Page History
...
- errors in generation of lattice,
- errors in generation of look-up table,
- errors in indexing - association of data with look-up table,
- wrong lattice model.
A few cross-check crosschecks are presented below in order to address this issue.
Lattice
Triclinic crystal cell primitive vectors
We use a few methods from pyimgalgos.FiberIndexing to generate lattice:
...
| Code Block |
|---|
# Triclinic crystal cell parameters: # a = 18.55 A # b = 27.19 A # c = 4.86 A # alpha = 90.00 deg # beta = 90.00 deg # gamma = 78.47 deg # 3-d space primitive vectors: # a1 = (18.55, 0.0, 0.0) # a2 = (-5.435623727109098, 26.645523961582906, 0.0) # a3 = (0.0, 0.0, 4.8601) |
Reciprocal space primitive vectors
b1, b2, b3 = reciprocal_from_bravias(a1, a2, a3) - converts 3-d primitive vectors to reciprocal space primitive vectors.
...
| Code Block |
|---|
# reciprocal space primitive vectors: # b1 = [ 0.05390836 0.01099718 -0. ] # b2 = [ 0. 0.03752976 0. ] # b3 = [ 0. -0. 0.20575708] |
Lattice generator and test
Then, call to method
x, y, z, r, h, k, l = lattice(b1, b2, b3, hmax, kmax, lmax, cdtype)
...
| Code Block |
|---|
h.shape: (13, 9)
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
row: -4 -3 -2 -1 0 1 2 3 4
k.shape: (13, 9)
row: -6 -6 -6 -6 -6 -6 -6 -6 -6
row: -5 -5 -5 -5 -5 -5 -5 -5 -5
row: -4 -4 -4 -4 -4 -4 -4 -4 -4
row: -3 -3 -3 -3 -3 -3 -3 -3 -3
row: -2 -2 -2 -2 -2 -2 -2 -2 -2
row: -1 -1 -1 -1 -1 -1 -1 -1 -1
row: 0 0 0 0 0 0 0 0 0
row: 1 1 1 1 1 1 1 1 1
row: 2 2 2 2 2 2 2 2 2
row: 3 3 3 3 3 3 3 3 3
row: 4 4 4 4 4 4 4 4 4
row: 5 5 5 5 5 5 5 5 5
row: 6 6 6 6 6 6 6 6 6
l.shape: (13, 9)
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
row: 0 0 0 0 0 0 0 0 0
x coords.shape: (13, 9)
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
row: -0.2156 -0.1617 -0.1078 -0.0539 0.0000 0.0539 0.1078 0.1617 0.2156
y coords.shape: (13, 9)
row: -0.2692 -0.2582 -0.2472 -0.2362 -0.2252 -0.2142 -0.2032 -0.1922 -0.1812
row: -0.2316 -0.2206 -0.2096 -0.1986 -0.1876 -0.1767 -0.1657 -0.1547 -0.1437
row: -0.1941 -0.1831 -0.1721 -0.1611 -0.1501 -0.1391 -0.1281 -0.1171 -0.1061
row: -0.1566 -0.1456 -0.1346 -0.1236 -0.1126 -0.1016 -0.0906 -0.0796 -0.0686
row: -0.1190 -0.1081 -0.0971 -0.0861 -0.0751 -0.0641 -0.0531 -0.0421 -0.0311
row: -0.0815 -0.0705 -0.0595 -0.0485 -0.0375 -0.0265 -0.0155 -0.0045 0.0065
row: -0.0440 -0.0330 -0.0220 -0.0110 0.0000 0.0110 0.0220 0.0330 0.0440
row: -0.0065 0.0045 0.0155 0.0265 0.0375 0.0485 0.0595 0.0705 0.0815
row: 0.0311 0.0421 0.0531 0.0641 0.0751 0.0861 0.0971 0.1081 0.1190
row: 0.0686 0.0796 0.0906 0.1016 0.1126 0.1236 0.1346 0.1456 0.1566
row: 0.1061 0.1171 0.1281 0.1391 0.1501 0.1611 0.1721 0.1831 0.1941
row: 0.1437 0.1547 0.1657 0.1767 0.1876 0.1986 0.2096 0.2206 0.2316
row: 0.1812 0.1922 0.2032 0.2142 0.2252 0.2362 0.2472 0.2582 0.2692
z coords.shape: (13, 9)
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
row: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
r of lattice nodes.shape: (13, 9)
row: 0.3449 0.3046 0.2697 0.2423 0.2252 0.2209 0.2300 0.2512 0.2817
row: 0.3165 0.2736 0.2357 0.2058 0.1876 0.1847 0.1977 0.2238 0.2591
row: 0.2901 0.2443 0.2031 0.1699 0.1501 0.1492 0.1675 0.1997 0.2403
row: 0.2665 0.2176 0.1724 0.1348 0.1126 0.1150 0.1408 0.1803 0.2263
row: 0.2463 0.1945 0.1451 0.1015 0.0751 0.0837 0.1202 0.1671 0.2179
row: 0.2305 0.1764 0.1232 0.0725 0.0375 0.0601 0.1089 0.1618 0.2157
row: 0.2201 0.1651 0.1100 0.0550 0.0000 0.0550 0.1100 0.1651 0.2201
