Taurine on SENJU¶
Fit the amino-sulfonic acid taurine to six time-of-flight neutron single-crystal datasets from SENJU at J-PARC together, each reflection measured at its own wavelength.
The project is the catalogue case sc-neut-tof_taurine-senju, the one the command line and the
app's Examples open. Banks 2 to 6 share bank 1's three extinction terms, from the start.
Fitting 
Joint sc neut tof Bragg 
Crystal structure
import easydiffraction as edi
Load the project¶
project_path = edi.download_data('sc-neut-tof_taurine-senju', destination='data')
project = edi.Project.load(project_path)
structure = project.structures['taurine']
senju_1 = project.experiments['senju_1']
senju_2 = project.experiments['senju_2']
senju_3 = project.experiments['senju_3']
senju_4 = project.experiments['senju_4']
senju_5 = project.experiments['senju_5']
senju_6 = project.experiments['senju_6']
project.display.constraints()
Data 'sc-neut-tof_taurine-senju' is at data/sc-neut-tof_taurine-senju-b5deb357e7e8/sc-neut-tof_taurine-senju
The project marks what its fit frees. The fit below frees it in stages, so start with all of it fixed.
for parameter in project.free_parameters:
parameter.free = False
project.display.pattern('senju_1')
Perform the analysis¶
The fit follows diffraction-lib's change of model for this case: isotropic displacements first, then anisotropic tensors. diffraction-lib does not fit the positions, which this case does, so they get a stage of their own.
Scales, every site isotropic¶
Each bank's scale, with every site's displacement isotropic for now.
for site in structure.atom_sites:
site.adp_type = 'Biso'
for experiment in project.experiments:
experiment.linked_structures['taurine'].scale.free = True
project.display.parameters.free()
project.analysis.fit()
project.display.fit.results()
edi fit: joint project sc-neut-tof_taurine-senju, 6 banks (senju_1, senju_2, senju_3, senju_4, senju_5, senju_6), 947 pts fitted / 1540 loaded, 6 free
iter time (s) wR(F²) (%) reduced χ² change
179.47 5665.97
1 0.003 51.73 470.74 91.7% ↓
2 0.006 51.73 470.73
done · converged · 2 iters · reduced χ² 470.73 · wR(F²) 51.73 % · 0.01 s
project.display.pattern('senju_1')
Isotropic displacements¶
Every site's isotropic displacement.
for site in structure.atom_sites:
site.adp_iso.free = True
project.analysis.fit()
project.display.fit.results()
edi fit: joint project sc-neut-tof_taurine-senju, 6 banks (senju_1, senju_2, senju_3, senju_4, senju_5, senju_6), 947 pts fitted / 1540 loaded, 20 free
iter time (s) wR(F²) (%) reduced χ² change
51.73 477.84
1 0.005 31.17 173.48 63.7% ↓
2 0.010 27.18 131.89 24.0% ↓
3 0.014 26.94 129.62 1.7% ↓
4 0.018 26.94 129.57
5 0.021 26.94 129.56
6 0.027 26.94 129.56
done · converged · 6 iters · reduced χ² 129.56 · wR(F²) 26.94 % · 0.03 s
project.display.pattern('senju_1')
Extinction¶
Bank 1's three extinction terms, which the other banks share.
senju_1.extinction.coefficient_11.free = True
senju_1.extinction.coefficient_22.free = True
senju_1.extinction.coefficient_33.free = True
project.analysis.fit()
project.display.fit.results()
edi fit: joint project sc-neut-tof_taurine-senju, 6 banks (senju_1, senju_2, senju_3, senju_4, senju_5, senju_6), 947 pts fitted / 1540 loaded, 23 free
iter time (s) wR(F²) (%) reduced χ² change
26.94 129.98
1 0.003 22.14 87.84 32.4% ↓
2 0.008 20.47 75.09 14.5% ↓
3 0.012 20.27 73.57 2.0% ↓
4 0.016 20.26 73.55
5 0.021 20.26 73.55
done · converged · 5 iters · reduced χ² 73.55 · wR(F²) 20.26 % · 0.03 s
project.display.pattern('senju_1')
Positions¶
All fourteen sites' coordinates.
for site in structure.atom_sites:
site.fract_x.free = True
site.fract_y.free = True
site.fract_z.free = True
project.analysis.fit()
project.display.fit.results()
edi fit: joint project sc-neut-tof_taurine-senju, 6 banks (senju_1, senju_2, senju_3, senju_4, senju_5, senju_6), 947 pts fitted / 1540 loaded, 65 free
iter time (s) wR(F²) (%) reduced χ² change
20.26 77.05
1 0.006 17.17 55.36 28.2% ↓
2 0.013 17.04 54.51 1.5% ↓
3 0.019 17.04 54.49
4 0.025 17.04 54.49
done · converged · 4 iters · reduced χ² 54.49 · wR(F²) 17.04 % · 0.04 s
project.display.pattern('senju_1')
Anisotropic displacements¶
Back to anisotropic displacements (edi converts the values), with every tensor component free.
for site in structure.atom_sites:
site.adp_type = 'beta'
for tensor in structure.atom_site_aniso:
tensor.adp_11.free = True
tensor.adp_22.free = True
tensor.adp_33.free = True
tensor.adp_12.free = True
tensor.adp_13.free = True
tensor.adp_23.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.S1.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.O1.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.O2.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.O3.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.N1.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H1.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H2.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H3.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.C1.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H11.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H12.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.C2.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H21.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
/tmp/ipykernel_4219/4011545669.py:4: UserWarning: crysta.domain.dependent_free_ignored: parameter 'taurine.atom_site.H22.adp_iso' is constrained by 'the equivalent isotropic value of its beta tensor'; free = True is ignored and it stays dependent (cannot be fitted: set by a constraint)
tensor.adp_11.free = True
project.analysis.fit()
project.display.fit.results()
edi fit: joint project sc-neut-tof_taurine-senju, 6 banks (senju_1, senju_2, senju_3, senju_4, senju_5, senju_6), 947 pts fitted / 1540 loaded, 135 free
iter time (s) wR(F²) (%) reduced χ² change
17.04 59.19
1 0.015 13.02 34.56 41.6% ↓
2 0.031 12.20 30.32 12.3% ↓
3 0.046 12.19 30.27 0.2% ↓
4 0.068 12.19 30.27
done · converged · 4 iters · reduced χ² 30.27 · wR(F²) 12.19 % · 0.13 s
project.display.pattern('senju_1')
project.display.fit.correlations()
project.display.structure('taurine')
Save the project¶
project.save_as('sc-neut-tof_taurine-senju')
project.report.save_html('sc-neut-tof_taurine-senju.html')
Saving project to 'sc-neut-tof_taurine-senju'
Saving report to 'sc-neut-tof_taurine-senju.html'