@ccp-nc/crystvis-js 0.4.13

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Files changed (100) hide show
  1. package/.eslintrc.json +16 -0
  2. package/.github/workflows/test-mocha.yml +30 -0
  3. package/.vscode/settings.json +4 -0
  4. package/LICENSE +21 -0
  5. package/README.html +1127 -0
  6. package/README.md +76 -0
  7. package/demo/demo.css +30 -0
  8. package/demo/index.html +76 -0
  9. package/demo/main.js +143 -0
  10. package/docs/.nojekyll +0 -0
  11. package/docs-tutorials/Events.md +57 -0
  12. package/docs-tutorials/Queries.md +50 -0
  13. package/fonts/Rubik/OFL.txt +93 -0
  14. package/fonts/Rubik/README.txt +77 -0
  15. package/fonts/Rubik/Rubik-Italic-VariableFont_wght.ttf +0 -0
  16. package/fonts/Rubik/Rubik-VariableFont_wght.ttf +0 -0
  17. package/fonts/Rubik/static/Rubik-Black.ttf +0 -0
  18. package/fonts/Rubik/static/Rubik-BlackItalic.ttf +0 -0
  19. package/fonts/Rubik/static/Rubik-Bold.ttf +0 -0
  20. package/fonts/Rubik/static/Rubik-BoldItalic.ttf +0 -0
  21. package/fonts/Rubik/static/Rubik-ExtraBold.ttf +0 -0
  22. package/fonts/Rubik/static/Rubik-ExtraBoldItalic.ttf +0 -0
  23. package/fonts/Rubik/static/Rubik-Italic.ttf +0 -0
  24. package/fonts/Rubik/static/Rubik-Light.ttf +0 -0
  25. package/fonts/Rubik/static/Rubik-LightItalic.ttf +0 -0
  26. package/fonts/Rubik/static/Rubik-Medium.ttf +0 -0
  27. package/fonts/Rubik/static/Rubik-MediumItalic.ttf +0 -0
  28. package/fonts/Rubik/static/Rubik-Regular.ttf +0 -0
  29. package/fonts/Rubik/static/Rubik-SemiBold.ttf +0 -0
  30. package/fonts/Rubik/static/Rubik-SemiBoldItalic.ttf +0 -0
  31. package/index.html +25 -0
  32. package/index.js +11 -0
  33. package/jsconf.json +14 -0
  34. package/lib/assets/fonts/Rubik-Medium.fnt +297 -0
  35. package/lib/assets/fonts/Rubik-Medium.png +0 -0
  36. package/lib/assets/fonts/bmpfonts.in.js +16 -0
  37. package/lib/assets/fonts/bmpfonts.js +9 -0
  38. package/lib/assets/fonts/font.js +82 -0
  39. package/lib/assets/fonts/index.js +14 -0
  40. package/lib/assets/fonts/threebmfont.js +28 -0
  41. package/lib/data.js +125 -0
  42. package/lib/formats/cell.js +114 -0
  43. package/lib/formats/cif.js +22 -0
  44. package/lib/formats/magres.js +337 -0
  45. package/lib/formats/xyz.js +124 -0
  46. package/lib/loader.js +87 -0
  47. package/lib/model.js +2076 -0
  48. package/lib/modelview.js +382 -0
  49. package/lib/nmrdata.js +2898 -0
  50. package/lib/orbit.js +1233 -0
  51. package/lib/primitives/atoms.js +261 -0
  52. package/lib/primitives/cell.js +160 -0
  53. package/lib/primitives/dither.js +156 -0
  54. package/lib/primitives/ellipsoid.js +183 -0
  55. package/lib/primitives/geometries.js +20 -0
  56. package/lib/primitives/index.js +48 -0
  57. package/lib/primitives/isosurface.js +171 -0
  58. package/lib/primitives/shapes.js +100 -0
  59. package/lib/primitives/sprites.js +172 -0
  60. package/lib/query.js +158 -0
  61. package/lib/render.js +440 -0
  62. package/lib/selbox.js +361 -0
  63. package/lib/shaders/aura.frag +26 -0
  64. package/lib/shaders/aura.vert +37 -0
  65. package/lib/shaders/dither.frag +42 -0
  66. package/lib/shaders/dither.vert +8 -0
  67. package/lib/shaders/index.in.js +17 -0
  68. package/lib/shaders/index.js +25 -0
  69. package/lib/shaders/msdf300.frag +25 -0
  70. package/lib/shaders/msdf300.vert +45 -0
  71. package/lib/tensor.js +227 -0
  72. package/lib/utils.js +168 -0
  73. package/lib/visualizer.js +480 -0
  74. package/package.json +106 -0
  75. package/scripts/build-bundle.js +17 -0
  76. package/scripts/build-fonts.js +43 -0
  77. package/scripts/build-resources.js +46 -0
  78. package/scripts/plugins-shim.js +10 -0
  79. package/test/chemdata.js +69 -0
  80. package/test/data/CHA.cif +74 -0
  81. package/test/data/H2O.xyz +8 -0
  82. package/test/data/H2_bound.xyz +4 -0
  83. package/test/data/ethanol.cell +25 -0
  84. package/test/data/ethanol.magres +238 -0
  85. package/test/data/example_single.cif +789 -0
  86. package/test/data/frac.cell +8 -0
  87. package/test/data/org.cif +427 -0
  88. package/test/data/pyridine.xyz +13 -0
  89. package/test/data/si8.xyz +10 -0
  90. package/test/loader.js +107 -0
  91. package/test/model.js +368 -0
  92. package/test/query.js +135 -0
  93. package/test/tensor.js +133 -0
  94. package/test/test-html/examples.js +1485 -0
  95. package/test/test-html/index.html +33 -0
  96. package/test/test-html/index.js +279 -0
  97. package/tools/compile_colors.py +120 -0
  98. package/tools/compile_periodic.py +96 -0
  99. package/tools/ptable.json +497 -0
  100. package/tools/test +5844 -0
@@ -0,0 +1,69 @@
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+ 'use strict';
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+
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+ import chai from 'chai'
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+ import chaiAlmost from 'chai-almost'
