Single-crystal fit: Tb₂Ti₂O₇, HEiDi¶
The same staged fit as the Python tutorial, on the command line. The command line fits whatever the project marks free with () after a value, so each stage marks its parameters in the project's files with a text editor and runs edi fit, which writes the fitted values back into the project for the next stage.
Get the project¶
edi download-data sc-neut-cwl_tb2ti2o7-heidi
python -m edi download-data sc-neut-cwl_tb2ti2o7-heidi
Start with nothing free¶
The project marks what its finished fit frees. Remove every (), so the stages below free one group at a time.
In experiments/heidi.edi, remove the () from every value; they now read:
_extinction.domain_radius 25
_extinction.mosaic_spread 0
tb2ti2o7 4In structures/tb2ti2o7.edi, remove the () from every value; they now read:
O1 O 0.33 0.125 0.125 f 48 1 0.0026 Uani
Tb 0.0026 0.0026 0.0026 0 0 0The same for every other row (3 more).
Scale¶
The scale brings the calculated intensities to the measured ones.
In experiments/heidi.edi, add () after the values the stage frees:
tb2ti2o7 4()edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
python -m edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
edi fit: project sc-neut-cwl_tb2ti2o7-heidi, 220 pts fitted / 220 loaded, 1 free
iter time (s) wR(F²) (%) reduced χ² change
22.22 75.58
1 0.010 19.62 58.90 22.1% ↓
2 0.021 19.62 58.90
done · converged · 2 iters · reduced χ² 58.90 · wR(F²) 19.62 % · 0.03 s
refined parameters (1 free):
name parameter start value s.u. change
scale experiment.linked_structures[tb2ti2o7].scale 4 4.477 0.061 11.9% ↑
- start the value before the fit
- value the fitted value
- s.u. its standard uncertainty
- change how far the fit moved it, in % of the start: ↑ up, ↓ down
O1's position¶
The one coordinate the symmetry leaves free.
In structures/tb2ti2o7.edi, add () after the values the stage frees:
O1 O 0.33() 0.125 0.125 f 48 1 0.0026 Uaniedi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
python -m edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
edi fit: project sc-neut-cwl_tb2ti2o7-heidi, 220 pts fitted / 220 loaded, 2 free
iter time (s) wR(F²) (%) reduced χ² change
19.62 59.17
1 0.013 14.74 33.42 43.5% ↓
2 0.076 14.74 33.42
done · converged · 2 iters · reduced χ² 33.42 · wR(F²) 14.74 % · 0.10 s
refined parameters (2 free):
name parameter start value s.u. change
scale experiment.linked_structures[tb2ti2o7].scale 4.477 4.555 0.046 1.7% ↑
x structure.atom_sites[O1].fract_x 0.33000 0.32803 0.00015 0.6% ↓
- start the value before the fit
- value the fitted value
- s.u. its standard uncertainty
- change how far the fit moved it, in % of the start: ↑ up, ↓ down
Anisotropic displacements¶
In structures/tb2ti2o7.edi, add () after the values the stage frees:
Tb 0.0026() 0.0026 0.0026 0() 0 0
Ti 0.0026() 0.0026 0.0026 0() 0 0The same for every other row (2 more).
edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
python -m edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
edi fit: project sc-neut-cwl_tb2ti2o7-heidi, 220 pts fitted / 220 loaded, 10 free
iter time (s) wR(F²) (%) reduced χ² change
14.74 34.69
1 0.016 6.20 6.13 82.3% ↓
2 0.028 6.09 5.93 3.3% ↓
3 0.047 6.09 5.93
done · converged · 3 iters · reduced χ² 5.93 · wR(F²) 6.09 % · 0.06 s
refined parameters (10 free):
name parameter start value s.u. change
scale experiment.linked_structures[tb2ti2o7].scale 4.555 5.269 0.041 15.7% ↑
U₁₁, Ų structure.atom_site_aniso[O1].adp_11 0.00260 0.00632 0.00025 143.3% ↑
U₂₂, Ų structure.atom_site_aniso[O1].adp_22 0.00260 0.00434 0.00017 66.9% ↑
U₂₃, Ų structure.atom_site_aniso[O1].adp_23 0.00000 0.00192 0.00019
U₁₁, Ų structure.atom_site_aniso[O2].adp_11 0.00260 0.00332 0.00023 27.6% ↑
U₁₁, Ų structure.atom_site_aniso[Tb].adp_11 0.00260 0.00578 0.00016 122.2% ↑
U₁₂, Ų structure.atom_site_aniso[Tb].adp_12 0.00000 -0.00234 0.00016
U₁₁, Ų structure.atom_site_aniso[Ti].adp_11 0.00260 0.00515 0.00027 98.1% ↑
U₁₂, Ų structure.atom_site_aniso[Ti].adp_12 0.00000 -6.2e-4 3.5e-4
x structure.atom_sites[O1].fract_x 0.32803 0.327960 0.000067
- start the value before the fit
- value the fitted value
- s.u. its standard uncertainty
- change how far the fit moved it, in % of the start: ↑ up, ↓ down
Extinction¶
The domain radius and the mosaic spread.
In experiments/heidi.edi, add () after the values the stage frees:
_extinction.domain_radius 25()
_extinction.mosaic_spread 0()edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
python -m edi fit sc-neut-cwl_tb2ti2o7-heidi --verbosity full
edi fit: project sc-neut-cwl_tb2ti2o7-heidi, 220 pts fitted / 220 loaded, 12 free
iter time (s) wR(F²) (%) reduced χ² change
6.09 5.98
1 0.014 3.86 2.40 59.9% ↓
2 0.026 3.18 1.63 32.1% ↓
3 0.037 2.97 1.42 13.1% ↓
4 0.048 2.92 1.38 2.9% ↓
5 0.069 2.91 1.37 0.7% ↓
6 0.081 2.88 1.34 2.0% ↓
7 0.092 2.88 1.33 0.4% ↓
8 0.103 2.88 1.33
9 0.113 2.88 1.33
10 0.126 2.88 1.33
done · converged · 10 iters · reduced χ² 1.33 · wR(F²) 2.88 % · 0.14 s
refined parameters (12 free):
name parameter start value s.u. change
Domain radius, μm experiment.extinction.domain_radius 25 3.0 1.8 88.1% ↓
Mosaic spread, rad⁻¹ experiment.extinction.mosaic_spread 0 2.733e3 0.093e3
scale experiment.linked_structures[tb2ti2o7].scale 5.269 5.900 0.036 12.0% ↑
U₁₁, Ų structure.atom_site_aniso[O1].adp_11 0.00632 0.00742 0.00012 17.4% ↑
U₂₂, Ų structure.atom_site_aniso[O1].adp_22 0.00434 0.005533 0.000084 27.5% ↑
U₂₃, Ų structure.atom_site_aniso[O1].adp_23 0.00192 0.001926 0.000087 0.3% ↑
U₁₁, Ų structure.atom_site_aniso[O2].adp_11 0.00332 0.00442 0.00012 33.2% ↑
U₁₁, Ų structure.atom_site_aniso[Tb].adp_11 0.00578 0.006965 0.000084 20.5% ↑
U₁₂, Ų structure.atom_site_aniso[Tb].adp_12 -0.00234 -0.002266 0.000075 3.1% ↑
U₁₁, Ų structure.atom_site_aniso[Ti].adp_11 0.00515 0.00617 0.00014 19.8% ↑
U₁₂, Ų structure.atom_site_aniso[Ti].adp_12 -6.20e-4 -2.7e-4 1.7e-4 55.7% ↑
x structure.atom_sites[O1].fract_x 0.32796 0.327981 0.000032
- start the value before the fit
- value the fitted value
- s.u. its standard uncertainty
- change how far the fit moved it, in % of the start: ↑ up, ↓ down
Report¶
Write the HTML report of the fitted project and open it in a browser.
The standalone executable has no report; use the Python package.
python -m edi report sc-neut-cwl_tb2ti2o7-heidi --output sc-neut-cwl_tb2ti2o7-heidi.html