pymatgen.analysis.diffusion.neb.tests.test_pathfinder module

class DistinctPathFinderTest(methodName='runTest')

Bases: PymatgenTest

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.

test_get_paths()

test_max_path_length()

class IDPPSolverTest(methodName='runTest')

Bases: TestCase

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.

final_struct = Structure Summary Lattice     abc : 10.411723299877 12.0783517723596 9.47759961582329  angles : 90.0 90.0 90.0  volume : 1191.8693444977544       A : 10.411723299877 0.0 0.0       B : 0.0 12.0783517723596 0.0       C : 0.0 0.0 9.47759961582329     pbc : True True True PeriodicSite: Li (5.185, 6.182, 2.417) [0.498, 0.5118, 0.2551] PeriodicSite: Li (5.227, 11.94, 2.321) [0.502, 0.9882, 0.2449] PeriodicSite: Li (5.182, 12.07, 7.085) [0.4977, 0.999, 0.7475] PeriodicSite: Li (5.23, 6.051, 7.132) [0.5023, 0.501, 0.7525] PeriodicSite: Li (0.0005125, 3.018, 0.004327) [4.922e-05, 0.2499, 0.0004565] PeriodicSite: Li (10.41, 3.021, 4.734) [1.0, 0.2501, 0.4995] PeriodicSite: Li (10.41, 9.058, 0.003074) [0.9995, 0.75, 0.0003243] PeriodicSite: Li (0.005658, 9.059, 4.736) [0.0005434, 0.75, 0.4997] PeriodicSite: Li (5.206, 3.02, 2.369) [0.5, 0.25, 0.25] PeriodicSite: Li (5.206, 3.02, 7.108) [0.5, 0.25, 0.75] PeriodicSite: Li (5.206, 9.059, 7.108) [0.5, 0.75, 0.75] PeriodicSite: Li (10.41, 12.06, 0.008545) [0.9997, 0.9989, 0.0009016] PeriodicSite: Li (0.003162, 12.07, 4.738) [0.0003037, 0.9996, 0.5] PeriodicSite: Li (10.41, 6.043, 0.0004624) [0.9997, 0.5004, 4.879e-05] PeriodicSite: Li (0.002981, 6.053, 4.73) [0.0002863, 0.5011, 0.4991] PeriodicSite: Fe (8.141, 1.511, 2.487) [0.7819, 0.1251, 0.2624] PeriodicSite: Fe (8.141, 1.506, 7.228) [0.7819, 0.1247, 0.7626] PeriodicSite: Fe (8.1, 7.569, 2.472) [0.778, 0.6266, 0.2608] PeriodicSite: Fe (8.137, 7.545, 7.235) [0.7816, 0.6247, 0.7633] PeriodicSite: Fe (2.947, 1.502, 4.613) [0.283, 0.1243, 0.4867] PeriodicSite: Fe (2.938, 1.504, 9.355) [0.2822, 0.1245, 0.9871] PeriodicSite: Fe (2.957, 7.578, 4.609) [0.284, 0.6274, 0.4863] PeriodicSite: Fe (2.96, 7.565, 9.381) [0.2842, 0.6264, 0.9898] PeriodicSite: Fe (2.27, 4.528, 2.252) [0.2181, 0.3749, 0.2376] PeriodicSite: Fe (2.271, 4.533, 6.988) [0.2181, 0.3753, 0.7374] PeriodicSite: Fe (2.312, 10.55, 2.267) [0.222, 0.8734, 0.2392] PeriodicSite: Fe (2.274, 10.57, 6.982) [0.2184, 0.8753, 0.7367] PeriodicSite: Fe (7.465, 4.537, 0.1261) [0.717, 0.3757, 0.0133] PeriodicSite: Fe (7.473, 4.535, 4.861) [0.7178, 0.3755, 0.5129] PeriodicSite: Fe (7.455, 10.54, 0.1303) [0.716, 0.8726, 0.01374] PeriodicSite: Fe (7.452, 10.55, 4.836) [0.7158, 0.8736, 0.5102] PeriodicSite: P (6.198, 1.507, 0.3753) [0.5953, 0.1248, 0.0396] PeriodicSite: P (6.211, 1.514, 5.111) [0.5966, 0.1253, 0.5393] PeriodicSite: P (6.196, 7.548, 0.3633) [0.5951, 0.6249, 