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+
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+ import {
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+ getVdwRadius,
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+ getIsotopeList,
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+ getElementData,
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+ getIsotopeData
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+ } from '../lib/data.js';
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+
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+ chai.use(chaiAlmost(1e-3));
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+
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+ const expect = chai.expect;
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+
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+ describe('#nmrdata', function() {
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+
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+ it('should find the right VdW radius for elements', function() {
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+
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+ const vdwH = getVdwRadius('H');
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+ const vdwX = getVdwRadius('X'); // Unknown
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+
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+ expect(vdwH).to.equal(1.2);
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+ expect(vdwX).to.equal(1.77);
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+ });
27
+
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+ it('should properly load the isotopes for a given element', function() {
29
+
30
+ const isosH = getIsotopeList('H');
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+ const isosHe = getIsotopeList('He');
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+
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+ expect(isosH).to.deep.equal(['1', '2']);
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+ expect(isosHe).to.deep.equal(['3', '4']);
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+
36
+ });
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+
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+ it('should properly find the correct NMR data for an element', function() {
39
+
40
+ const dataH = getElementData('H');
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+
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+ expect(dataH.symbol).to.equal('H');
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+ expect(dataH.Z).to.equal(1);
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+
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+ expect(dataH.maxiso).to.equal('1');
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+ expect(dataH.maxiso_NMR).to.equal('1');
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+ expect(dataH.maxiso_Q).to.equal('2');
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+
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+ });
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+
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+ it('should properly find the correct NMR data for an isotope', function() {
52
+
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+ const dataC12 = getIsotopeData('C'); // Most abundant C isotope
54
+ const dataC13 = getIsotopeData('C', 'nmr'); // Most abundant NMR active one
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+ const dataCna = getIsotopeData('C', 'Q'); // Doesn't exist
56
+
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+ expect(dataC12.A).to.equal(12);
58
+ expect(dataC13.A).to.equal(13);
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+ expect(dataCna).to.equal(null);
60
+
61
+ const dataH2 = getIsotopeData('H', 'Q'); // Deuterium
62
+
63
+ expect(dataH2.A).to.equal(2);
64
+ expect(dataH2.spin).to.equal(1.0);
65
+ expect(dataH2.gamma).to.almost.equal(41066279.1);
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+ expect(dataH2.Q).to.almost.equal(2.86);
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+
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+ });
69
+ });
@@ -0,0 +1,74 @@
1
+ data_CHA
2
+ #**************************************************************************
3
+ #
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+ # CIF taken from the IZA-SC Database of Zeolite Structures
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+ # Ch. Baerlocher and L.B. McCusker
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+ # Database of Zeolite Structures: http://www.iza-structure.org/databases/
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+ #
8
+ # The atom coordinates and the cell parameters were optimized with DLS76
9
+ # assuming a pure SiO2 composition.
