|
2 | 2 | "cells": [ |
3 | 3 | { |
4 | 4 | "cell_type": "code", |
5 | | - "execution_count": 55, |
| 5 | + "execution_count": 1, |
6 | 6 | "id": "2b4ff90d-5a58-4202-ac2a-874168a2c6a2", |
7 | 7 | "metadata": {}, |
8 | 8 | "outputs": [], |
9 | 9 | "source": [ |
10 | | - "from easydiffraction.core.categories import CategoryItem, CategoryCollection\n", |
11 | | - "from easydiffraction.core.datablocks import DatablockItem, DatablockCollection\n", |
12 | | - "from easydiffraction.core.guards import RangeValidator, \\\n", |
13 | | - " ListValidator, RegexValidator\n", |
14 | | - "from easydiffraction.core.parameters import DescriptorStr, Parameter\n", |
15 | | - "from easydiffraction.crystallography.cif import CifHandler\n", |
16 | | - "from easydiffraction.utils.logging import log # type: ignore\n", |
17 | | - "from easydiffraction.sample_models.components.cell import Cell # type: ignore\n", |
18 | | - "from easydiffraction.sample_models.components.space_group import SpaceGroup # type: ignore\n", |
19 | | - "from easydiffraction.sample_models.collections.atom_sites import AtomSite, AtomSites # type: ignore\n", |
20 | | - "from easydiffraction.sample_models.sample_model import BaseSampleModel, SampleModel\n", |
21 | | - "from easydiffraction.sample_models.sample_models import SampleModels\n", |
22 | | - "from easydiffraction.analysis.collections.constraints import Constraint\n", |
23 | | - "from easydiffraction.analysis.collections.constraints import Constraints" |
| 10 | + "from easydiffraction.sample_models.components.cell import Cell\n", |
| 11 | + "from easydiffraction.sample_models.components.space_group import SpaceGroup\n", |
| 12 | + "from easydiffraction.sample_models.collections.atom_sites import AtomSite, AtomSites\n", |
| 13 | + "from easydiffraction.sample_models.sample_model import SampleModel\n", |
| 14 | + "from easydiffraction.sample_models.sample_models import SampleModels" |
24 | 15 | ] |
25 | 16 | }, |
26 | 17 | { |
27 | 18 | "cell_type": "code", |
28 | | - "execution_count": 56, |
| 19 | + "execution_count": 2, |
29 | 20 | "id": "1100c5b2-e00c-4513-bd2e-e30742d47e67", |
30 | 21 | "metadata": {}, |
31 | 22 | "outputs": [], |
32 | 23 | "source": [ |
33 | 24 | "from easydiffraction.utils.logging import Logger\n", |
34 | 25 | "\n", |
35 | 26 | "Logger.configure(\n", |
36 | | - " level=Logger.Level.INFO,\n", |
| 27 | + " level=Logger.Level.DEBUG,\n", |
37 | 28 | " mode=Logger.Mode.COMPACT,\n", |
38 | 29 | " reaction=Logger.Reaction.WARN,\n", |
39 | 30 | ")" |
40 | 31 | ] |
41 | 32 | }, |
42 | 33 | { |
43 | 34 | "cell_type": "code", |
44 | | - "execution_count": 57, |
| 35 | + "execution_count": 3, |
45 | 36 | "id": "a1a30af4-91c9-4015-9c96-a571fd1a711a", |
46 | 37 | "metadata": { |
47 | 38 | "scrolled": true |
48 | 39 | }, |
49 | | - "outputs": [], |
| 40 | + "outputs": [ |
| 41 | + { |
| 42 | + "name": "stdout", |
| 43 | + "output_type": "stream", |
| 44 | + "text": [ |
| 45 | + "\u001b[32mDEBUG \u001b[0m Setting \u001b[1m<\u001b[0m\u001b[1;95mlabel\u001b[0m\u001b[1m>\u001b[0m to validated \u001b[32m'La'\u001b[0m. \n", |
| 46 | + "\u001b[32mDEBUG \u001b[0m Setting \u001b[1m<\u001b[0m\u001b[1;95mtype_symbol\u001b[0m\u001b[1m>\u001b[0m to validated \u001b[32m'La'\u001b[0m. \n", |
| 47 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mfract_x\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 48 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mfract_y\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 49 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mfract_z\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 50 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mwyckoff_letter\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[32m'a'\u001b[0m. \n", |
| 51 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95moccupancy\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m1.0\u001b[0m. \n", |
| 52 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mb_iso\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 53 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95madp_type\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[32m'Biso'\u001b[0m. \n" |
| 54 | + ] |
| 55 | + } |
| 56 | + ], |
50 | 57 | "source": [ |
