1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
|
Using the XrayDB xraydb.sqlite
=====================================
All the data for the X-ray database is held in the SQLite3 file
``xraydb.sqlite``. To use with SQLite, this file is all you need. While
many programs and languages can access SQLite files, basic
usage with the ``sqlite3`` program (available from Windows, Mac OS X, and
Linux) can be as simple as::
system~> sqlite3 xraydb.sqlite
sqlite> .headers on
sqlite> select * from elements where atomic_number=47;
atomic_number|element|name|molar_mass|density
47|Ag|silver|107.868|10.48
That is, you can retrieve the data using standard SQL queries built-in to
SQLite. Of course, the expectation is that you'd want to use this database
within a programming environment. Currently, wrappers exist only for
Python.
Overall Database Schema
-----------------------------
The schema for the SQLite3 database describes where data is held in the
database, and how to access it. The schema for the current version (4)
looks like this::
Table Version (id integer primary key,
tag text,
date text,
notes text);
Table elements (atomic_number integer primary key,
element text,
name text,
molar_mass real,
density real);
Table xray_levels (id integer primary key,
element text,
iupac_symbol text,
absorption_edge real,
fluorescence_yield real,
jump_ratio real);
Table xray_transitions (id integer primary key,
element text,
iupac_symbol text,
siegbahn_symbol text,
initial_level text,
final_level text,
emission_energy real,
intensity real);
Table Coster_Kronig (id integer primary key,
element text,
initial_level text,
final_level text,
transition_probability real,
total_transition_probability real);
Table photoabsorption (id integer primary key,
element text,
log_energy text,
log_photoabsorption text,
log_photoabsorption_spline text);
Table scattering (id integer primary key,
element text,
log_energy text,
log_coherent_scatter text,
log_coherent_scatter_spline text,
log_incoherent_scatter text,
log_incoherent_scatter_spline text);
Table Waasmaier (id integer primary key,
atomic_number integer,
element text,
ion text,
offset real,
scale text,
exponents text);
Table KeskiRahkonen_Krause (id integer primary key,
atomic_number integer,
element text,
edge text,
width float);
Table Krause_Oliver (id integer primary key,
atomic_number integer,
element text,
edge text,
width float);
Table corelevel_widths (id integer primary key,
atomic_number integer,
element text,
edge text,
width float);
Table Chantler (id integer primary key,
element text,
sigma_mu real,
mue_f2 real,
density real,
corr_henke float,
corr_cl35 float,
corr_nucl float,
energy text,
f1 text,
f2 text,
mu_photo text,
mu_incoh text,
mu_total text);
More details for each table are given below.
.. note::
in the tables below the type of `json array` means that arrays of numerical
data are stored in the database as text of JSON-encoded arrays.
.. _db_version_sect:
Version Table
-----------------
The `Version` table holds data about the revisions to the database file
itself. Each row represents a single revision.
.. index:: DB Table of Database Versions
.. _db_version_table:
DB Table of Database Versions
+----------------------+--------------+---------------------------------------+
| Column | Type | Description |
+======================+==============+=======================================+
| id | integer | counter (primary tag) |
+----------------------+--------------+---------------------------------------+
| tag | text | version name |
+----------------------+--------------+---------------------------------------+
| date | text | date string |
+----------------------+--------------+---------------------------------------+
| notes | text | notes on changes for version |
+----------------------+--------------+---------------------------------------+
.. _db_elements_sect:
Elements Table
-----------------
The `elements` table holds basic data about each element. Each row
represents an element.
.. index:: DB Table of Basic Properties of the Elements
.. _db_elements_table:
DB Table of Basic Properties of the Elements
+----------------------+--------------+---------------------------------------+
| Column | Type | Description |
+======================+==============+=======================================+
| atomic_number | integer | Atomic Number, Z |
+----------------------+--------------+---------------------------------------+
| element | text | Atomic symbol |
+----------------------+--------------+---------------------------------------+
| name | text | English name of element |
+----------------------+--------------+---------------------------------------+
| molar_mass | float | Atomic mass in AMU |
+----------------------+--------------+---------------------------------------+
| density | float | Density of pure element (gr/cm^3) |
+----------------------+--------------+---------------------------------------+
.. _db_xray_levels_sect:
Xray_Levels Table
------------------------
The `xray_levels` table holds data for electronic levels of atoms. Each row
represents a core electronic level.
.. index:: DB Table of X-ray Levels
.. _db_xray_levels_table:
DB Table of X-ray and core electronic levels. `fluorescence yield`
gives the probability of an empty level refilling by X-ray
fluorescence. The `jump ratio` is the ratio of values for photo-electric
cross section (that is, from :ref:`db_photoabsorption_sect`) 1 eV above
the absorption edge to that 1 eV below the absorption edge. See
:ref:`Table of X-ray Edges <xraydb-edge_table>`
+----------------------+--------------+---------------------------------------+
| Column | Type | Description |
+======================+==============+=======================================+
| id | integer | Index (primary key) |
+----------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+----------------------+--------------+---------------------------------------+
| iupac_symbol | text | IUPAC symbol for level ('K','L3',...) |
+----------------------+--------------+---------------------------------------+
| absorption_edge | float | binding energy for level (eV) |
+----------------------+--------------+---------------------------------------+
| fluorescence_yield | float | fluorescence yield (fraction) |
+----------------------+--------------+---------------------------------------+
| jump_ratio | float | ratio of mu_photo across edge |
+----------------------+--------------+---------------------------------------+
.. _db_xray_trans_sect:
Xray_Transitions Table
------------------------
The `xray_transitions` table holds data for transitions between electronic levels
of atoms. Each row represents a transition between two levels.