10
+ #
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+ #**************************************************************************
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+
13
+ _cell_length_a 13.6750(0)
14
+ _cell_length_b 13.6750(0)
15
+ _cell_length_c 14.7670(0)
16
+ _cell_angle_alpha 90.0000(0)
17
+ _cell_angle_beta 90.0000(0)
18
+ _cell_angle_gamma 120.0000(0)
19
+
20
+ _symmetry_space_group_name_H-M 'R -3 m'
21
+ _symmetry_Int_Tables_number 166
22
+ _symmetry_cell_setting trigonal
23
+
24
+ loop_
25
+ _symmetry_equiv_pos_as_xyz
26
+ '+x,+y,+z'
27
+ '2/3+x,1/3+y,1/3+z'
28
+ '1/3+x,2/3+y,2/3+z'
29
+ '-y,+x-y,+z'
30
+ '2/3-y,1/3+x-y,1/3+z'
31
+ '1/3-y,2/3+x-y,2/3+z'
32
+ '-x+y,-x,+z'
33
+ '2/3-x+y,1/3-x,1/3+z'
34
+ '1/3-x+y,2/3-x,2/3+z'
35
+ '-y,-x,+z'
36
+ '2/3-y,1/3-x,1/3+z'
37
+ '1/3-y,2/3-x,2/3+z'
38
+ '-x+y,+y,+z'
39
+ '2/3-x+y,1/3+y,1/3+z'
40
+ '1/3-x+y,2/3+y,2/3+z'
41
+ '+x,+x-y,+z'
42
+ '2/3+x,1/3+x-y,1/3+z'
43
+ '1/3+x,2/3+x-y,2/3+z'
44
+ '-x,-y,-z'
45
+ '2/3-x,1/3-y,1/3-z'
46
+ '1/3-x,2/3-y,2/3-z'
47
+ '+y,-x+y,-z'
48
+ '2/3+y,1/3-x+y,1/3-z'
49
+ '1/3+y,2/3-x+y,2/3-z'
50
+ '+x-y,+x,-z'
51
+ '2/3+x-y,1/3+x,1/3-z'
52
+ '1/3+x-y,2/3+x,2/3-z'
53
+ '+y,+x,-z'
54
+ '2/3+y,1/3+x,1/3-z'
55
+ '1/3+y,2/3+x,2/3-z'
56
+ '+x-y,-y,-z'
57
+ '2/3+x-y,1/3-y,1/3-z'
58
+ '1/3+x-y,2/3-y,2/3-z'
59
+ '-x,-x+y,-z'
60
+ '2/3-x,1/3-x+y,1/3-z'
61
+ '1/3-x,2/3-x+y,2/3-z'
62
+
63
+ loop_
64
+ _atom_site_label
65
+ _atom_site_type_symbol
66
+ _atom_site_fract_x
67
+ _atom_site_fract_y
68
+ _atom_site_fract_z
69
+ O1 O 0.9020 0.0980 0.1227
70
+ O2 O 0.9767 0.3101 0.1667
71
+ O3 O 0.1203 0.2405 0.1315
72
+ O4 O 0.0000 0.2577 0.0000
73
+ T1 Si 0.9997 0.2264 0.1051
74
+
@@ -0,0 +1,8 @@
1
+ 6
2
+ Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0" Properties=species:S:1:pos:R:3 pbc="T T T"
3
+ O 0.00000000 0.00000000 0.11926200
4
+ H 0.00000000 0.76323900 -0.47704700
5
+ H 0.00000000 -0.76323900 -0.47704700
6
+ O 5.00000000 0.00000000 0.11926200
7
+ H 5.00000000 0.76323900 9.522953
8
+ H 5.00000000 9.236761 9.522953
@@ -0,0 +1,4 @@
1
+ 2
2
+ Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0" Properties=species:S:1:pos:R:3 pbc="T T T"
3
+ H 0.2 0.2 0.2
4
+ H 9.8 9.8 9.8
@@ -0,0 +1,25 @@
1
+ #######################################################
2
+ #CASTEP cell file: ethanol.cell
3
+ #Created using the Atomic Simulation Environment (ASE)#
4
+ #######################################################
5
+
6
+ %BLOCK LATTICE_CART
7
+ ANG
8
+ 6.000000 0.000000 0.000000
9
+ 0.000000 6.000000 0.000000
10
+ 0.000000 0.000000 6.000000
11
+ %ENDBLOCK LATTICE_CART
12
+
13
+ %BLOCK POSITIONS_ABS
14
+ ANG
15
+ H 2.129659 2.823711 2.349943
16
+ H 3.182454 2.075799 3.559623
17
+ H 3.868130 3.197626 2.370217
18
+ H 1.869295 3.974874 4.564773
19
+ H 2.561231 5.078941 3.371865
20
+ H 4.060671 3.677653 5.297066
21
+ C 2.996000 2.996000 2.996000
22
+ C 2.752085 4.164107 3.937396
23
+ O 3.895314 4.458074 4.741964
24
+ %ENDBLOCK POSITIONS_ABS
25
+
@@ -0,0 +1,238 @@
