diff --git a/anharmonic/other/isotope.py b/anharmonic/other/isotope.py index fc3af53a..f6283f4d 100644 --- a/anharmonic/other/isotope.py +++ b/anharmonic/other/isotope.py @@ -10,8 +10,8 @@ def get_mass_variances(primitive): symbols = primitive.get_chemical_symbols() mass_variances = [] for s in symbols: - masses = np.array([x[0] for x in isotope_data[s]]) - fractions = np.array([x[1] for x in isotope_data[s]]) + masses = np.array([x[1] for x in isotope_data[s]]) + fractions = np.array([x[2] for x in isotope_data[s]]) m_ave = np.dot(masses, fractions) g = np.dot(fractions, (1 - masses / m_ave) ** 2) mass_variances.append(g) diff --git a/phonopy/structure/atoms.py b/phonopy/structure/atoms.py index c021f43b..2ba677ea 100644 --- a/phonopy/structure/atoms.py +++ b/phonopy/structure/atoms.py @@ -404,125 +404,179 @@ symbol_map = { # K. J. R. Rosman and P. D. P. Taylor (2003). # "Atomic weights of the elements. Review 2000 (IUPAC Technical Report)" isotope_data = { - 'H': [[1, 0.999885], [2, 0.000115]], - 'He': [[3, 0.00000134], [4, 0.99999866]], - 'Li': [[6, 0.0759], [7, 0.9241]], - 'Be': [[9, 1.0000]], - 'B': [[10, 0.199], [11, 0.801]], - 'C': [[12, 0.9893], [13, 0.0107]], - 'N': [[14, 0.99636], [15, 0.00364]], - 'O': [[16, 0.99757], [17, 0.00038], [18, 0.00205]], - 'F': [[19, 1.0000]], - 'Ne': [[20, 0.9048], [21, 0.0027], [22, 0.0925]], - 'Na': [[23, 1.0000]], - 'Mg': [[24, 0.7899], [25, 0.1000], [26, 0.1101]], - 'Al': [[27, 1.0000]], - 'Si': [[28, 0.92223], [29, 0.04685], [30, 0.03092]], - 'P': [[31, 1.0000]], - 'S': [[32, 0.9499], [33, 0.0075], [34, 0.0425], [36, 0.0001]], - 'Cl': [[35, 0.7576], [37, 0.2424]], - 'Ar': [[36, 0.003365], [38, 0.000632], [40, 0.996003]], - 'K': [[39, 0.932581], [40, 0.000117], [41, 0.067302]], - 'Ca': [[40, 0.96941], [42, 0.00647], [43, 0.00135], [44, 0.02086], - [46, 0.00004], [48, 0.00187]], - 'Sc': [[45, 1.0000]], - 'Ti': [[46, 0.0825], [47, 0.0744], [48, 0.7372], [49, 0.0541], - [50, 0.0518]], - 'V': [[50, 0.00250], [51, 0.99750]], - 'Cr': [[50, 0.04345], [52, 0.83789], [53, 0.09501], [54, 0.02365]], - 'Mn': [[55, 1.0000]], - 'Fe': [[54, 0.05845], [56, 0.91754], [57, 0.02119], [58, 0.00282]], - 'Co': [[59, 1.0000]], - 'Ni': [[58, 0.680769], [60, 0.262231], [61, 0.011399], [62, 0.036345], - [64, 0.009256]], - 'Cu': [[63, 0.6915], [65, 0.3085]], - 'Zn': [[64, 0.48268], [66, 0.27975], [67, 0.04102], [68, 0.19024], - [70, 0.00631]], - 'Ga': [[69, 0.60108], [71, 0.39892]], - 'Ge': [[70, 0.2038], [72, 0.2731], [73, 0.0776], [74, 0.3672], - [76, 0.0783]], - 'As': [[75, 1.0000]], - 'Se': [[74, 0.0089], [76, 0.0937], [77, 0.0763], [78, 0.2377], - [80, 0.4961], [82, 0.0873]], - 'Br': [[79, 0.5069], [81, 0.4931]], - 'Kr': [[78, 0.00355], [80, 0.02286], [82, 0.11593], [83, 0.11500], - [84, 0.56987], [86, 0.17279]], - 'Rb': [[85, 0.7217], [87, 0.2783]], - 'Sr': [[84, 0.0056], [86, 0.0986], [87, 0.0700], [88, 0.8258]], - 'Y': [[89, 1.0000]], - 'Zr': [[90, 0.5145], [91, 0.1122], [92, 0.1715], [94, 0.1738], - [96, 0.0280]], - 'Nb': [[93, 