pymatgen.util.testing module

Common test support for pymatgen test scripts.

This single module should provide all the common functionality for pymatgen tests in a single location, so that test scripts can just import it and work right away.

class PymatgenTest(methodName='runTest')[source]

Bases: TestCase

Extends unittest.TestCase with functions (taken from numpy.testing.utils) that support the comparison of arrays.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

MODULE_DIR = PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util')[source]

STRUCTURES_DIR = PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/structures')[source]

TEST_FILES_DIR = PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/../../test_files')[source]

TEST_STRUCTURES = {'BaNiO3': <pymatgen.alchemy.materials.TransformedStructure object>, 'CsCl': Structure Summary Lattice abc : 4.209 4.209 4.209 angles : 90.0 90.0 90.0 volume : 74.56530132899998 A : 4.209 0.0 0.0 B : 0.0 4.209 0.0 C : 0.0 0.0 4.209 pbc : True True True PeriodicSite: Cs (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Cl (2.1045, 2.1045, 2.1045) [0.5000, 0.5000, 0.5000], 'Graphite': Structure Summary Lattice abc : 2.4700000000000006 2.47 6.8 angles : 90.0 90.0 120.00000000000001 volume : 35.928033824449685 A : -1.2350000000000005 -2.139082747347564 -3.024877593893963e-16 B : -1.2349999999999997 2.139082747347564 1.5124387969469814e-16 C : 0.0 0.0 -6.8 pbc : True True True PeriodicSite: C0+ (-1.2350, -0.7132, -5.1000) [0.6667, 0.3333, 0.7500] PeriodicSite: C0+ (-1.2350, 0.7132, -1.7000) [0.3333, 0.6667, 0.2500] PeriodicSite: C0+ (0.0000, 0.0000, -5.1000) [0.0000, 0.0000, 0.7500] PeriodicSite: C0+ (0.0000, 0.0000, -1.7000) [0.0000, 0.0000, 0.2500], 'He_BCC': Structure Summary Lattice abc : 2.737172073807164 2.7371720737557492 2.73717207 angles : 109.47122060669534 109.47122060631484 109.47122066304705 volume : 15.786447515629305 A : 2.58063058 0.0 -0.91239069 B : -1.29031529 2.23489164 -0.91239069 C : 0.0 0.0 2.73717207 pbc : True True True PeriodicSite: He (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000], 'K2O2': Structure Summary Lattice abc : 4.862375062662279 4.862375062662278 6.361 angles : 90.0 90.0 91.89149308502677 volume : 150.30921504900002 A : 3.3810000000000002 -3.4945000000000004 0.0 B : 3.381 3.4944999999999995 4.2795282396204257e-16 C : 0.0 0.0 -6.361 pbc : True True True PeriodicSite: K+ (1.6905, -1.0861, -1.5902) [0.4054, 0.0946, 0.2500] PeriodicSite: K+ (1.6905, 1.0861, -4.7707) [0.0946, 0.4054, 0.7500] PeriodicSite: K+ (5.0715, 1.0861, -4.7707) [0.5946, 0.9054, 0.7500] PeriodicSite: K+ (5.0715, -1.0861, -1.5902) [0.9054, 0.5946, 0.2500] PeriodicSite: O- (3.3810, -0.6262, -3.6417) [0.5896, 0.4104, 0.5725] PeriodicSite: O- (3.3810, 0.6262, -2.7193) [0.4104, 0.5896, 0.4275] PeriodicSite: O- (3.3810, -2.8683, -0.4612) [0.9104, 0.0896, 0.0725] PeriodicSite: O- (3.3810, 2.8683, -5.8998) [0.0896, 0.9104, 0.9275], 'La2CoO4F': Structure Summary Lattice abc : 6.847249 6.847249 5.748369 angles : 90.0 90.0 132.754623 volume : 197.89340779864318 A : 6.847249 0.0 4.192730785407457e-16 B : -4.648323410186749 5.027714027499061 4.192730785407457e-16 C : 0.0 0.0 5.748369 pbc : True True True PeriodicSite: La3+ (-3.0614, 4.3336, 2.7708) [0.1380, 0.8620, 0.4820] PeriodicSite: La3+ (5.2603, 0.6941, 2.9775) [0.8620, 0.1380, 0.5180] PeriodicSite: La3+ (-0.4875, 3.2079, 5.6450) [0.3620, 0.6380, 0.9820] PeriodicSite: La3+ (2.6864, 1.8198, 0.1033) [0.6380, 0.3620, 0.0180] PeriodicSite: Co3+ (1.0995, 2.5139, 2.8742) [0.5000, 0.5000, 0.5000] PeriodicSite: Co3+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (-0.9933, 3.4292, 3.2966) [0.3180, 0.6821, 0.5735] PeriodicSite: O2- (3.1922, 1.5986, 2.4518) [0.6821, 0.3180, 0.4265] PeriodicSite: O2- (-2.5555, 4.1124, 0.4224) [0.1820, 0.8179, 0.0735] PeriodicSite: O2- (4.7545, 0.9153, 5.3260) [0.8179, 0.1820, 0.9265] PeriodicSite: O2- (1.4256, 