.. index:: DB Table of X-ray Transitions
.. _db_xray_trans_table:
DB Table of X-ray Transitions. Both IUPAC and Siegbahn symbols are given (see
:ref:`Table of X-ray emission lines <xraydb-lines_table>`), as
well as the initial and final levels. The `intensity` is the relative
intensity of the transition for a given `initial level`.
+----------------------+--------------+---------------------------------------+
| Column | Type | Description |
+======================+==============+=======================================+
| id | integer | Index (primary key) |
+----------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+----------------------+--------------+---------------------------------------+
| iupac_symbol | text | IUPAC symbol for transition |
+----------------------+--------------+---------------------------------------+
| siegbahn_symbol | text | Siegbahn symbol for transition |
+----------------------+--------------+---------------------------------------+
| initial_level | text | IUPAC symbol for initial level |
+----------------------+--------------+---------------------------------------+
| final_level | text | IUPAC symbol for final level |
+----------------------+--------------+---------------------------------------+
| emission_energy | float | fluorescence energy (eV) |
+----------------------+--------------+---------------------------------------+
| intensity | float | relative intensity for transition |
+----------------------+--------------+---------------------------------------+
.. _db_photoabsorption_sect:
Photoabsorption Table
------------------------
The `photoabsorption` table holds data for the photo-electric absorption
cross sections in cm^2/gr. Each row represents an element.
.. index:: DB Table of Photoabsorption Cross Sections
.. _db_photoabsorption_table:
DB Table of Photoabsorption Cross Sections. JSON-encoded arrays are held
for logs of energy, cross section, and cross section spline (second
derivative useful for spline interpolation).
+----------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+============================+==============+=======================================+
| id | integer | Index (primary key) |
+----------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+----------------------------+--------------+---------------------------------------+
| log_energy | json array | log of Energy values (eV) |
+----------------------------+--------------+---------------------------------------+
| log_photoabsorption | json array | log of cross section (cm^2/gr) |
+----------------------------+--------------+---------------------------------------+
| log_photoabsorption_spline | json array | log of cross section spline |
+----------------------------+--------------+---------------------------------------+
.. _db_scattering_sect:
Scattering Table
------------------------
The `scattering` table holds data for the coherent and incoherent X-ray scattering
cross sections, in cm^2/gr. Each row represents an element.
.. index:: DB Table of Coherent and Incoherent Scattering Cross Sections
.. _db_scattering_table:
DB Table of Coherent and Incoherent Scattering Cross Sections. JSON-encoded
arrays are held for logs of energy, cross section, and cross section spline
(second derivative useful for spline interpolation).
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| log_energy | json array | log of Energy values (eV) |
+-------------------------------+--------------+---------------------------------------+
| log_coherent_scatter | json array | log of cross section (cm^2/gr) |
+-------------------------------+--------------+---------------------------------------+
| log_coherent_scatter_spline | json array | log of cross section spline |
+-------------------------------+--------------+---------------------------------------+
| log_incoherent_scatter | json array | log of cross section (cm^2/gr) |
+-------------------------------+--------------+---------------------------------------+
| log_incoherent_scatter_spline | json array | log of cross section spline |
+-------------------------------+--------------+---------------------------------------+
.. _db_costerkronig_sect:
Coster_Kronig Table
------------------------
The `Coster_Kronig` table holds data for energy levels, partial and total
transition probabilities for the Coster-Kronig transitions (Auger processes
in which the empty core level is filled from an electron in a higher level
with the same principle quantum number). The partial probability describes
direct transitions, while the total probability includes cascade effects.
Each row represents a transition.
.. index:: DB Table of Coster-Kronig Transitions
.. _db_costerkronig_table:
DB Table of Coster-Kronig Transitions.
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| initial_level | text | IUPAC symbol for initial level |
+-------------------------------+--------------+---------------------------------------+
| final_level | text | IUPAC symbol for final level |
+-------------------------------+--------------+---------------------------------------+
| transition_probability | float | direct transition probability |
+-------------------------------+--------------+---------------------------------------+
| total_transition_probability | float | total transition probability |
+-------------------------------+--------------+---------------------------------------+
.. _db_waasmaier_sect:
Waasmaier Table
------------------------
The `Waasmaier` table holds data for calculating elastic X-ray scattering
factors :math:`f_0(k)`, from :cite:`Waasmaier_Kirfel`. The scattering
factor is unitless, and :math:`k=\sin(\theta)/\lambda` where :math:`\theta`
is the scattering angle and :math:`\lambda` is the X-ray wavelength.
available for many common ionic states for each element. Each row
represents an ion.
