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Adding Tutorial for Easy Use of OmniXAS #3

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3088c51
Added tutorial folder with a Jupyter Notebook walkthrough and all nec…
niyucao Sep 15, 2025
70c416f
Adjusted tutorial notebook to make sure everything runs properly and …
niyucao Sep 25, 2025
c803e27
Deleted unnecessary folders and added a random seed in tutorial noteb…
niyucao Oct 6, 2025
f6e18b1
Further removed additional unnecessary files for the tutorial. Only n…
niyucao Oct 6, 2025
8e29599
Moved random seed to cell where the NN is trained.
niyucao Oct 7, 2025
51fedfa
Removed python dependent files and fixed random seed for various diff…
niyucao Oct 8, 2025
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Binary file added tutorial_omnixas/CU_FEFF.npz
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221 changes: 221 additions & 0 deletions tutorial_omnixas/FEFF/Cu/mp-1005792/FEFF-XANES/008_Cu/feff.inp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,221 @@
* This FEFF.inp file generated by pymatgen
TITLE comment: None given
TITLE Source:
TITLE Structure Summary: Sm8 Cu4 As12 O4
TITLE Reduced formula: Sm2CuAs3O
TITLE space group: (Pnma), space number: (62)
TITLE abc: 3.991376 3.999568 34.822541
TITLE angles: 90.000000 90.000000 90.000000
TITLE sites: 28
* 1 Sm 0.750000 0.751232 0.966883
* 2 Sm 0.250000 0.251232 0.533117
* 3 Sm 0.750000 0.748768 0.466883
* 4 Sm 0.250000 0.248768 0.033117
* 5 Sm 0.250000 0.307973 0.824177
* 6 Sm 0.750000 0.807973 0.675823
* 7 Sm 0.250000 0.192027 0.324177
* 8 Sm 0.750000 0.692027 0.175823
* 9 Cu 0.250000 0.808380 0.750036
* 10 Cu 0.750000 0.308380 0.749964
* 11 Cu 0.250000 0.691620 0.250036
* 12 Cu 0.750000 0.191620 0.249964
* 13 As 0.250000 0.830992 0.892979
* 14 As 0.750000 0.330992 0.607021
* 15 As 0.250000 0.669008 0.392979
* 16 As 0.750000 0.169008 0.107021
* 17 As 0.750000 0.251288 0.894095
* 18 As 0.250000 0.751288 0.605905
* 19 As 0.750000 0.248712 0.394095
* 20 As 0.250000 0.748712 0.105905
* 21 As 0.250000 0.309052 0.705477
* 22 As 0.750000 0.809052 0.794523
* 23 As 0.250000 0.190948 0.205477
* 24 As 0.750000 0.690948 0.294523
* 25 O 0.750000 0.251299 0.000135
* 26 O 0.250000 0.751299 0.499865
* 27 O 0.750000 0.248701 0.500135
* 28 O 0.250000 0.748701 0.999865

CONTROL 1 1 1 1 1 1
COREHOLE RPA
S02 0
EXCHANGE 0 0.0 0.0 2
SCF 7.0 0 100 0.2 3
FMS 9.0 0
XANES 4 0.04 0.1
EDGE K
RPATH -1
EGRID
k_grid -1 0 0.04
k_grid 0 6 0.04

POTENTIALS
*ipot Z tag lmax1 lmax2 xnatph(stoichometry) spinph
******- **- ****- ******- ******- ********************** ********
0 29 Cu -1 -1 0.0001 0
1 62 Sm -1 -1 8 0
2 29 Cu -1 -1 4 0
3 33 As -1 -1 12 0
4 8 O -1 -1 4 0

ATOMS
* x y z ipot Atom Distance Number
**********- ********- ********- ****** ****** ********** ********
0 0 0 0 Cu 0 0
-1.99569 0.002688 1.54915 3 As 2.52639 59
1.99569 0.002688 1.54915 3 As 2.52639 155
0 -1.9971 -1.55166 3 As 2.52904 80
0 2.00247 -1.55166 3 As 2.53328 126
-1.99569 -1.99978 -0.002507 2 Cu 2.82523 4