51 | 58 | "s1 = AtomSite(label='La', type_symbol='La')" |
52 | 59 | ] |
53 | 60 | }, |
54 | 61 | { |
55 | 62 | "cell_type": "code", |
56 | | - "execution_count": 58, |
| 63 | + "execution_count": 4, |
57 | 64 | "id": "5f8217f7-e8cf-4202-8369-ced7438657f2", |
58 | 65 | "metadata": {}, |
59 | | - "outputs": [], |
| 66 | + "outputs": [ |
| 67 | + { |
| 68 | + "name": "stdout", |
| 69 | + "output_type": "stream", |
| 70 | + "text": [ |
| 71 | + "\u001b[32mDEBUG \u001b[0m Setting \u001b[1m<\u001b[0m\u001b[1;95matom_site.La.fract_x\u001b[0m\u001b[1m>\u001b[0m to validated \u001b[1;36m1.234\u001b[0m. \n" |
| 72 | + ] |
| 73 | + } |
| 74 | + ], |
60 | 75 | "source": [ |
61 | 76 | "s1.fract_x.value = 1.234" |
62 | 77 | ] |
63 | 78 | }, |
64 | 79 | { |
65 | 80 | "cell_type": "code", |
66 | | - "execution_count": 59, |
| 81 | + "execution_count": 5, |
67 | 82 | "id": "4c9cf2fe-7f72-4b9d-a574-5eb8c40223c4", |
68 | 83 | "metadata": {}, |
69 | 84 | "outputs": [ |
70 | 85 | { |
71 | 86 | "name": "stdout", |
72 | 87 | "output_type": "stream", |
73 | 88 | "text": [ |
74 | | - "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.La.fract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'xyz'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. \n" |
| 89 | + "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.La.fract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'xyz'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. Keeping current \u001b[1;36m1.234\u001b[0m. \n" |
75 | 90 | ] |
76 | 91 | } |
77 | 92 | ], |
|
81 | 96 | }, |
82 | 97 | { |
83 | 98 | "cell_type": "code", |
84 | | - "execution_count": 60, |
| 99 | + "execution_count": 6, |
85 | 100 | "id": "cba23ca5-a865-428b-b1c8-90e38787e593", |
86 | 101 | "metadata": {}, |
87 | 102 | "outputs": [ |
88 | 103 | { |
89 | 104 | "name": "stdout", |
90 | 105 | "output_type": "stream", |
91 | 106 | "text": [ |
92 | | - "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.La.fract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'qwe'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. \n" |
| 107 | + "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.La.fract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'qwe'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. Keeping current \u001b[1;36m1.234\u001b[0m. \n" |
93 | 108 | ] |
94 | 109 | } |
95 | 110 | ], |
|
99 | 114 | }, |
100 | 115 | { |
101 | 116 | "cell_type": "code", |
102 | | - "execution_count": 61, |
| 117 | + "execution_count": 7, |
103 | 118 | "id": "3ba30971-177b-40e4-b477-e79a00341f87", |
104 | 119 | "metadata": {}, |
105 | 120 | "outputs": [ |
106 | 121 | { |
107 | 122 | "name": "stdout", |
108 | 123 | "output_type": "stream", |
109 | 124 | "text": [ |
110 | | - "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95mfract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'uuuu'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. \n" |
| 125 | + "\u001b[32mDEBUG \u001b[0m Setting \u001b[1m<\u001b[0m\u001b[1;95mlabel\u001b[0m\u001b[1m>\u001b[0m to validated \u001b[32m'Si'\u001b[0m. \n", |
| 126 | + "\u001b[32mDEBUG \u001b[0m Setting \u001b[1m<\u001b[0m\u001b[1;95mtype_symbol\u001b[0m\u001b[1m>\u001b[0m to validated \u001b[32m'Si'\u001b[0m. \n", |
| 127 | + "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95mfract_x\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'uuuu'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not float. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 128 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mfract_y\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 129 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mfract_z\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 130 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mwyckoff_letter\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[32m'a'\u001b[0m. \n", |
| 131 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95moccupancy\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m1.0\u001b[0m. \n", |
| 132 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mb_iso\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m0.0\u001b[0m. \n", |