1.0000]], - 'Mo': [[92, 0.1477], [94, 0.0923], [95, 0.1590], [96, 0.1668], - [97, 0.0956], [98, 0.2419], [100, 0.0967]], + 'H': [[1, 1.0078250319, 0.999885], [2, 2.0141017779, 0.000115]], + 'He': [[3, 3.0160293094, 0.00000134], [4, 4.0026032497, 0.99999866]], + 'Li': [[6, 6.0151223, 0.0759], [7, 7.0160041, 0.9241]], + 'Be': [[9, 9.0121822, 1.0000]], + 'B': [[10, 10.0129371, 0.199], [11, 11.0093055, 0.801]], + 'C': [[12, 12, 0.9893], [13, 13.003354838, 0.0107]], + 'N': [[14, 14.0030740074, 0.99636], [15, 15.000108973, 0.00364]], + 'O': [[16, 15.9949146223, 0.99757], [17, 16.99913150, 0.00038], + [18, 17.9991604, 0.00205]], + 'F': [[19, 18.99840320, 1.0000]], + 'Ne': [[20, 19.992440176, 0.9048], [21, 20.99384674, 0.0027], + [22, 21.99138550, 0.0925]], + 'Na': [[23, 22.98976966, 1.0000]], + 'Mg': [[24, 23.98504187, 0.7899], [25, 24.98583700, 0.1000], + [26, 25.98259300, 0.1101]], + 'Al': [[27, 26.98153841, 1.0000]], + 'Si': [[28, 27.97692649, 0.92223], [29, 28.97649468, 0.04685], + [30, 29.97377018, 0.03092]], + 'P': [[31, 30.97376149, 1.0000]], + 'S': [[32, 31.97207073, 0.9499], [33, 32.97145854, 0.0075], + [34, 33.96786687, 0.0425], [36, 35.96708088, 0.0001]], + 'Cl': [[35, 34.96885271, 0.7576], [37, 36.96590260, 0.2424]], + 'Ar': [[36, 35.96754626, 0.003365], [38, 37.9627322, 0.000632], + [40, 39.962383124, 0.996003]], + 'K': [[39, 38.96370, 0.932581], [40, 39.96399867, 0.000117], + [41, 40.96182597, 0.067302]], + 'Ca': [[40, 39.9625912, 0.96941], [42, 41.9586183, 0.00647], + [43, 42.9587668, 0.00135], [44, 43.9554811, 0.02086], + [46, 45.9536927, 0.00004], [48, 47.952533, 0.00187]], + 'Sc': [[45, 44.9559102, 1.0000]], + 'Ti': [[46, 45.9526295, 0.0825], [47, 46.9517637, 0.0744], + [48, 47.9479470, 0.7372], [49, 48.9478707, 0.0541], + [50, 49.9447920, 0.0518]], + 'V': [[50, 49.9471627, 0.00250], [51, 50.9439635, 0.99750]], + 'Cr': [[50, 49.9460495, 0.04345], [52, 51.9405115, 0.83789], + [53, 52.9406534, 0.09501], [54, 53.9388846, 0.02365]], + 'Mn': [[55, 54.9380493, 1.0000]], + 'Fe': [[54, 53.9396147, 0.05845], [56, 55.9349418, 0.91754], + [57, 56.9353983, 0.02119], [58, 57.9332801, 0.00282]], + 'Co': [[59, 58.9331999, 1.0000]], + 'Ni': [[58, 57.9353477, 0.680769], [60, 59.9307903, 0.262231], + [61, 60.9310601, 0.011399], [62, 61.9283484, 0.036345], + [64, 63.9279692, 0.009256]], + 'Cu': [[63, 62.9296007, 0.6915], [65, 64.9277938, 0.3085]], + 'Zn': [[64, 63.9291461, 0.48268], [66, 65.9260364, 0.27975], + [67, 66.9271305, 0.04102], [68, 67.9248473, 0.19024], + [70, 69.925325, 0.00631]], + 'Ga': [[69, 68.925581, 0.60108], [71, 70.9247073, 0.39892]], + 'Ge': [[70, 69.9242500, 0.2038], [72, 71.9220763, 0.2731], + [73, 72.9234595, 0.0776], [74, 73.9211784, 0.3672], + [76, 75.921402, 0.0783]], + 'As': [[75, 74.9215966, 1.0000]], + 'Se': [[74, 73.9224767, 0.0089], [76, 75.9192143, 0.0937], + [77, 76.9199148, 0.0763], [78, 77.9173097, 0.2377], + [80, 79.9165221, 0.4961], [82, 81.9167003, 0.0873]], + 'Br': [[79, 78.9183379, 0.5069], [81, 80.916291, 0.4931]], + 'Kr': [[78, 