-1.99569 1.99978 -0.002507 2 Cu 2.82523 41
1.99569 -1.99978 -0.002507 2 Cu 2.82523 83
1.99569 1.99978 -0.002507 2 Cu 2.82523 129
0 1.99816 2.58178 1 Sm 3.26469 153
-1.99569 -0.001628 -2.58428 1 Sm 3.26517 5
1.99569 -0.001628 -2.58428 1 Sm 3.26517 84
0 -2.00141 2.58178 1 Sm 3.26668 103
-3.99138 0 0 2 Cu 3.99138 61
3.99138 0 0 2 Cu 3.99138 144
0 -3.99957 0 2 Cu 3.99957 108
0 3.99957 0 2 Cu 3.99957 152
-3.99138 -1.9971 -1.55166 3 As 4.72516 1
3.99138 -1.9971 -1.55166 3 As 4.72516 69
-3.99138 2.00247 -1.55166 3 As 4.72743 38
3.99138 2.00247 -1.55166 3 As 4.72743 116
-1.99569 -3.99688 1.54915 3 As 4.72839 22
1.99569 -3.99688 1.54915 3 As 4.72839 105
-1.99569 4.00226 1.54915 3 As 4.73294 53
1.99569 4.00226 1.54915 3 As 4.73294 149
0 0.090438 4.97764 3 As 4.97846 156
0 -0.228343 -5.01901 3 As 5.0242 81
-3.99138 1.99816 2.58178 1 Sm 5.15648 57
3.99138 1.99816 2.58178 1 Sm 5.15648 141
-3.99138 -2.00141 2.58178 1 Sm 5.15774 20
3.99138 -2.00141 2.58178 1 Sm 5.15774 95
-1.99569 3.99794 -2.58428 1 Sm 5.16186 42
1.99569 3.99794 -2.58428 1 Sm 5.16186 130
-1.99569 -4.0012 -2.58428 1 Sm 5.16439 11
1.99569 -4.0012 -2.58428 1 Sm 5.16439 90
-3.99138 -3.99957 0 2 Cu 5.65045 25
-3.99138 3.99957 0 2 Cu 5.65045 56
3.99138 -3.99957 0 2 Cu 5.65045 98
3.99138 3.99957 0 2 Cu 5.65045 140
-1.99569 1.77144 5.0165 3 As 5.68208 54
1.99569 1.77144 5.0165 3 As 5.68208 150
-1.99569 -1.90935 -4.98015 3 As 5.69475 3
1.99569 -1.90935 -4.98015 3 As 5.69475 82
-1.99569 2.09022 -4.98015 3 As 5.75792 40
1.99569 2.09022 -4.98015 3 As 5.75792 128
-1.99569 -2.22813 5.0165 3 As 5.8406 19
1.99569 -2.22813 5.0165 3 As 5.8406 102
-5.98706 0.002688 1.54915 3 As 6.18424 66
5.98706 0.002688 1.54915 3 As 6.18424 142
0 -5.99666 -1.55166 3 As 6.19416 86
0 6.00204 -1.55166 3 As 6.19937 122
0 3.77122 -5.01901 3 As 6.27794 127
-5.98706 -1.99978 -0.002507 2 Cu 6.31222 15
-5.98706 1.99978 -0.002507 2 Cu 6.31222 47
5.98706 -1.99978 -0.002507 2 Cu 6.31222 72
5.98706 1.99978 -0.002507 2 Cu 6.31222 119
-1.99569 -5.99935 -0.002507 2 Cu 6.32258 10
-1.99569 5.99935 -0.002507 2 Cu 6.32258 36
1.99569 -5.99935 -0.002507 2 Cu 6.32258 89
1.99569 5.99935 -0.002507 2 Cu 6.32258 124
0 -3.90913 4.97764 3 As 6.32915 107
-3.99138 0.090438 4.97764 3 As 6.38092 60
3.99138 0.090438 4.97764 3 As 6.38092 143
-3.99138 -0.228343 -5.01901 3 As 6.41667 2
3.99138 -0.228343 -5.01901 3 As 6.41667 70
0 4.09001 4.97764 3 As 6.44244 151
-5.98706 -0.001628 -2.58428 1 Sm 6.521 16
5.98706 -0.001628 -2.58428 1 Sm 6.521 73
0 5.99772 2.58178 1 Sm 6.5298 148
0 -6.00098 2.58178 1 Sm 6.53279 109
0 -4.22791 -5.01901 3 As 6.56244 87
-5.98706 -3.99688 1.54915 3 As 7.36341 32
5.98706 -3.99688 1.54915 3 As 7.36341 96
-5.98706 4.00226 1.54915 3 As 7.36633 62
5.98706 4.00226 1.54915 3 As 7.36633 137
-3.99138 -5.99666 -1.55166 3 As 7.36877 7
3.99138 -5.99666 -1.55166 3 As 7.36877 75
-3.99138 6.00204 -1.55166 3 As 7.37314 34
3.99138 6.00204 -1.55166 3 As 7.37314 114
-3.99138 3.77122 -5.01901 3 As 7.43933 39
3.99138 3.77122 -5.01901 3 As 7.43933 117
-3.99138 -3.90913 4.97764 3 As 7.4826 24