3.8686, 1.4371) [0.7305, 0.7695, 0.2500] PeriodicSite: O2- (1.8728, 3.6730, 4.3113) [0.7695, 0.7305, 0.7500] PeriodicSite: O2- (0.3261, 1.3547, 1.4371) [0.2305, 0.2695, 0.2500] PeriodicSite: O2- (0.7734, 1.1591, 4.3113) [0.2695, 0.2305, 0.7500] PeriodicSite: F- (-2.3242, 2.5139, 4.3113) [0.0000, 0.5000, 0.7500] PeriodicSite: F2- (3.4236, 0.0000, 1.4371) [0.5000, 0.0000, 0.2500], 'Li10GeP2S12': Structure Summary Lattice abc : 8.69407 8.69407 12.5994 angles : 90.0 90.0 90.0 volume : 952.3489977658411 A : -8.69407 0.0 -5.323582498531514e-16 B : 5.323582498531514e-16 -8.69407 -5.323582498531514e-16 C : 0.0 0.0 -12.5994 pbc : True True True PeriodicSite: Li:0.691 (-6.4658, -6.3310, -10.2912) [0.7437, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -2.3630, -10.2912) [0.2563, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -2.1187, -3.9915) [0.7718, 0.2437, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -6.5753, -3.9915) [0.2282, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-6.5753, -1.9840, -8.6079) [0.7563, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -6.7101, -8.6079) [0.2437, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -6.4658, -2.3082) [0.7282, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -2.2283, -2.3082) [0.2718, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-6.5753, -6.7101, -8.6079) [0.7563, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -1.9840, -8.6079) [0.2437, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -2.2283, -2.3082) [0.7282, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -6.4658, -2.3082) [0.2718, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-6.4658, -2.3630, -10.2912) [0.7437, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -6.3310, -10.2912) [0.2563, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -6.5753, -3.9915) [0.7718, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -2.1187, -3.9915) [0.2282, 0.2437, 0.3168] PeriodicSite: Li (0.0000, -4.3470, -0.6980) [0.0000, 0.5000, 0.0554] PeriodicSite: Li (0.0000, -4.3470, -6.9977) [0.0000, 0.5000, 0.5554] PeriodicSite: Li (-4.3470, 0.0000, -5.6017) [0.5000, 0.0000, 0.4446] PeriodicSite: Li (-4.3470, 0.0000, -11.9014) [0.5000, 0.0000, 0.9446] PeriodicSite: Li:0.643 (-6.5527, -6.5527, -0.0000) [0.7537, 0.7537, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -2.1413, -0.0000) [0.2463, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-6.4884, -2.2057, -6.2997) [0.7463, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -6.4884, -6.2997) [0.2537, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-6.4884, -6.4884, -6.2997) [0.7463, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -2.2057, -6.2997) [0.2537, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-6.5527, -2.1413, -0.0000) [0.7537, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -6.5527, -0.0000) [0.2463, 0.7537, 0.0000] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -3.8970) [0.0000, 0.5000, 0.3093] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -10.1967) [0.0000, 0.5000, 0.8093] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -2.4027) [0.5000, 0.0000, 0.1907] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -8.7024) [0.5000, 0.0000, 0.6907] PeriodicSite: P (0.0000, 0.0000, -6.2997) [0.0000, 0.0000, 0.5000] PeriodicSite: P (-4.3470, -4.3470, -0.0000) [0.5000, 0.5000, 0.0000] PeriodicSite: S (-8.6941, -7.0918, -7.4299) [1.0000, 0.8157, 0.5897] PeriodicSite: S (0.0000, -1.6023, -7.4299) [0.0000, 0.1843, 0.5897] PeriodicSite: S (-5.9494, -4.3470, -1.1302) [0.6843, 0.5000, 0.0897] PeriodicSite: S (-2.7447, -4.3470, -1.1302) [0.3157, 0.5000, 0.0897] PeriodicSite: S (-4.3470, -2.7447, -11.4692) [0.5000, 0.3157, 0.9103] PeriodicSite: S (-4.3470, -5.9494, -11.4692) [0.5000, 0.6843, 0.9103] PeriodicSite: S (-7.0918, 0.0000, -5.1695) [0.8157, 0.0000, 0.4103] PeriodicSite: S (-1.6023, 0.0000, -5.1695) [0.1843, 0.0000, 