77.920388, 0.00355], [80, 79.916379, 0.02286], + [82, 81.9134850, 0.11593], [83, 82.914137, 0.11500], + [84, 83.911508, 0.56987], [86, 85.910615, 0.17279]], + 'Rb': [[85, 84.9117924, 0.7217], [87, 86.9091858, 0.2783]], + 'Sr': [[84, 83.913426, 0.0056], [86, 85.9092647, 0.0986], + [87, 86.9088816, 0.0700], [88, 87.9056167, 0.8258]], + 'Y': [[89, 88.9058485, 1.0000]], + 'Zr': [[90, 89.9047022, 0.5145], [91, 90.9056434, 0.1122], + [92, 91.9050386, 0.1715], [94, 93.9063144, 0.1738], + [96, 95.908275, 0.0280]], + 'Nb': [[93, 92.9063762, 1.0000]], + 'Mo': [[92, 91.906810, 0.1477], [94, 93.9050867, 0.0923], + [95, 94.9058406, 0.1590], [96, 95.9046780, 0.1668], + [97, 96.9060201, 0.0956], [98, 97.905406, 0.2419], + [100, 99.907476, 0.0967]], 'Tc': None, - 'Ru': [[96, 0.0554], [98, 0.0187], [99, 0.1276], [100, 0.1260], - [101, 0.1706], [102, 0.3155], [104, 0.1862]], - 'Rh': [[103, 1.0000]], - 'Pd': [[102, 0.0102], [104, 0.1114], [105, 0.2233], [106, 0.2733], - [108, 0.2646], [110, 0.1172]], - 'Ag': [[107, 0.51839], [109, 0.48161]], - 'Cd': [[106, 0.0125], [108, 0.0089], [110, 0.1249], [111, 0.1280], - [112, 0.2413], [113, 0.1222], [114, 0.2873], [116, 0.0749]], - 'In': [[113, 0.0429], [115, 0.9571]], - 'Sn': [[112, 0.0097], [114, 0.0066], [115, 0.0034], [116, 0.1454], - [117, 0.0768], [118, 0.2422], [119, 0.0859], [120, 0.3258], - [112, 0.0463], [124, 0.0579]], - 'Sb': [[121, 0.5721], [123, 0.4279]], - 'Te': [[120, 0.0009], [122, 0.0255], [123, 0.0089], [124, 0.0474], - [125, 0.0707], [126, 0.1884], [128, 0.3174], [130, 0.3408]], - 'I': [[127, 1.0000]], - 'Xe': [[124, 0.000952], [126, 0.000890], [128, 0.019102], [129, 0.264006], - [130, 0.040710], [131, 0.212324], [132, 0.269086], [134, 0.104357], - [136, 0.088573]], - 'Cs': [[133, 1.0000]], - 'Ba': [[130, 0.00106], [132, 0.00101], [134, 0.02417], [135, 0.06592], - [136, 0.07854], [137, 0.11232], [138, 0.71698]], - 'La': [[138, 0.00090], [139, 0.99910]], - 'Ce': [[136, 0.00185], [138, 0.00251], [140, 0.88450], [142, 0.11114]], - 'Pr': [[141, 1.0000]], - 'Nd': [[142, 0.272], [143, 0.122], [144, 0.238], [145, 0.083], - [146, 0.172], [148, 0.057], [150, 0.056]], + 'Ru': [[96, 95.907604, 0.0554], [98, 97.905287, 0.0187], + [99, 98.9059385, 0.1276], [100, 99.9042189, 0.1260], + [101, 100.9055815, 0.1706], [102, 101.9043488, 0.3155], + [104, 103.905430, 0.1862]], + 'Rh': [[103, 102.905504, 1.0000]], + 'Pd': [[102, 101.905607, 0.0102], [104, 103.904034, 0.1114], + [105, 104.905083, 0.2233], [106, 105.903484, 0.2733], + [108, 107.903895, 0.2646], [110, 109.905153, 0.1172]], + 'Ag': [[107, 106.905093, 0.51839], [109, 108.904756, 0.48161]], + 'Cd': [[106, 105.906458, 0.0125], [108, 107.904183, 0.0089], + [110, 109.903006, 0.1249], [111, 110.904182, 0.1280], + [112, 111.9027577, 0.2413], [113, 112.9044014, 0.1222], + [114, 113.9033586, 0.2873], [116, 115.904756, 0.0749]], + 'In': [[113, 112.904062, 0.0429], [115, 114.903879, 0.9571]], + 'Sn': [[112, 111.904822, 0.0097], [114, 113.902783, 0.0066], + [115, 114.903347, 0.0034], [116, 