3.99138 -3.90913 4.97764 3 As 7.4826 97
-3.99138 4.09001 4.97764 3 As 7.57866 55
3.99138 4.09001 4.97764 3 As 7.57866 139
-5.98706 3.99794 -2.58428 1 Sm 7.64899 48
5.98706 3.99794 -2.58428 1 Sm 7.64899 120
-5.98706 -4.0012 -2.58428 1 Sm 7.65069 18
5.98706 -4.0012 -2.58428 1 Sm 7.65069 78
-3.99138 5.99772 2.58178 1 Sm 7.65306 52
3.99138 5.99772 2.58178 1 Sm 7.65306 136
-3.99138 -6.00098 2.58178 1 Sm 7.65561 26
3.99138 -6.00098 2.58178 1 Sm 7.65561 99
-3.99138 -4.22791 -5.01901 3 As 7.68093 8
3.99138 -4.22791 -5.01901 3 As 7.68093 76
0 1.77122 -7.55367 1 Sm 7.75855 131
-1.99569 -0.228567 7.55116 1 Sm 7.81377 21
1.99569 -0.228567 7.55116 1 Sm 7.81377 104
0 -2.22835 -7.55367 1 Sm 7.8755 85
-1.99569 5.77101 5.0165 3 As 7.90269 50
1.99569 5.77101 5.0165 3 As 7.90269 146
-1.99569 -5.90891 -4.98015 3 As 7.98122 9
1.99569 -5.90891 -4.98015 3 As 7.98122 88
-7.98275 0 0 2 Cu 7.98275 67
7.98275 0 0 2 Cu 7.98275 134
0 -7.99914 0 2 Cu 7.99914 112
0 7.99914 0 2 Cu 7.99914 147
-5.98706 1.77144 5.0165 3 As 8.00926 63
5.98706 1.77144 5.0165 3 As 8.00926 138
-5.98706 -1.90935 -4.98015 3 As 8.01825 14
5.98706 -1.90935 -4.98015 3 As 8.01825 71
-5.98706 2.09022 -4.98015 3 As 8.06324 46
5.98706 2.09022 -4.98015 3 As 8.06324 118
-1.99569 6.08979 -4.98015 3 As 8.11604 35
1.99569 6.08979 -4.98015 3 As 8.11604 123
-5.98706 -2.22813 5.0165 3 As 8.12248 30
5.98706 -2.22813 5.0165 3 As 8.12248 94
-1.99569 -6.22769 5.0165 3 As 8.2421 23
1.99569 -6.22769 5.0165 3 As 8.2421 106
-7.98275 -1.9971 -1.55166 3 As 8.37379 13
7.98275 -1.9971 -1.55166 3 As 8.37379 68
-7.98275 2.00247 -1.55166 3 As 8.37507 45
7.98275 2.00247 -1.55166 3 As 8.37507 113
-1.99569 -7.99645 1.54915 3 As 8.38605 28
1.99569 -7.99645 1.54915 3 As 8.38605 111
-1.99569 8.00182 1.54915 3 As 8.39118 49
1.99569 8.00182 1.54915 3 As 8.39118 145
-5.98706 -5.99935 -0.002507 2 Cu 8.47568 17
-5.98706 5.99935 -0.002507 2 Cu 8.47568 44
5.98706 -5.99935 -0.002507 2 Cu 8.47568 77
5.98706 5.99935 -0.002507 2 Cu 8.47568 115
-7.98275 1.99816 2.58178 1 Sm 8.62453 65
7.98275 1.99816 2.58178 1 Sm 8.62453 133
-7.98275 -2.00141 2.58178 1 Sm 8.62529 31
7.98275 -2.00141 2.58178 1 Sm 8.62529 92
-1.99569 7.99751 -2.58428 1 Sm 8.63837 37
1.99569 7.99751 -2.58428 1 Sm 8.63837 125
-1.99569 -8.00076 -2.58428 1 Sm 8.64138 12
1.99569 -8.00076 -2.58428 1 Sm 8.64138 91
-1.99569 3.771 7.55116 1 Sm 8.67314 58
1.99569 3.771 7.55116 1 Sm 8.67314 154
0 -0.23869 8.69968 4 O 8.70295 101
0 -0.228299 -8.71159 4 O 8.71458 79
-3.99138 1.77122 -7.55367 1 Sm 8.72504 43
3.99138 1.77122 -7.55367 1 Sm 8.72504 121
-3.99138 -2.22835 -7.55367 1 Sm 8.82919 6
3.99138 -2.22835 -7.55367 1 Sm 8.82919 74
-1.99569 -4.22813 7.55116 1 Sm 8.88144 27
1.99569 -4.22813 7.55116 1 Sm 8.88144 110
-7.98275 -3.99957 0 2 Cu 8.92865 33
-7.98275 3.99957 0 2 Cu 8.92865 64
7.98275 -3.99957 0 2 Cu 8.92865 93
7.98275 3.99957 0 2 Cu 8.92865 132
-3.99138 -7.99914 0 2 Cu 8.93965 29
-3.99138 7.99914 0 2 Cu 8.93965 51
3.99138 -7.99914 0 2 Cu 8.93965 100
3.99138 7.99914 0 2 Cu 8.93965 135
END
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