0.4103] PeriodicSite: S (-8.6941, -6.0937, -11.4025) [1.0000, 0.7009, 0.9050] PeriodicSite: S (0.0000, -2.6004, -11.4025) [0.0000, 0.2991, 0.9050] PeriodicSite: S (-6.9474, -4.3470, -5.1028) [0.7991, 0.5000, 0.4050] PeriodicSite: S (-1.7466, -4.3470, -5.1028) [0.2009, 0.5000, 0.4050] PeriodicSite: S (-4.3470, -1.7466, -7.4966) [0.5000, 0.2009, 0.5950] PeriodicSite: S (-4.3470, -6.9474, -7.4966) [0.5000, 0.7991, 0.5950] PeriodicSite: S (-6.0937, 0.0000, -1.1969) [0.7009, 0.0000, 0.0950] PeriodicSite: S (-2.6004, 0.0000, -1.1969) [0.2991, 0.0000, 0.0950] PeriodicSite: S (0.0000, -2.6169, -2.6282) [0.0000, 0.3010, 0.2086] PeriodicSite: S (-8.6941, -6.0772, -2.6282) [1.0000, 0.6990, 0.2086] PeriodicSite: S (-1.7301, -4.3470, -8.9279) [0.1990, 0.5000, 0.7086] PeriodicSite: S (-6.9640, -4.3470, -8.9279) [0.8010, 0.5000, 0.7086] PeriodicSite: S (-4.3470, -6.9640, -3.6715) [0.5000, 0.8010, 0.2914] PeriodicSite: S (-4.3470, -1.7301, -3.6715) [0.5000, 0.1990, 0.2914] PeriodicSite: S (-2.6169, 0.0000, -9.9712) [0.3010, 0.0000, 0.7914] PeriodicSite: S (-6.0772, 0.0000, -9.9712) [0.6990, 0.0000, 0.7914], 'Li2O': Structure Summary Lattice abc : 3.291071792359756 3.291071899625086 3.2910720568557887 angles : 60.12971043288485 60.12970952137675 60.12970313039097 volume : 25.279668381289053 A : 2.91738857 0.09789437 1.52000466 B : 0.96463406 2.75503561 1.52000466 C : 0.13320635 0.09789443 3.28691771 pbc : True True True PeriodicSite: O2- (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (3.0121, 2.2136, 4.7463) [0.7502, 0.7502, 0.7502] PeriodicSite: Li+ (1.0031, 0.7372, 1.5806) [0.2498, 0.2498, 0.2498], 'Li2O2': Structure Summary Lattice abc : 3.1830000000000007 3.1830000000000003 7.7258 angles : 90.0 90.0 120.00000000000001 volume : 67.7871492344378 A : -1.5915000000000006 -2.756558860245869 -3.898050761686025e-16 B : -1.5914999999999992 2.756558860245869 1.9490253808430124e-16 C : 0.0 0.0 -7.7258 pbc : True True True PeriodicSite: Li+ (0.0000, 0.0000, -3.8629) [0.0000, 0.0000, 0.5000] PeriodicSite: Li+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (-1.5915, -0.9190, -5.7943) [0.6667, 0.3333, 0.7500] PeriodicSite: Li+ (-1.5915, 0.9190, -1.9314) [0.3333, 0.6667, 0.2500] PeriodicSite: O- (-1.5915, -0.9190, -1.1566) [0.6667, 0.3333, 0.1497] PeriodicSite: O- (-1.5915, 0.9190, -6.5692) [0.3333, 0.6667, 0.8503] PeriodicSite: O- (-1.5915, 0.9190, -5.0195) [0.3333, 0.6667, 0.6497] PeriodicSite: O- (-1.5915, -0.9190, -2.7063) [0.6667, 0.3333, 0.3503], 'Li3V2(PO4)3': Structure Summary Lattice abc : 8.64068 8.67265 8.64068 angles : 61.21317 61.3442 61.21317 volume : 470.7978186322687 A : -2.470939478415996 -7.168424451387926 -4.143609518420984 B : -7.600861301025969 0.0 -4.17633397910965 C : 0.0 0.0 -8.64068 pbc : True True True PeriodicSite: Li0+ (-9.8221, -7.1201, -8.1771) [0.9933, 0.9693, 0.0015] PeriodicSite: Li0+ (-5.2652, -3.5733, -8.6603) [0.4985, 0.5307, 0.5067] PeriodicSite: Li0+ (-6.0857, -1.1171, -6.7518) [0.1558, 0.7500, 0.3442] PeriodicSite: Li0+ (-3.9986, -6.0875, -10.1861) [0.8492, 0.2500, 0.6508] PeriodicSite: Li0+ (-4.4741, -5.3421, -5.9052) [0.7452, 0.3464, 0.1586] PeriodicSite: Li0+ (-2.0112, -2.4471, -8.5778) [0.3414, 0.1536, 0.7548] PeriodicSite: V0+ (-8.6165, -6.1274, -14.5645) [0.8548, 0.8558, 0.8621] PeriodicSite: V0+ (-6.4732, -4.5730, -10.9092) [0.6379, 0.6442, 0.6452] PeriodicSite: V0+ (-3.5744, -2.5407, -5.9951) [0.3544, 0.3550, 0.3522] PeriodicSite: V0+ (-1.4669, -1.0591, -2.4754) [0.1478, 0.1450, 0.1456] PeriodicSite: P0+ (-7.8497, -1.7789, -9.7592) [0.2482, 0.9521, 0.5503] PeriodicSite: P0+ (-6.5114, -6.8080, -8.3997) [0.9497, 0.5479, 0.2518] PeriodicSite: P0+ (-6.8308, -3.2786, -5.3958) [0.4574, 0.7500, 0.0426] PeriodicSite: P0+ (-3.2537, -3.9267, -11.5417) [0.5478, 0.2500, 0.9522] PeriodicSite: P0+ (-3.5598, -0.2774, -8.5391) [0.0387, 0.4558, 0.7494] PeriodicSite: P0+ (-2.1909, -5.3806, -7.2809) [0.7506, 0.0442, 0.4613] PeriodicSite: O0+ (-8.3983, -5.1136, -10.9141) [0.7133, 0.8730, 0.4991] PeriodicSite: O0+ (-6.5103, -3.5115, -12.5689) [0.4899, 0.6973, 0.8827] PeriodicSite: O0+ (-7.4256, -0.5548, -10.6251) [0.0774, 0.9518, 0.7325] PeriodicSite: O0+ (-7.9453, -1.4000, -8.2592) [0.1953, 0.9818, 0.3876] PeriodicSite: O0+ (-6.7928, -2.9117, -9.8164) [0.4062, 0.7617, 0.5732] PeriodicSite: O0+ (-5.7536, -6.2988, -11.6913) [0.8787, 0.4713, 0.7039] PeriodicSite: O0+ (-7.9023, -6.6440, -7.7347) [0.9268, 0.7384, 0.0938] PeriodicSite: O0+ (-6.0633, -5.5016, -9.1213) [0.7675, 0.5482, 0.4226] PeriodicSite: O0+ (-7.6267, -4.4251, -5.9980) [0.6173, 0.8027, 0.0101] PeriodicSite: O0+ (-7.5702, -1.8930, -5.4665) [0.2641, 0.9101, 0.0661] PeriodicSite: O0+ (-4.4855, -4.0749, -10.6051) [0.5685, 0.4053, 0.7588] PeriodicSite: O0+ (-4.7679, -0.0067, -9.4196) [0.0009, 0.6270, 0.7867] PeriodicSite: O0+ (-5.3896, -7.0627, -7.3776) [0.9852, 0.3888, 0.1934] PeriodicSite: O0+ (-5.5557, -3.1102, -6.2999) [0.4339, 0.5899, 0.2359] PeriodicSite: O0+ (-2.5509, -5.3129, -11.5157) [0.7412, 0.0947, 0.9316] PeriodicSite: O0+ (-2.3963, -2.7970, -10.9316) [0.3902, 0.1884, 0.9869] PeriodicSite: O0+ (-3.8311, -1.6586, -7.8407) [0.2314, 0.4288, 0.5892] PeriodicSite: O0+ (-2.2016, -0.4825, -9.2908) [0.0673, 0.2678, 0.9135] PeriodicSite: O0+ (-3.2143, -4.2040, -7.1387) [0.5865, 0.2322, 0.4327] PeriodicSite: O0+ (-4.2162, -0.8054, -5.2624) [0.1124, 0.5182, 0.3047] PeriodicSite: O0+ (-2.1852, -5.7069, -8.7871) [0.7961, 0.0287, 0.6213] PeriodicSite: O0+ (-2.7916, -6.5290, -6.3923) [0.9108, 0.0712, 0.2686] PeriodicSite: O0+ (-3.6360, -3.6778, -4.3760) [0.5131, 0.3116, 0.1098] PeriodicSite: O0+ (-1.6028, -2.1976, -6.1825) [0.3066, 0.1112, 0.5148], 'LiFePO4': Structure Summary Lattice abc : 4.7448 6.0657700000000006 10.41037 angles : 90.50178999999999 90.00019 90.00362 volume : 299.60796771125047 A : 0.0 0.0 -4.7448 B : -0.053122654367700306 -6.065537365280947 0.00038324092231544317 C : 10.41036999994276 0.0 3.452209424235223e-05 pbc : True True True PeriodicSite: Li (10.3571, -6.0655, 0.0004) [0.0000, 1.0000, 1.0000] PeriodicSite: Li (-0.0265, -3.0328, -4.7446) [1.0000, 0.5000, 0.0000] PeriodicSite: Li (5.1521, -6.0655, -2.3720) [0.5000, 1.0000, 0.5000] PeriodicSite: Li (5.1786, -3.0328, -2.3723) [0.5000, 0.5000, 0.5000] PeriodicSite: Fe (2.2647, -1.5372, -2.4912) [0.5251, 0.2534, 0.2188] PeriodicSite: Fe (2.8873, -4.5282, -0.1187) [0.0251, 0.7465, 0.2812] PeriodicSite: Fe (7.4699, -1.5374, -4.6259) [0.9750, 0.2535, 0.7188] PeriodicSite: Fe (8.0925, -4.5281, -2.2531) [0.4749, 0.7465, 0.7812] PeriodicSite: P (0.9432, -4.5594, -2.7614) [0.5821, 0.7517, 0.0944] PeriodicSite: P (4.2088, -1.5061, -0.3893) [0.0821, 0.2483, 0.4056] PeriodicSite: P (6.1483, -4.5597, -4.3551) [0.9179, 0.7517, 0.5944] PeriodicSite: P (9.4141, -1.5060, -1.9829) [0.4179, 0.2483, 0.9056] PeriodicSite: O (0.4361, -1.5232, -1.3833) [0.2916, 0.2511, 0.0432] PeriodicSite: O (0.9618, -4.5518, -1.2263) [0.2585, 0.7504, 0.0962] PeriodicSite: O (1.6753, -5.7983, -3.3849) [0.7135, 0.9559, 0.1658] PeriodicSite: O (1.6950, -3.3276, -3.3983) [0.7163, 0.5486, 0.1656] PeriodicSite: O (3.4570, -2.7380, -1.0261) [0.2163, 0.4514, 0.3344] PeriodicSite: O (3.4767, -0.2672, -1.0127) [0.2135, 0.0441, 0.3342] PeriodicSite: O (4.1902, -1.5137, -3.5989) [0.7585, 0.2495, 0.4038] PeriodicSite: O (4.7159, -4.5425, -3.7555) [0.7916, 0.7489, 0.4568] PeriodicSite: O (5.6412, -1.5231, -0.9889) [0.2084, 0.2511, 0.5432] PeriodicSite: O (6.1670, -4.5519, -1.1455) [0.2415, 0.7505, 0.5962] PeriodicSite: O (6.8801, -5.7988, -3.7318) [0.7866, 0.9560, 0.6658] PeriodicSite: O (6.9004, -3.3280, -3.7181) [0.7837, 0.5487, 0.6656] PeriodicSite: O (8.6620, -2.7376, -1.3457) [0.2837, 0.4513, 0.8344] PeriodicSite: O (8.6823, -0.2668, -1.3597) [0.2866, 0.0440, 0.8342] PeriodicSite: O (9.3954, -1.5138, -3.5181) [0.7415, 0.2496, 0.9038] PeriodicSite: O (9.9213, -4.5424, -3.3610) [0.7084, 0.7489, 0.9568], 