| 133 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95madp_type\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[32m'Biso'\u001b[0m. \n" |
111 | 134 | ] |
112 | 135 | } |
113 | 136 | ], |
|
117 | 140 | }, |
118 | 141 | { |
119 | 142 | "cell_type": "code", |
120 | | - "execution_count": 62, |
| 143 | + "execution_count": 8, |
121 | 144 | "id": "992966e7-6bb7-4bc7-bbff-80acfea6fd2c", |
122 | 145 | "metadata": {}, |
123 | 146 | "outputs": [], |
|
127 | 150 | }, |
128 | 151 | { |
129 | 152 | "cell_type": "code", |
130 | | - "execution_count": 63, |
| 153 | + "execution_count": 9, |
131 | 154 | "id": "50ef6ebd-097d-4df2-93dc-39243bdba6fd", |
132 | 155 | "metadata": {}, |
133 | 156 | "outputs": [ |
134 | 157 | { |
135 | 158 | "name": "stdout", |
136 | 159 | "output_type": "stream", |
137 | 160 | "text": [ |
138 | | - "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.Si.fract_x.free\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'abc'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not bool \n" |
| 161 | + "\u001b[33mWARNING \u001b[0m Type mismatch for \u001b[1m<\u001b[0m\u001b[1;95matom_site.Si.fract_x.free\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[32m'abc'\u001b[0m \u001b[1m(\u001b[0mstr\u001b[1m)\u001b[0m is not bool. \n" |
139 | 162 | ] |
140 | 163 | } |
141 | 164 | ], |
|
145 | 168 | }, |
146 | 169 | { |
147 | 170 | "cell_type": "code", |
148 | | - "execution_count": 64, |
| 171 | + "execution_count": 10, |
149 | 172 | "id": "2c46e9ca-f68d-4b71-b783-6660f357322c", |
150 | 173 | "metadata": {}, |
151 | | - "outputs": [], |
| 174 | + "outputs": [ |
| 175 | + { |
| 176 | + "name": "stdout", |
| 177 | + "output_type": "stream", |
| 178 | + "text": [ |
| 179 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mlength_a\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 180 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mlength_b\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 181 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mlength_c\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 182 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_alpha\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n", |
| 183 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_beta\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n", |
| 184 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_gamma\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n" |
| 185 | + ] |
| 186 | + } |
| 187 | + ], |
152 | 188 | "source": [ |
153 | 189 | "c = Cell()" |
154 | 190 | ] |
155 | 191 | }, |
156 | 192 | { |
157 | 193 | "cell_type": "code", |
158 | | - "execution_count": 65, |
| 194 | + "execution_count": 11, |
159 | 195 | "id": "8e3fee6f-dc71-49a0-bf67-6f85f4ba83cd", |
160 | 196 | "metadata": {}, |
161 | 197 | "outputs": [ |
162 | 198 | { |
163 | 199 | "name": "stdout", |
164 | 200 | "output_type": "stream", |
165 | 201 | "text": [ |
166 | | - "\u001b[33mWARNING \u001b[0m Value mismatch for \u001b[1m<\u001b[0m\u001b[1;95mlength_b\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[1;36m-8.8\u001b[0m is outside of \u001b[1m[\u001b[0m\u001b[1;36m0\u001b[0m, \u001b[1;36m1000\u001b[0m\u001b[1m]\u001b[0m. \n" |
| 202 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mlength_a\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 203 | + "\u001b[33mWARNING \u001b[0m Value mismatch for \u001b[1m<\u001b[0m\u001b[1;95mlength_b\u001b[0m\u001b[1m>\u001b[0m. Provided \u001b[1;36m-8.8\u001b[0m is outside of \u001b[1m[\u001b[0m\u001b[1;36m0\u001b[0m, \u001b[1;36m1000\u001b[0m\u001b[1m]\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 204 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mlength_c\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m10.0\u001b[0m. \n", |
| 205 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_alpha\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n", |
| 206 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_beta\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n", |
| 207 | + "\u001b[32mDEBUG \u001b[0m No value provided for \u001b[1m<\u001b[0m\u001b[1;95mangle_gamma\u001b[0m\u001b[1m>\u001b[0m. Using default \u001b[1;36m90.0\u001b[0m. \n" |
167 | 208 | ] |
168 | 209 | } |
169 | 210 | ], |
|
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