.. index:: DB Table of Elastic Scattering Cross Section Coefficients
.. _db_waasmaier_table:
DB Table of Elastic Scattering Cross Section Coefficients
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| atomic_number | integer | Atomic Number, Z |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| ion | text | symbol for element and ionization |
+-------------------------------+--------------+---------------------------------------+
| offset | float | offset value |
+-------------------------------+--------------+---------------------------------------+
| scale | json array | coefficients for calculation |
+-------------------------------+--------------+---------------------------------------+
| exponents | json array | coefficients for calculation |
+-------------------------------+--------------+---------------------------------------+
.. _db_keski_sect:
KeskiRahkonen_Krause Table
------------------------------
The `KeskiRahkonen_Krause` table holds data for energy widths of the core electronic
levels from :cite:`Keski_Krause`. Values are in eV, and each row represents an
energy level for an element.
.. index:: DB Table of Core Hole Widths
.. _db_keski_table:
DB Table of Core Hole Widths from Keski-Rahkonen and Krause
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| atomic_number | integer | Atomic Number, Z |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| edge | text | IUPAC symbol for energy level ('K') |
+-------------------------------+--------------+---------------------------------------+
| width | float | width of level (eV) |
+-------------------------------+--------------+---------------------------------------+
Krause_Oliver Table
------------------------------
The `Krause_Oliver` table holds data for energy widths of the core electronic
levels from :cite:`Krause_Oliver`. Values are in eV, and each row represents an
energy level for an element.
.. index:: DB Table of Core Hole Widths
.. _db_krause_table:
DB Table of Core Hole Widths from Krause and Oliver
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| atomic_number | integer | Atomic Number, Z |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| edge | text | IUPAC symbol for energy level ('K') |
+-------------------------------+--------------+---------------------------------------+
| width | float | width of level (eV) |
+-------------------------------+--------------+---------------------------------------+
Compton Energies Table
------------------------------
The `Compton_energies` table holds data for median (90 deg scattering) and mean
values of the energies of Compton scattered X-rays, and the mean values of the
Compton-scattered electrons as a function of incident X-ray energy. There is
only 1 row in this table, with all columns being json-encoded arrays of floats.
These values should be finely-spaced enough for linear interpolation
.. index:: DB Table of Compton Energies
.. _db_compton_table:
DB Table of Compton-scattered energies.
+---------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===========================+==============+=======================================+
| incident | json_array | Incident X-ray energies (eV) |
+---------------------------+--------------+---------------------------------------+
| xray_90deg | json_array | Median scattered X-ray energies (eV) |
+---------------------------+--------------+---------------------------------------+
| xray_mean | json_array | Mean scattered X-ray energies (eV) |
+---------------------------+--------------+---------------------------------------+
| electron_mean | json_array | Mean scattered electron energies (eV) |
+---------------------------+--------------+---------------------------------------+
.. _db_chantler_sect:
Chantler Table
------------------------------
The `Chantler` table holds data for resonant X-ray scattering factors
:math:`f'(E)` and :math:`f''(E)` as well as photo-electric absorption,
coherent, and incoherent scattering factors from :cite:`Chantler`. As
with other tables, scattering factors are unitless, and cross sections are
in cm^2/gr. Each row represents an element.
.. index:: DB Table of resonant scattering and mass attenuation coefficients from Chantler
.. _db_chantler_table:
DB Table of resonant scattering and mass attenuation coefficients from Chantler.
+-------------------------------+--------------+---------------------------------------+
| Column | Type | Description |
+===============================+==============+=======================================+
| id | integer | Index (primary key) |
+-------------------------------+--------------+---------------------------------------+
| element | text | Atomic symbol for element |
+-------------------------------+--------------+---------------------------------------+
| mue_f2 | float | factor to convert mu(E) to f''(E) |
+-------------------------------+--------------+---------------------------------------+
| density | float | atomic density (gr/cm^3) |
+-------------------------------+--------------+---------------------------------------+
| corr_henke | float | Henke correction to f`(E) |
+-------------------------------+--------------+---------------------------------------+
| corr_cl35 | float | Cromer-Liberman correction to f`(E) |
+-------------------------------+--------------+---------------------------------------+
| corr_nucl | float | nuclear correction to f`(E) |
+-------------------------------+--------------+---------------------------------------+
| energy | json array | energies for interpolation |
+-------------------------------+--------------+---------------------------------------+
| f1 | json array | f'(E) (e) |
+-------------------------------+--------------+---------------------------------------+
| f2 | json array | f''(E) (e) |
+-------------------------------+--------------+---------------------------------------+
| mu_photo | json array | photoabsorption mu(E) (cm^2/gr) |
+-------------------------------+--------------+---------------------------------------+
| mu_incoh | json array | incoherent scattering (cm^2/gr) |
+-------------------------------+--------------+---------------------------------------+
| mu_total | json array | total attenuation (cm^2/gr) |
+-------------------------------+--------------+---------------------------------------+
|