115.901745, 0.1454], + [117, 116.902955, 0.0768], [118, 117.901608, 0.2422], + [119, 118.903311, 0.0859], [120, 119.9021985, 0.3258], + [122, 121.9034411, 0.0463], [124, 123.9052745, 0.0579]], + 'Sb': [[121, 120.9038222, 0.5721], [123, 122.9042160, 0.4279]], + 'Te': [[120, 119.904026, 0.0009], [122, 121.9030558, 0.0255], + [123, 122.9042711, 0.0089], [124, 123.9028188, 0.0474], + [125, 124.9044241, 0.0707], [126, 125.9033049, 0.1884], + [128, 127.9044615, 0.3174], [130, 129.9062229, 0.3408]], + 'I': [[127, 126.904468, 1.0000]], + 'Xe': [[124, 123.9058954, 0.000952], [126, 125.904268, 0.000890], + [128, 127.9035305, 0.019102], [129, 128.9047799, 0.264006], + [130, 129.9035089, 0.040710], [131, 130.9050828, 0.212324], + [132, 131.9041546, 0.269086], [134, 133.9053945, 0.104357], + [136, 135.907220, 0.088573]], + 'Cs': [[133, 132.905447, 1.0000]], + 'Ba': [[130, 129.906311, 0.00106], [132, 131.905056, 0.00101], + [134, 133.904504, 0.02417], [135, 134.905684, 0.06592], + [136, 135.904571, 0.07854], [137, 136.905822, 0.11232], + [138, 137.905242, 0.71698]], + 'La': [[138, 137.907108, 0.00090], [139, 138.906349, 0.99910]], + 'Ce': [[136, 135.907140, 0.00185], [138, 137.905986, 0.00251], + [140, 139.905435, 0.88450], [142, 141.909241, 0.11114]], + 'Pr': [[141, 140.907648, 1.0000]], + 'Nd': [[142, 141.907719, 0.272], [143, 142.909810, 0.122], + [144, 143.910083, 0.238], [145, 144.912569, 0.083], + [146, 145.913113, 0.172], [148, 147.916889, 0.057], + [150, 149.920887, 0.056]], 'Pm': None, - 'Sm': [[144, 0.0307], [147, 0.1499], [148, 0.1124], [149, 0.1382], - [150, 0.0738], [152, 0.2675], [154, 0.2275]], - 'Eu': [[151, 0.4781], [153, 0.5219]], - 'Gd': [[152, 0.0020], [154, 0.0218], [155, 0.1480], [156, 0.2047], - [157, 0.1565], [158, 0.2484], [160, 0.2186]], - 'Tb': [[159, 1.0000]], - 'Dy': [[156, 0.00056], [158, 0.00095], [160, 0.02329], [161, 0.18889], - [162, 0.25475], [163, 0.24896], [164, 0.28260]], - 'Ho': [[165, 1.0000]], - 'Eu': [[162, 0.00139], [164, 0.01601], [166, 0.33503], [167, 0.22869], - [168, 0.26978], [170, 0.14910]], - 'Tm': [[169, 1.0000]], - 'Yb': [[168, 0.0013], [170, 0.0304], [171, 0.1428], [172, 0.2183], - [173, 0.1613], [174, 0.3183], [176, 0.1276]], - 'Lu': [[175, 0.9741], [176, 0.0259]], - 'Hf': [[174, 0.0016], [176, 0.0526], [177, 0.1860], [178, 0.2728], - [179, 0.1362], [180, 0.3508]], - 'Ta': [[180, 0.00012], [181, 0.99988]], - 'W': [[180, 0.0012], [182, 0.2650], [183, 0.1431], [184, 0.3064], - [186, 0.2843]], - 'Re': [[185, 0.3740], [187, 0.6260]], - 'Os': [[184, 0.0002], [186, 0.0159], [187, 0.0196], [188, 0.1324], - [189, 0.1615], [190, 0.2626], [192, 0.4078]], - 'Ir': [[191, 0.373], [193, 0.627]], - 'Pt': [[190, 0.00014], [192, 0.00782], [194, 0.32967], [195, 0.33832], - [196, 0.25242], [198, 0.07163]], - 'Au': [[197, 1.0000]], - 'Hg': [[196, 0.0015], [198, 0.0997], [199, 0.1687], [200, 0.2310], - [201, 0.1318], [202, 0.2986], [204, 0.0687]], - 'Tl': [[203, 0.2952], [205, 0.7048]], - 'Pb': [[204, 0.014], [206, 0.241], [207, 0.221], [208, 