)
203-
204-
# %% [markdown]
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# ### Perform Fit 1/5
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#
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# Set parameters to be refined.
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# %%
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model.cell.length_a.free = True
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expt.instrument.calib_d_to_tof_offset.free = True
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expt.linked_phases['ncaf'].scale.free = True
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# %% [markdown]
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# Show free parameters after selection.
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# %%
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project.analysis.show_free_params()
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# %% [markdown]
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# #### Run Fit
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224-
# %%
225-
project.analysis.fit()
266+
project.analysis.fit_mode = 'joint'
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227268
# %% [markdown]
228269
# ### Plot Measured vs Calculated
229270

230271
# %%
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project.plot_meas_vs_calc(expt_name='wish',
272+
project.plot_meas_vs_calc(expt_name='wish_5_6',
232273
show_residual=True)
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234275
# %%
235-
project.plot_meas_vs_calc(expt_name='wish',
236-
x_min=37000, x_max=40000,
276+
project.plot_meas_vs_calc(expt_name='wish_4_7',
237277
show_residual=True)
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239279
# %% [markdown]
240-
# ### Perform Fit 2/5
280+
# ### Perform Fit
241281
#
242-
# Set more parameters to be refined.
243-
244-
# %%
245-
expt.peak.broad_gauss_sigma_2.free = True
246-
expt.peak.broad_mix_beta_0.free = True
247-
expt.peak.broad_mix_beta_1.free = True
248-
expt.peak.asym_alpha_0.free = True
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expt.peak.asym_alpha_1.free = True
250-
251-
# %% [markdown]
252-
# Show free parameters after selection.
253-
254-
# %%
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project.analysis.show_free_params()
256-
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# %% [markdown]
258-
# #### Run Fit
259-
260-
# %%
261-
project.analysis.fit()
262-
263-
# %% [markdown]
264-
# #### Plot Measured vs Calculated
265-
266-
# %%
267-
project.plot_meas_vs_calc(expt_name='wish',
268-
show_residual=True)
269-
270-
# %%
271-
project.plot_meas_vs_calc(expt_name='wish',
272-
x_min=37000, x_max=40000,
273-
show_residual=True)
274-
275-
276-
# %% [markdown]
277-
# ### Perform Fit 3/5
278-
#
279-
# Set more parameters to be refined.
282+
# Set parameters to be refined.
280283

281284
# %%
282285
model.atom_sites['Ca'].fract_x.free = True
@@ -290,45 +293,33 @@
290293
model.atom_sites['F2'].fract_z.free = True
291294
model.atom_sites['F3'].fract_x.free = True
292295

293-
# %% [markdown]
294-
# Show free parameters after selection.
295-
296-
# %%
297-
project.analysis.show_free_params()
298-
299-
# %% [markdown]
300-
# #### Run Fit
301-
302-
# %%
303-
project.analysis.fit()
304-
305-
# %% [markdown]
306-
# #### Plot Measured vs Calculated
307-
308-
# %%
309-
project.plot_meas_vs_calc(expt_name='wish',
310-
show_residual=True)
311-
312-
# %%
313-
project.plot_meas_vs_calc(expt_name='wish',
314-
x_min=37000, x_max=40000,
315-
show_residual=True)
316-
317-
# %% [markdown]
318-
# ### Perform Fit 4/5
319-
#
320-
# Set more parameters to be refined.
321-
322-
# %%
323-
expt.instrument.calib_d_to_tof_linear.free = True
324-
325296
model.atom_sites['Ca'].b_iso.free = True
326297
model.atom_sites['Al'].b_iso.free = True
327298
model.atom_sites['Na'].b_iso.free = True
328299
model.atom_sites['F1'].b_iso.free = True
329300
model.atom_sites['F2'].b_iso.free = True
330301
model.atom_sites['F3'].b_iso.free = True
331302

303+
# %%
304+
expt1.linked_phases['ncaf'].scale.free = True
305+
expt1.instrument.calib_d_to_tof_offset.free = True
306+
expt1.instrument.calib_d_to_tof_linear.free = True
307+
expt1.peak.broad_gauss_sigma_2.free = True
308+
expt1.peak.broad_mix_beta_0.free = True
309+
expt1.peak.broad_mix_beta_1.free = True
310+
expt1.peak.asym_alpha_0.free = True
311+
expt1.peak.asym_alpha_1.free = True
312+
313+
expt2.linked_phases['ncaf'].scale.free = True
314+
expt2.instrument.calib_d_to_tof_linear.free = True
315+
expt2.instrument.calib_d_to_tof_offset.free = True
316+
expt2.peak.broad_gauss_sigma_1.free = True
317+
expt2.peak.broad_gauss_sigma_2.free = True
318+
expt2.peak.broad_mix_beta_0.free = True
319+
expt2.peak.broad_mix_beta_1.free = True
320+
expt2.peak.asym_alpha_0.free = True
321+
expt2.peak.asym_alpha_1.free = True
322+
332323
# %% [markdown]
333324
# Show free parameters after selection.
334325

@@ -345,12 +336,11 @@
345336
# #### Plot Measured vs Calculated
346337

347338
# %%
348-
project.plot_meas_vs_calc(expt_name='wish',
339+
project.plot_meas_vs_calc(expt_name='wish_5_6',
349340
show_residual=True)
350341

351342
# %%
352-
project.plot_meas_vs_calc(expt_name='wish',
353-
x_min=37000, x_max=40000,
343+
project.plot_meas_vs_calc(expt_name='wish_4_7',
354344
show_residual=True)
355345

356346
# %% [markdown]

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