1
+ #$magres-abinitio-v1.0
2
+ # Generated by format.py. For format definition and code samples see http://www.ccpnc.ac.uk/pmwiki.php/CCPNC/Fileformat
3
+ [calculation]
4
+ calc_code CASTEP
5
+ calc_code_version 7.0
6
+ calc_comment
7
+ calc_kpoint_mp_grid 1 1 1
8
+ calc_code_hgversion 0d37235409d7+ magres-efg 2013-02-07
9
+ calc_cutoffenergy 4.0000000000000000E+01
10
+ calc_xcfunctional PBE
11
+ calc_kpoint_mp_offset 0.25000000 0.25000000 0.25000000
12
+ calc_code_platform linux_x86_64_ifort12
13
+ units calc_cutoffenergy Hartree
14
+ calc_name ethanol
15
+ [/calculation]
16
+ [atoms]
17
+ units lattice Angstrom
18
+ units atom Angstrom
19
+ lattice 6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0
20
+ symmetry P1
21
+ atom H H 1 2.129659 2.823711 2.349943
22
+ atom H H 2 3.182454 2.075799 3.559623
23
+ atom H H 3 3.86813 3.197626 2.370217
24
+ atom H H 4 1.869295 3.974874 4.564773
25
+ atom H H 5 2.561231 5.078941 3.371865
26
+ atom H H 6 4.060671 3.677653 5.297066
27
+ atom C C 1 2.996 2.996 2.996
28
+ atom C C 2 2.752085 4.164107 3.937396
29
+ atom O O 1 3.895314 4.458074 4.741964
30
+ [/atoms]
31
+ [magres]
32
+ units sus 10^-6.cm^3.mol^-1
33
+ units ms ppm
34
+ units efg au
35
+ units isc_fc 10^19.T^2.J^-1
36
+ units isc 10^19.T^2.J^-1
37
+ units isc_fc 10^19.T^2.J^-1
38
+ units isc 10^19.T^2.J^-1
39
+ sus 1 0 0 0 1 0 0 0 1
40
+ ms H 1 30.2981796159 1.2051069281 3.67274492938 1.96313294552 27.5765250451 2.57545224195 4.21834131673 2.16271307552 30.9031525163
41
+ ms H 2 26.9742092612 -0.420221330647 0.603628166501 -0.387611330052 35.3313827464 -1.80447967738 -0.578564493964 -1.44841641969 28.4625610177
42
+ ms H 3 29.9943370458 0.804017870839 -3.41596793698 -0.538358436872 27.8109854077 -0.130246475692 -3.56604211569 -0.0418632950686 32.5029379989
43
+ ms H 4 32.2898154856 0.584330480731 -1.63639006642 0.778952021344 22.6711049351 1.80797334282 -0.0810936558433 2.01393309009 25.9791612443
44
+ ms H 5 25.946849893 -2.77588906551 3.75442739434 -1.77463107727 29.7225814726 -0.398037457666 3.04599241075 -1.46601607492 26.5018075671
45
+ ms H 6 28.6085193533 -2.06023026024 4.73450589133 -0.308253194156 32.9520121318 -6.48661920164 4.68678352951 -5.89383717672 34.3943957639
46
+ ms C 1 150.363398078 -10.1551572591 -0.228392095331 0.262621541636 160.896219614 23.0932964082 7.6058979745 15.6796898709 158.142036855
47
+ ms C 2 133.676840084 0.262423773157 30.3803502689 3.67357096609 87.087341646 13.766471363 33.4352726046 12.5980254544 108.80723859
48
+ ms O 1 246.617726076 4.67835886314 23.439961146 -25.5598430959 289.39716395 -21.152670085 18.297484257 -4.25541343242 268.070670505
49
+ efg_local H 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
50
+ efg_local H 2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
51
+ efg_local H 3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
52
+ efg_local H 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
53
+ efg_local H 5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
54