0.524]], - 'Bi': [[209, 1.0000]], + 'Sm': [[144, 143.911996, 0.0307], [147, 146.914894, 0.1499], + [148, 147.914818, 0.1124], [149, 148.917180, 0.1382], + [150, 149.917272, 0.0738], [152, 151.919729, 0.2675], + [154, 153.922206, 0.2275]], + 'Eu': [[151, 150.919846, 0.4781], [153, 152.921227, 0.5219]], + 'Gd': [[152, 151.919789, 0.0020], [154, 153.920862, 0.0218], + [155, 154.922619, 0.1480], [156, 155.922120, 0.2047], + [157, 156.923957, 0.1565], [158, 157.924101, 0.2484], + [160, 159.927051, 0.2186]], + 'Tb': [[159, 158.925343, 1.0000]], + 'Dy': [[156, 155.924278, 0.00056], [158, 157.924405, 0.00095], + [160, 159.925194, 0.02329], [161, 160.926930, 0.18889], + [162, 161.926795, 0.25475], [163, 162.928728, 0.24896], + [164, 163.929171, 0.28260]], + 'Ho': [[165, 164.930319, 1.0000]], + 'Eu': [[162, 161.928775, 0.00139], [164, 163.929197, 0.01601], + [166, 165.930290, 0.33503], [167, 166.932046, 0.22869], + [168, 167.932368, 0.26978], [170, 169.935461, 0.14910]], + 'Tm': [[169, 168.934211, 1.0000]], + 'Yb': [[168, 167.933895, 0.0013], [170, 169.934759, 0.0304], + [171, 170.936323, 0.1428], [172, 171.936378, 0.2183], + [173, 172.938207, 0.1613], [174, 173.938858, 0.3183], + [176, 175.942569, 0.1276]], + 'Lu': [[175, 174.9407682, 0.9741], [176, 175.9426827, 0.0259]], + 'Hf': [[174, 173.940042, 0.0016], [176, 175.941403, 0.0526], + [177, 176.9432204, 0.1860], [178, 177.9436981, 0.2728], + [179, 178.9458154, 0.1362], [180, 179.9465488, 0.3508]], + 'Ta': [[180, 179.947466, 0.00012], [181, 180.947996, 0.99988]], + 'W': [[180, 179.946706, 0.0012], [182, 181.948205, 0.2650], + [183, 182.9502242, 0.1431], [184, 183.9509323, 0.3064], + [186, 185.95436, 0.2843]], + 'Re': [[185, 184.952955, 0.3740], [187, 186.9557505, 0.6260]], + 'Os': [[184, 183.952491, 0.0002], [186, 185.953838, 0.0159], + [187, 186.9557476, 0.0196], [188, 187.9558357, 0.1324], + [189, 188.958145, 0.1615], [190, 189.958445, 0.2626], + [192, 191.961479, 0.4078]], + 'Ir': [[191, 190.960591, 0.373], [193, 192.962923, 0.627]], + 'Pt': [[190, 189.959930, 0.00014], [192, 191.961035, 0.00782], + [194, 193.962663, 0.32967], [195, 194.964774, 0.33832], + [196, 195.964934, 0.25242], [198, 197.967875, 0.07163]], + 'Au': [[197, 196.966551, 1.0000]], + 'Hg': [[196, 195.965814, 0.0015], [198, 197.966752, 0.0997], + [199, 198.968262, 0.1687], [200, 199.968309, 0.2310], + [201, 200.970285, 0.1318], [202, 201.970625, 0.2986], + [204, 203.973475, 0.0687]], + 'Tl': [[203, 202.972329, 0.2952], [205, 204.974412, 0.7048]], + 'Pb': [[204, 203.973028, 0.014], [206, 205.974449, 0.241], + [207, 206.975880, 0.221], [208, 207.976636, 0.524]], + 'Bi': [[209, 208.980384, 1.0000]], 'Po': None, 'At': None, 'Rn': None, 'Fr': None, 'Ra': None, 'Ac': None, - 'Th': [[232, 1.0000]], - 'Pa': [[231, 1.0000]], - 'U': [[234, 0.000054], [235, 0.007204], [238, 0.992742]] + 'Th': [[232, 232.0380495, 1.0000]], + 'Pa': [[231, 231.03588, 1.0000]], + 'U': [[234, 234.0409447, 0.000054], [235, 235.0439222, 0.007204], + [238, 238.0507835, 0.992742]] }