Single-crystal fit: Pr₂NiO₄, 5C2¶
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_pr2nio4-5c2
python -m edi download-data sc-neut-cwl_pr2nio4-5c2
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/llb_5c2.edi, remove the () from every value; they now read:
pr2nio4 4In structures/pr2nio4.edi, remove the () from every value; they now read:
Pr Pr 0 0 0.362 i 8 1 0 Bani
O2 O 0 0 0.176 i 8 0.722965 0 BaniThe same for every other row (6 more).
Scale¶
The scale brings the calculated intensities to the measured ones.
In experiments/llb_5c2.edi, add () after the values the stage frees:
pr2nio4 4()edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
python -m edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
edi fit: project sc-neut-cwl_pr2nio4-5c2, 198 pts fitted / 198 loaded, 1 free
iter time (s) wR(F²) (%) reduced χ² change
115.85 6415.49
1 0.042 49.30 1161.93 81.9% ↓
2 0.055 49.30 1161.93
done · converged · 2 iters · reduced χ² 1161.93 · wR(F²) 49.30 % · 0.07 s
refined parameters (1 free):
name parameter start value s.u. change
scale experiment.linked_structures[pr2nio4].scale 4 1.814 0.074 54.6% ↓
- 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
Positions¶
The coordinates each site's symmetry leaves free.
In structures/pr2nio4.edi, add () after the values the stage frees:
Pr Pr 0 0 0.362() i 8 1 0 Bani
O2 O 0 0 0.176() i 8 0.722965 0 BaniThe same for every other row (1 more).
edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
python -m edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
edi fit: project sc-neut-cwl_pr2nio4-5c2, 198 pts fitted / 198 loaded, 6 free
iter time (s) wR(F²) (%) reduced χ² change
49.30 1192.18
1 0.043 47.49 1106.20 7.2% ↓
2 0.084 46.77 1072.93 3.0% ↓
3 0.106 46.69 1069.03 0.4% ↓
4 0.118 46.64 1067.00 0.2% ↓
5 0.136 46.63 1066.25 0.1% ↓
6 0.168 46.61 1065.55 0.1% ↓
7 0.199 46.60 1065.20
8 0.221 46.60 1064.86
9 0.234 46.59 1064.67
10 0.257 46.59 1064.48
11 0.267 46.59 1064.37
12 0.275 46.58 1064.26
13 0.294 46.58 1064.19
14 0.304 46.58 1064.13
15 0.313 46.58 1064.09
16 0.326 46.58 1064.05
17 0.335 46.58 1064.02
18 0.345 46.58 1063.99
19 0.357 46.58 1063.98
20 0.368 46.58 1063.96
21 0.397 46.58 1063.95
22 0.406 46.58 1063.94
23 0.418 46.58 1063.93
done · converged · 23 iters · reduced χ² 1063.93 · wR(F²) 46.58 % · 0.44 s
refined parameters (6 free):
name parameter start value s.u. change
scale experiment.linked_structures[pr2nio4].scale 1.814 1.887 0.075 4.0% ↑
z structure.atom_sites[O2].fract_z 0.17600 0.1742 0.0011 1.0% ↓
x structure.atom_sites[Od].fract_x 0.07500 0.053 0.011 29.9% ↓
y structure.atom_sites[Od].fract_y 0.07500 0.067 0.011 10.6% ↓
z structure.atom_sites[Od].fract_z 0.17500 0.1727 0.0039 1.3% ↓
z structure.atom_sites[Pr].fract_z 0.36200 0.36026 0.00078 0.5% ↓
- 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
The interstitial displacement¶
The isotropic displacement of the interstitial oxygen Od.