'NaFePO4': Structure Summary Lattice abc : 4.9955 6.28746 10.440590000000002 angles : 90.0 89.97269 90.0 volume : 327.9285211911844 A : 0.0 0.0 -4.9955 B : 3.849958881883509e-16 -6.28746 -3.849958881883509e-16 C : -10.440588813976833 0.0 -0.004976500966151329 pbc : True True True PeriodicSite: Na (-10.4402, -6.2870, -5.0004) [1.0000, 0.9999, 1.0000] PeriodicSite: Na (-10.4402, -3.1442, -5.0004) [1.0000, 0.5001, 1.0000] PeriodicSite: Na (-5.2197, -6.2870, -2.5005) [0.5001, 0.9999, 0.4999] PeriodicSite: Na (-5.2197, -3.1442, -2.5005) [0.5001, 0.5001, 0.4999] PeriodicSite: Fe (-8.2056, -1.5719, -2.6193) [0.5235, 0.2500, 0.7859] PeriodicSite: Fe (-7.4584, -4.7156, -0.1238) [0.0241, 0.7500, 0.7144] PeriodicSite: Fe (-2.9844, -1.5719, -4.8792) [0.9764, 0.2500, 0.2859] PeriodicSite: Fe (-2.2367, -4.7156, -2.3805) [0.4763, 0.7500, 0.2142] PeriodicSite: P (-9.3366, -4.7156, -2.8377) [0.5672, 0.7500, 0.8943] PeriodicSite: P (-6.3250, -1.5719, -0.3370) [0.0669, 0.2500, 0.6058] PeriodicSite: P (-4.1164, -4.7156, -4.6625) [0.9329, 0.7500, 0.3943] PeriodicSite: P (-1.1040, -1.5719, -2.1641) [0.4331, 0.2500, 0.1057] PeriodicSite: O (-10.0753, -1.5719, -1.6636) [0.3321, 0.2500, 0.9650] PeriodicSite: O (-9.2800, -4.7156, -1.2986) [0.2591, 0.7500, 0.8888] PeriodicSite: O (-8.6132, -5.9528, -3.4881) [0.6974, 0.9468, 0.8250] PeriodicSite: O (-8.6132, -3.4783, -3.4881) [0.6974, 0.5532, 0.8250] PeriodicSite: O (-7.0467, -2.8104, -0.9879) [0.1971, 0.4470, 0.6749] PeriodicSite: O (-7.0467, -0.3333, -0.9879) [0.1971, 0.0530, 0.6749] PeriodicSite: O (-6.3830, -1.5719, -3.7937) [0.7588, 0.2500, 0.6114] PeriodicSite: O (-5.5841, -4.7156, -4.1557) [0.8314, 0.7500, 0.5348] PeriodicSite: O (-4.8549, -1.5719, -0.8420) [0.1681, 0.2500, 0.4650] PeriodicSite: O (-4.0586, -4.7156, -1.2059) [0.2410, 0.7500, 0.3887] PeriodicSite: O (-3.3933, -5.9537, -4.0111) [0.8026, 0.9469, 0.3250] PeriodicSite: O (-3.3933, -3.4775, -4.0111) [0.8026, 0.5531, 0.3250] PeriodicSite: O (-1.8263, -2.8099, -1.5129) [0.3027, 0.4469, 0.1749] PeriodicSite: O (-1.8263, -0.3338, -1.5129) [0.3027, 0.0531, 0.1749] PeriodicSite: O (-1.1622, -1.5719, -3.7030) [0.7412, 0.2500, 0.1113] PeriodicSite: O (-0.3650, -4.7156, -3.3387) [0.6683, 0.7500, 0.0350], 'Pb2TiZrO6': Structure Summary Lattice abc : 4.505383 5.67298 5.67298 angles : 90.0 90.0 90.0 volume : 144.99539884709878 A : 0.0 0.0 4.505383 B : 5.67298 0.0 0.0 C : 0.0 5.67298 0.0 pbc : True True True PeriodicSite: Zr (2.8365, 0.0000, 2.4376) [0.5410, 0.5000, -0.0000] PeriodicSite: Ti (0.0000, 2.8365, 2.4188) [0.5369, -0.0000, 0.5000] PeriodicSite: Pb (0.0000, 0.0000, 4.4114) [0.9791, -0.0000, -0.0000] PeriodicSite: Pb (2.8365, 2.8365, 4.4114) [0.9791, 0.5000, 0.5000] PeriodicSite: O (1.3704, 1.4661, 2.8748) [0.6381, 0.2416, 0.2584] PeriodicSite: O (1.3704, 4.2069, 2.8748) [0.6381, 0.2416, 0.7416] PeriodicSite: O (4.3026, 1.4661, 2.8748) [0.6381, 0.7584, 0.2584] PeriodicSite: O (4.3026, 4.2069, 2.8748) [0.6381, 0.7584, 0.7416] PeriodicSite: O (0.0000, 2.8365, 0.6698) [0.1487, -0.0000, 0.5000] PeriodicSite: O (2.8365, 0.0000, 0.4587) [0.1018, 0.5000, -0.0000], 'Si': Structure Summary Lattice abc : 3.8401979337 3.840198994344244 3.8401979337177736 angles : 119.99999086398421 90.0 60.0000091373222 volume : 40.04479464425159 A : 3.8401979337 0.0 0.0 B : 1.9200989668 3.3257101909 0.0 C : 0.0 -2.2171384943 3.1355090603 pbc : True True True PeriodicSite: Si (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Si (3.8402, 0.0000, 2.3516) [0.7500, 0.5000, 0.7500], 'SiO2': Structure Summary Lattice abc : 5.0277818 5.0277817873408415 5.51891759 angles : 90.0 90.0 120.00000005747829 volume : 120.81959693044213 A : 5.0277818 6e-08 -0.0 B : -2.51389095 4.35418672 0.0 C : -0.0 0.0 5.51891759 pbc : True True True PeriodicSite: Si (1.3140, 2.2760, 5.5189) [0.5227, 0.5227, 1.0000] PeriodicSite: Si (2.3997, -0.0000, 3.6792) [0.4773, -0.0000, 0.6667] PeriodicSite: Si (3.8279, 2.0782, 1.8396) [1.0000, 