+ efg_local H 6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
55
+ efg_local C 1 -0.0250863245422 -0.0201770085446 -0.00412773044863 -0.0201770085446 0.019590013125 0.034603122236 -0.00412773044863 0.034603122236 0.00549631141718
56
+ efg_local C 2 0.18069118986 0.0616787382743 0.26613664065 0.0616787382743 -0.179575675203 0.11466220516 0.26613664065 0.11466220516 -0.00111551465673
57
+ efg_local O 1 0.118861288007 0.135560088603 1.49199510969 0.135560088603 0.0010287580134 -0.861525967236 1.49199510969 -0.861525967236 -0.11989004602
58
+ efg_nonlocal H 1 -0.248884029127 -0.15886792949 -0.510061683836 -0.15886792949 0.31790645627 -0.164617997629 -0.510061683836 -0.164617997629 -0.0690224271437
59
+ efg_nonlocal H 2 0.413666682454 0.14659469133 -0.101224264464 0.14659469133 -0.557394043688 0.377626548075 -0.101224264464 0.377626548075 0.143727361235
60
+ efg_nonlocal H 3 -0.240472505532 -0.1201678195 0.512637552144 -0.1201678195 0.352737517928 0.0258286832003 0.512637552144 0.0258286832003 -0.112265012396
61
+ efg_nonlocal H 4 -0.47263265592 -0.148232439756 0.491190116538 -0.148232439756 0.40383299567 0.0474885223735 0.491190116538 0.0474885223735 0.06879966025
62
+ efg_nonlocal H 5 0.345536759085 0.227490107486 -0.192663085782 0.227490107486 -0.428940178047 0.468128657615 -0.192663085782 0.468128657615 0.083403418962
63
+ efg_nonlocal H 6 0.682455309103 0.347422629338 -0.345110329811 0.347422629338 -0.57839260253 1.04274527009 -0.345110329811 1.04274527009 -0.104062706573
64
+ efg_nonlocal C 1 0.130515539747 -0.00113106162527 -0.0103315568603 -0.00113106162527 -0.0778325541782 -0.186058494954 -0.0103315568603 -0.186058494954 -0.0526829855687
65
+ efg_nonlocal C 2 -0.10120809182 -0.0606319177341 -0.25184927724 -0.0606319177341 0.10366108656 -0.201110715697 -0.25184927724 -0.201110715697 -0.00245299473989
66
+ efg_nonlocal O 1 -0.0499340762424 -0.0597999337628 -0.341995493801 -0.0597999337628 0.070460923598 0.0611629807928 -0.341995493801 0.0611629807928 -0.0205268473556
67
+ efg H 1 0.12793404309 0.0514298737569 0.20226839328 0.0514298737569 -0.133531745662 0.0414560149276 0.20226839328 0.0414560149276 0.00559770257191
68
+ efg H 2 -0.133979130361 -0.0609040781878 0.0374120243967 -0.0609040781878 0.157638296763 -0.184442244602 0.0374120243967 -0.184442244602 -0.0236591664019
69
+ efg H 3 0.12986839977 0.0652645621537 -0.201061065166 0.0652645621537 -0.128376570683 -0.0454082281587 -0.201061065166 -0.0454082281587 -0.00149182908676
70
+ efg H 4 0.125522205339 0.060319384091 -0.183473060621 0.060319384091 -0.129847323513 -0.040585650492 -0.183473060621 -0.040585650492 0.00432511817317
71
+ efg H 5 -0.126596501712 -0.0582754965986 0.0467662219879 -0.0582754965986 0.15405837804 -0.184288654121 0.0467662219879 -0.184288654121 -0.0274618763279
72
+ efg H 6 -0.190199778929 -0.0789692888392 0.0920151083512 -0.0789692888392 0.199082123801 -0.306948344129 0.0920151083512 -0.306948344129 -0.00888234487242
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