In structures/pr2nio4.edi, add () after the values the stage frees:
Od O 0.053() 0.067() 0.1727() p 32 0.074654 0() Bisoedi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
python -m edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
edi fit: project sc-neut-cwl_pr2nio4-5c2, 198 pts fitted / 198 loaded, 7 free
iter time (s) wR(F²) (%) reduced χ² change
46.58 1069.49
1 0.018 46.53 1067.18 0.2% ↓
2 0.027 46.52 1066.73
3 0.039 46.51 1066.70
done · converged · 3 iters · reduced χ² 1066.70 · wR(F²) 46.51 % · 0.07 s
refined parameters (7 free):
name parameter start value s.u. change
scale experiment.linked_structures[pr2nio4].scale 1.887 1.887 0.075
z structure.atom_sites[O2].fract_z 0.17420 0.1744 0.0011 0.1% ↑
B iso, Ų structure.atom_sites[Od].adp_iso 0.000 -0.34 0.48
x structure.atom_sites[Od].fract_x 0.05300 0.0531 0.0091 0.1% ↑
y structure.atom_sites[Od].fract_y 0.06700 0.0664 0.0097 0.9% ↓
z structure.atom_sites[Od].fract_z 0.17270 0.1723 0.0033 0.2% ↓
z structure.atom_sites[Pr].fract_z 0.36026 0.36001 0.00086 0.1% ↓
- 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¶
Last, the tensors, each with the components its site symmetry leaves free.
In structures/pr2nio4.edi, add () after the values the stage frees:
Pr 0() 0() 0() 0 0 0
Ni 0() 0() 0() 0 0 0The same for every other row (3 more).
edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
python -m edi fit sc-neut-cwl_pr2nio4-5c2 --verbosity full
edi fit: project sc-neut-cwl_pr2nio4-5c2, 198 pts fitted / 198 loaded, 23 free
iter time (s) wR(F²) (%) reduced χ² change
46.51 1164.22
1 0.044 16.34 143.71 87.7% ↓
2 0.063 4.77 12.26 91.5% ↓
3 0.077 4.34 10.14 17.3% ↓
4 0.089 4.29 9.88 2.5% ↓
5 0.100 4.27 9.79 0.9% ↓
6 0.112 4.26 9.76 0.3% ↓
7 0.136 4.26 9.75 0.1% ↓
8 0.164 4.26 9.75
9 0.180 4.26 9.75
done · converged · 9 iters · reduced χ² 9.75 · wR(F²) 4.26 % · 0.21 s
refined parameters (23 free):
name parameter start value s.u. change
scale experiment.linked_structures[pr2nio4].scale 1.887 4.022 0.029 113.1% ↑
B₁₁, Ų structure.atom_site_aniso[Ni].adp_11 0.000 0.315 0.020
B₂₂, Ų structure.atom_site_aniso[Ni].adp_22 0.000 0.334 0.019
B₃₃, Ų structure.atom_site_aniso[Ni].adp_33 0.000 0.938 0.018
B₁₁, Ų structure.atom_site_aniso[O1].adp_11 0.000 0.581 0.028
B₁₂, Ų structure.atom_site_aniso[O1].adp_12 0.000 -0.164 0.017
B₂₂, Ų structure.atom_site_aniso[O1].adp_22 0.000 0.585 0.027
B₃₃, Ų structure.atom_site_aniso[O1].adp_33 0.000 2.570 0.032
B₁₁, Ų structure.atom_site_aniso[O2].adp_11 0.000 2.126 0.068
B₂₂, Ų structure.atom_site_aniso[O2].adp_22 0.000 2.172 0.065
B₃₃, Ų structure.atom_site_aniso[O2].adp_33 0.000 0.297 0.033
B₁₁, Ų structure.atom_site_aniso[Oi].adp_11 0.000 1.27 0.38
B₂₂, Ų structure.atom_site_aniso[Oi].adp_22 0.000 1.37 0.36
B₃₃, Ų structure.atom_site_aniso[Oi].adp_33 0.000 0.62 0.23
B₁₁, Ų structure.atom_site_aniso[Pr].adp_11 0.000 0.822 0.031
B₂₂, Ų structure.atom_site_aniso[Pr].adp_22 0.000 0.833 0.030
B₃₃, Ų structure.atom_site_aniso[Pr].adp_33 0.000 0.519 0.024
z structure.atom_sites[O2].fract_z 0.17440 0.173833 0.000095 0.3% ↓
B iso, Ų structure.atom_sites[Od].adp_iso -0.340 2.57 0.16 857.1% ↑
x structure.atom_sites[Od].fract_x 0.05310 0.0795 0.0022 49.7% ↑
y structure.atom_sites[Od].fract_y 0.06640 0.0741 0.0019 11.6% ↑
z structure.atom_sites[Od].fract_z 0.17230 0.17352 0.00069 0.7% ↑
z structure.atom_sites[Pr].fract_z 0.36001 0.359739 0.000076 0.1% ↓
- 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_pr2nio4-5c2 --output sc-neut-cwl_pr2nio4-5c2.html