0.4773, 0.3333] PeriodicSite: O (0.8313, 3.6543, 4.8051) [0.5850, 0.8393, 0.8707] PeriodicSite: O (-1.0664, 3.2469, 2.9655) [0.1607, 0.7457, 0.5373] PeriodicSite: O (0.2352, 1.8071, 1.1259) [0.2543, 0.4150, 0.2040] PeriodicSite: O (2.7491, 2.5470, 0.7137) [0.8393, 0.5850, 0.1293] PeriodicSite: O (3.3452, 0.6999, 2.5533) [0.7457, 0.1607, 0.4626] PeriodicSite: O (1.4474, 1.1073, 4.3929) [0.4150, 0.2543, 0.7960], 'Si_SiO2_Interface': Structure Summary Lattice abc : 10.160210588671637 10.160210588671637 29.156770002399192 angles : 90.0 90.0 59.99999999999999 volume : 2606.6064276838156 A : 10.160210588671637 0.0 6.221334688039882e-16 B : 5.080105294335819 8.799000477589283 6.221334688039882e-16 C : 0.0 0.0 29.156770002399192 pbc : True True True PeriodicSite: Si (10.3416, 3.8758, 9.3499) [0.7976, 0.4405, 0.3207] PeriodicSite: Si (13.9703, 5.1328, 9.3499) [1.0833, 0.5833, 0.3207] PeriodicSite: Si (7.4387, 6.3898, 9.3499) [0.3690, 0.7262, 0.3207] PeriodicSite: Si (11.0674, 7.6468, 9.3499) [0.6548, 0.8690, 0.3207] PeriodicSite: Si (9.6159, 0.1048, 9.3499) [0.9405, 0.0119, 0.3207] PeriodicSite: Si (3.0843, 1.3618, 9.3499) [0.2262, 0.1548, 0.3207] PeriodicSite: Si (6.7130, 2.6188, 9.3499) [0.5119, 0.2976, 0.3207] PeriodicSite: Si (10.3416, 3.8758, 11.7016) [0.7976, 0.4405, 0.4013] PeriodicSite: Si (13.9703, 5.1328, 11.7016) [1.0833, 0.5833, 0.4013] PeriodicSite: Si (7.4387, 6.3898, 11.7016) [0.3690, 0.7262, 0.4013] PeriodicSite: Si (11.0674, 7.6468, 11.7016) [0.6548, 0.8690, 0.4013] PeriodicSite: Si (9.6159, 0.1048, 11.7016) [0.9405, 0.0119, 0.4013] PeriodicSite: Si (3.0843, 1.3618, 11.7016) [0.2262, 0.1548, 0.4013] PeriodicSite: Si (6.7130, 2.6188, 11.7016) [0.5119, 0.2976, 0.4013] PeriodicSite: Si (3.8678, 2.0998, 13.7016) [0.2614, 0.2386, 0.4699] PeriodicSite: Si (6.4078, 6.4993, 13.7016) [0.2614, 0.7386, 0.4699] PeriodicSite: Si (8.9479, 2.0998, 13.7016) [0.7614, 0.2386, 0.4699] PeriodicSite: Si (11.4879, 6.4993, 13.7016) [0.7614, 0.7386, 0.4699] PeriodicSite: Si (4.9647, 4.3995, 15.5412) [0.2386, 0.5000, 0.5330] PeriodicSite: Si (2.4247, 0.0000, 15.5412) [0.2386, 0.0000, 0.5330] PeriodicSite: Si (10.0448, 4.3995, 15.5412) [0.7386, 0.5000, 0.5330] PeriodicSite: Si (7.5048, 0.0000, 15.5412) [0.7386, 0.0000, 0.5330] PeriodicSite: Si (1.3277, 2.2997, 17.3808) [0.0000, 0.2614, 0.5961] PeriodicSite: Si (3.8678, 6.6992, 17.3808) [0.0000, 0.7614, 0.5961] PeriodicSite: Si (6.4078, 2.2997, 17.3808) [0.5000, 0.2614, 0.5961] PeriodicSite: Si (8.9479, 6.6992, 17.3808) [0.5000, 0.7614, 0.5961] PeriodicSite: O (3.3800, 0.7072, 14.4153) [0.2925, 0.0804, 0.4944] PeriodicSite: O (5.9200, 5.1067, 14.4153) [0.2925, 0.5804, 0.4944] PeriodicSite: O (8.4601, 0.7072, 14.4153) [0.7925, 0.0804, 0.4944] PeriodicSite: O (11.0001, 5.1067, 14.4153) [0.7925, 0.5804, 0.4944] PeriodicSite: O (1.4625, 1.1188, 16.2550) [0.0804, 0.1271, 0.5575] PeriodicSite: O (4.0026, 5.5183, 16.2550) [0.0804, 0.6271, 0.5575] PeriodicSite: O (6.5426, 1.1188, 16.2550) [0.5804, 0.1271, 0.5575] PeriodicSite: O (9.0827, 5.5183, 16.2550) [0.5804, 0.6271, 0.5575] PeriodicSite: O (2.7777, 2.5735, 18.0946) [0.1271, 0.2925, 0.6206] PeriodicSite: O (5.3177, 6.9730, 18.0946) [0.1271, 0.7925, 0.6206] PeriodicSite: O (7.8578, 2.5735, 18.0946) [0.6271, 0.2925, 0.6206] PeriodicSite: O (10.3978, 6.9730, 18.0946) [0.6271, 0.7925, 0.6206] PeriodicSite: O (5.3177, 1.8260, 18.5067) [0.4196, 0.2075, 0.6347] PeriodicSite: O (7.8578, 6.2255, 18.5067) [0.4196, 0.7075, 0.6347] PeriodicSite: O (10.3978, 1.8260, 18.5067) [0.9196, 0.2075, 0.6347] PeriodicSite: O (12.9379, 6.2255, 18.5067) [0.9196, 0.7075, 0.6347] PeriodicSite: O (5.9200, 3.6923, 16.6671) [0.3729, 0.4196, 0.5716] PeriodicSite: O (8.4601, 8.0918, 16.6671) [0.3729, 0.9196, 0.5716] PeriodicSite: O (11.0001, 3.6923, 16.6671) [0.8729, 0.4196, 0.5716] PeriodicSite: O (13.5402, 8.0918, 16.6671) [0.8729, 0.9196, 0.5716] PeriodicSite: O (4.0026, 3.2807, 14.8274) [0.2075, 