row: 0.2157 0.1618 0.1089 0.0601 0.0375 0.0725 0.1232 0.1764 0.2305
row: 0.2179 0.1671 0.1202 0.0837 0.0751 0.1015 0.1451 0.1945 0.2463
row: 0.2263 0.1803 0.1408 0.1150 0.1126 0.1348 0.1724 0.2176 0.2665
row: 0.2403 0.1997 0.1675 0.1492 0.1501 0.1699 0.2031 0.2443 0.2901
row: 0.2591 0.2238 0.1977 0.1847 0.1876 0.2058 0.2357 0.2736 0.3165
row: 0.2817 0.2512 0.2300 0.2209 0.2252 0.2423 0.2697 0.3046 0.3449 |
Rotation of the crystal lattice
| Code Block |
|---|
xrot1, yrot1 = rotation(x, y, omega_deg) xrot2, zrot2 = rotation(xrot1, z, beta_deg) |
| Code Block |
|---|
xrot2.shape: (13, 9)
row: -0.0504 -0.0106 0.0292 0.0690 0.1088 0.1485 0.1883 0.2281 0.2679
row: -0.0685 -0.0287 0.0111 0.0508 0.0906 0.1304 0.1702 0.2100 0.2498
row: -0.0866 -0.0469 -0.0071 0.0327 0.0725 0.1123 0.1521 0.1919 0.2316
row: -0.1048 -0.0650 -0.0252 0.0146 0.0544 0.0942 0.1339 0.1737 0.2135
row: -0.1229 -0.0831 -0.0433 -0.0035 0.0363 0.0760 0.1158 0.1556 0.1954
row: -0.1410 -0.1012 -0.0614 -0.0217 0.0181 0.0579 0.0977 0.1375 0.1773
row: -0.1591 -0.1194 -0.0796 -0.0398 0.0000 0.0398 0.0796 0.1194 0.1591
row: -0.1773 -0.1375 -0.0977 -0.0579 -0.0181 0.0217 0.0614 0.1012 0.1410
row: -0.1954 -0.1556 -0.1158 -0.0760 -0.0363 0.0035 0.0433 0.0831 0.1229
row: -0.2135 -0.1737 -0.1339 -0.0942 -0.0544 -0.0146 0.0252 0.0650 0.1048
row: -0.2316 -0.1919 -0.1521 -0.1123 -0.0725 -0.0327 0.0071 0.0469 0.0866
row: -0.2498 -0.2100 -0.1702 -0.1304 -0.0906 -0.0508 -0.0111 0.0287 0.0685
row: -0.2679 -0.2281 -0.1883 -0.1485 -0.1088 -0.0690 -0.0292 0.0106 0.0504
yrot1.shape: (13, 9)
row: -0.3409 -0.3044 -0.2680 -0.2315 -0.1950 -0.1585 -0.1221 -0.0856 -0.0491
row: -0.3084 -0.2719 -0.2355 -0.1990 -0.1625 -0.1260 -0.0896 -0.0531 -0.0166
row: -0.2759 -0.2394 -0.2030 -0.1665 -0.1300 -0.0935 -0.0571 -0.0206 0.0159
row: -0.2434 -0.2069 -0.1705 -0.1340 -0.0975 -0.0610 -0.0245 0.0119 0.0484
row: -0.2109 -0.1744 -0.1380 -0.1015 -0.0650 -0.0285 0.0080 0.0444 0.0809
row: -0.1784 -0.1419 -0.1055 -0.0690 -0.0325 0.0040 0.0405 0.0769 0.1134
row: -0.1459 -0.1094 -0.0730 -0.0365 0.0000 0.0365 0.0730 0.1094 0.1459
row: -0.1134 -0.0769 -0.0405 -0.0040 0.0325 0.0690 0.1055 0.1419 0.1784
row: -0.0809 -0.0444 -0.0080 0.0285 0.0650 0.1015 0.1380 0.1744 0.2109
row: -0.0484 -0.0119 0.0245 0.0610 0.0975 0.1340 0.1705 0.2069 0.2434
row: -0.0159 0.0206 0.0571 0.0935 0.1300 0.1665 0.2030 0.2394 0.2759
row: 0.0166 0.0531 0.0896 0.1260 0.1625 0.1990 0.2355 0.2719 0.3084
row: 0.0491 0.0856 0.1221 0.1585 0.1950 0.2315 0.2680 0.3044 0.3409
zrot2.shape: (13, 9)
row: -0.0135 -0.0028 0.0078 0.0185 0.0291 0.0398 0.0505 0.0611 0.0718
row: -0.0184 -0.0077 0.0030 0.0136 0.0243 0.0349 0.0456 0.0563 0.0669
row: -0.0232 -0.0126 -0.0019 0.0088 0.0194 0.0301 0.0407 0.0514 0.0621
row: -0.0281 -0.0174 -0.0068 0.0039 0.0146 0.0252 0.0359 0.0466 0.0572
row: -0.0329 -0.0223 -0.0116 -0.0009 0.0097 0.0204 0.0310 0.0417 0.0524
row: -0.0378 -0.0271 -0.0165 -0.0058 0.0049 0.0155 0.0262 0.0368 0.0475
row: -0.0426 -0.0320 -0.0213 -0.0107 0.0000 0.0107 0.0213 0.0320 0.0426
row: -0.0475 -0.0368 -0.0262 -0.0155 -0.0049 0.0058 0.0165 0.0271 0.0378
row: -0.0524 -0.0417 -0.0310 -0.0204 -0.0097 0.0009 0.0116 0.0223 0.0329
row: -0.0572 -0.0466 -0.0359 -0.0252 -0.0146 -0.0039 0.0068 0.0174 0.0281
row: -0.0621 -0.0514 -0.0407 -0.0301 -0.0194 -0.0088 0.0019 0.0126 0.0232
row: -0.0669 -0.0563 -0.0456 -0.0349 -0.0243 -0.0136 -0.0030 0.0077 0.0184
row: -0.0718 -0.0611 -0.0505 -0.0398 -0.0291 -0.0185 -0.0078 0.0028 0.0135 |
Overview
Content Tools