0.3729, 0.5085] PeriodicSite: O (6.5426, 7.6802, 14.8274) [0.2075, 0.8729, 0.5085] PeriodicSite: O (9.0827, 3.2807, 14.8274) [0.7075, 0.3729, 0.5085] PeriodicSite: O (11.6227, 7.6802, 14.8274) [0.7075, 0.8729, 0.5085], 'Sn': Structure Summary Lattice abc : 6.65061477 6.65061477 6.65061477 angles : 90.0 90.0 90.0 volume : 294.16119253915326 A : 6.65061477 0.0 0.0 B : 0.0 6.65061477 0.0 C : 0.0 0.0 6.65061477 pbc : True True True PeriodicSite: Sn (2.4940, 5.8193, 2.4940) [0.3750, 0.8750, 0.3750] PeriodicSite: Sn (0.8313, 0.8313, 0.8313) [0.1250, 0.1250, 0.1250] PeriodicSite: Sn (2.4940, 2.4940, 5.8193) [0.3750, 0.3750, 0.8750] PeriodicSite: Sn (0.8313, 4.1566, 4.1566) [0.1250, 0.6250, 0.6250] PeriodicSite: Sn (5.8193, 5.8193, 5.8193) [0.8750, 0.8750, 0.8750] PeriodicSite: Sn (4.1566, 0.8313, 4.1566) [0.6250, 0.1250, 0.6250] PeriodicSite: Sn (5.8193, 2.4940, 2.4940) [0.8750, 0.3750, 0.3750] PeriodicSite: Sn (4.1566, 4.1566, 0.8313) [0.6250, 0.6250, 0.1250], 'SrTiO3': Structure Summary Lattice abc : 3.905 3.905 3.905 angles : 90.0 90.0 90.0 volume : 59.54744262499999 A : 3.905 0.0 2.391122875335207e-16 B : -2.391122875335207e-16 3.905 2.391122875335207e-16 C : 0.0 0.0 3.905 pbc : True True True PeriodicSite: Sr2+ (1.9525, 1.9525, 1.9525) [0.5000, 0.5000, 0.5000] PeriodicSite: Ti4+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (0.0000, 0.0000, 1.9525) [0.0000, 0.0000, 0.5000] PeriodicSite: O2- (-0.0000, 1.9525, 0.0000) [0.0000, 0.5000, 0.0000] PeriodicSite: O2- (1.9525, 0.0000, 0.0000) [0.5000, 0.0000, 0.0000], 'TiO2': <pymatgen.alchemy.materials.TransformedStructure object>, 'TlBiSe2': Structure Summary Lattice abc : 4.372201544153475 61.149528191254596 59.08304095958131 angles : 3.6737691014605547 58.80413768014368 59.97014152897428 volume : 825.8885392060803 A : 3.74140218 -0.00027862 2.26231209 B : -1.13595131 3.78041753 61.02198666 C : 0.036913 0.04093202 59.08301525 pbc : True True True PeriodicSite: Tl (2.5148, 3.6745, 63.4338) [0.9669, 0.9717, 0.0330] PeriodicSite: Tl (3.6037, 0.2035, 6.7146) [0.9793, 0.0537, 0.0207] PeriodicSite: Tl (3.5726, 0.5326, 10.9899) [0.9977, 0.1409, 0.0022] PeriodicSite: Tl (-0.2434, 0.8101, 13.0761) [0.0000, 0.2143, -0.0000] PeriodicSite: Tl (-0.2812, 1.1282, 76.5077) [0.0023, 0.2876, 0.9978] PeriodicSite: Tl (-0.3122, 1.4572, 80.7830) [0.0207, 0.3749, 0.9793] PeriodicSite: Tl (-0.3594, 1.7667, 85.0859) [0.0331, 0.4569, 0.9670] PeriodicSite: Bi (-0.4251, 2.0554, 89.4184) [0.0388, 0.5333, 0.9611] PeriodicSite: Bi (-0.5892, 2.2281, 93.9147) [0.0084, 0.5786, 0.9916] PeriodicSite: Bi (-0.6750, 2.4926, 98.2811) [0.0067, 0.6486, 0.9933] PeriodicSite: Bi (-0.8113, 2.7004, 43.5869) [0.0000, 0.7143, -0.0000] PeriodicSite: Bi (2.8309, 2.9491, 50.2379) [0.9934, 0.7801, 0.0066] PeriodicSite: Bi (2.7442, 3.2126, 54.6058) [0.9914, 0.8498, 0.0086] PeriodicSite: Bi (2.5805, 3.3856, 59.1013) [0.9611, 0.8952, 0.0389] PeriodicSite: Se (1.7377, 0.2085, 35.1484) [0.4743, 0.0495, 0.5256] PeriodicSite: Se (1.6987, 0.5271, 39.4370) [0.4897, 0.1339, 0.5104] PeriodicSite: Se (1.6462, 0.8311, 43.7478) [0.5002, 0.2145, 0.4998] PeriodicSite: Se (1.5935, 1.1347, 48.0594) [0.5106, 0.2949, 0.4893] PeriodicSite: Se (1.5531, 1.4514, 52.3505) [0.5255, 0.3788, 0.4747] PeriodicSite: Se (1.4871, 1.7413, 56.6824) [0.5312, 0.4556, 0.4685] PeriodicSite: Se (1.4204, 2.0277, 61.0185) [0.5364, 0.5314, 0.4634] PeriodicSite: Se (1.2436, 2.1850, 65.5372) [0.5013, 0.5726, 0.4986] PeriodicSite: Se (1.1826, 2.4786, 69.8633) [0.5087, 0.6503, 0.4913] PeriodicSite: Se (1.0777, 2.7207, 74.2599) [0.5000, 0.7143, 0.5000] PeriodicSite: Se (0.9728, 2.9625, 78.6564) [0.4913, 0.7782, 0.5088] PeriodicSite: Se (0.9121, 3.2562, 82.9823) [0.4987, 0.8560, 0.5014] PeriodicSite: Se (0.7353, 3.4138, 87.5010) [0.4636, 0.8973, 0.5365] PeriodicSite: Se (0.6680, 3.6996, 91.8379) [0.4687, 0.9729, 0.5316], 'VO2': <pymatgen.alchemy.materials.TransformedStructure object>}[source]

static assertArrayAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True)[source]: Tests if two arrays are almost equal to a tolerance. The CamelCase naming is so that it is consistent with standard unittest methods.

static assertArrayEqual(actual, desired, err_msg='', verbose=True)[source]

Tests if two arrays are equal. The CamelCase naming is so that it is: consistent with standard unittest methods.

static assertDictsAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True) → bool[source]: Tests if two arrays are almost equal to a tolerance. The CamelCase naming is so that it is consistent with standard unittest methods.

assertMSONable(obj, test_if_subclass=True)[source]

Tests if obj is MSONable and tries to verify whether the contract is fulfilled.

By default, the method tests whether obj is an instance of MSONable. This check can be deactivated by setting test_if_subclass to False.

static assertStrContentEqual(actual, desired, err_msg='', verbose=True)[source]: Tests if two strings are equal, ignoring things like trailing spaces, etc.

fn = PosixPath('/Users/shyue/repos/pymatgen/pymatgen/util/structures/SrTiO3.json')[source]

classmethod get_mp_structure(mpid: str) → Structure[source]

Get a structure from MP.

Parameters:: mpid – Materials Project id.
Returns:: Structure

classmethod get_structure(name: str) → Structure[source]

Get a structure from the template directories.

Parameters:: name – Name of a structure.
Returns:: Structure

serialize_with_pickle(objects, protocols=None, test_eq=True)[source]

Test whether the object(s) can be serialized and deserialized with pickle. This method tries to serialize the objects with pickle and the protocols specified in input. Then it deserializes the pickle format and compares the two objects with the __eq__ operator if test_eq is True.

Parameters:

objects – Object or list of objects.
protocols – List of pickle protocols to test. If protocols is None, HIGHEST_PROTOCOL is tested.
test_eq – If True, the deserialized object is compared with the original object using the __eq__ method.

Returns:

Nested list with the objects deserialized with the specified protocols.

warnings = <module 'warnings' from '/Users/shyue/miniconda3/envs/mavrl/lib/python3.9/warnings.py'>[source]