0.03833] PeriodicSite: P (6.22, 7.514, 5.12) [0.5974, 0.6221, 0.5402] PeriodicSite: P (0.9887, 1.504, 1.99) [0.09496, 0.1245, 0.2099] PeriodicSite: P (0.9865, 1.513, 6.727) [0.09475, 0.1253, 0.7098] PeriodicSite: P (0.9818, 7.544, 1.993) [0.0943, 0.6246, 0.2102] PeriodicSite: P (0.9911, 7.546, 6.738) [0.09519, 0.6248, 0.7109] PeriodicSite: P (4.214, 4.532, 4.364) [0.4047, 0.3752, 0.4604] PeriodicSite: P (4.2, 4.526, 9.105) [0.4034, 0.3747, 0.9607] PeriodicSite: P (4.216, 10.57, 4.376) [0.4049, 0.8751, 0.4617] PeriodicSite: P (4.191, 10.6, 9.097) [0.4026, 0.8779, 0.9598] PeriodicSite: P (9.423, 4.535, 2.749) [0.905, 0.3755, 0.2901] PeriodicSite: P (9.425, 4.526, 7.489) [0.9053, 0.3747, 0.7902] PeriodicSite: P (9.43, 10.57, 2.746) [0.9057, 0.8754, 0.2898] PeriodicSite: P (9.421, 10.57, 7.479) [0.9048, 0.8752, 0.7891] PeriodicSite: O (6.223, 1.527, 3.577) [0.5977, 0.1264, 0.3775] PeriodicSite: O (6.209, 1.513, 8.315) [0.5964, 0.1252, 0.8774] PeriodicSite: O (6.275, 7.44, 3.601) [0.6027, 0.616, 0.38] PeriodicSite: O (6.212, 7.545, 8.293) [0.5966, 0.6247, 0.875] PeriodicSite: O (0.9902, 1.512, 3.526) [0.0951, 0.1252, 0.372] PeriodicSite: O (0.9889, 1.512, 8.264) [0.09498, 0.1252, 0.8719] PeriodicSite: O (0.9898, 7.548, 3.529) [0.09506, 0.6249, 0.3724] PeriodicSite: O (0.9929, 7.54, 8.274) [0.09536, 0.6243, 0.873] PeriodicSite: O (4.189, 4.512, 1.161) [0.4023, 0.3736, 0.1225] PeriodicSite: O (4.202, 4.527, 5.901) [0.4036, 0.3748, 0.6226] PeriodicSite: O (4.137, 10.68, 1.137) [0.3973, 0.884, 0.12] PeriodicSite: O (4.2, 10.57, 5.923) [0.4034, 0.8753, 0.625] PeriodicSite: O (9.422, 4.527, 1.213) [0.9049, 0.3748, 0.128] PeriodicSite: O (9.423, 4.527, 5.953) [0.905, 0.3748, 0.6281] PeriodicSite: O (9.422, 10.57, 1.209) [0.9049, 0.8751, 0.1276] PeriodicSite: O (9.419, 10.58, 5.943) [0.9046, 0.8757, 0.627] PeriodicSite: O (9.968, 1.514, 1.379) [0.9574, 0.1253, 0.1455] PeriodicSite: O (9.966, 1.522, 6.119) [0.9572, 0.126, 0.6456] PeriodicSite: O (9.963, 7.543, 1.383) [0.9569, 0.6245, 0.1459] PeriodicSite: O (9.972, 7.541, 6.125) [0.9578, 0.6243, 0.6462] PeriodicSite: O (4.766, 1.52, 0.9751) [0.4577, 0.1259, 0.1029] PeriodicSite: O (4.778, 1.513, 5.718) [0.4589, 0.1253, 0.6033] PeriodicSite: O (4.763, 7.503, 0.9219) [0.4574, 0.6212, 0.09727] PeriodicSite: O (4.78, 7.542, 5.712) [0.4591, 0.6244, 0.6027] PeriodicSite: O (0.4439, 4.526, 3.36) [0.04263, 0.3747, 0.3545] PeriodicSite: O (0.4458, 4.517, 8.098) [0.04282, 0.374, 0.8544] PeriodicSite: O (0.4487, 10.57, 3.356) [0.0431, 0.8755, 0.3541] PeriodicSite: O (0.4398, 10.58, 8.092) [0.04224, 0.8757, 0.8538] PeriodicSite: O (5.646, 4.519, 3.764) [0.5423, 0.3741, 0.3971] PeriodicSite: O (5.634, 4.526, 8.498) [0.5411, 0.3747, 0.8967] PeriodicSite: O (5.649, 10.61, 3.817) [0.5426, 0.8788, 0.4027] PeriodicSite: O (5.632, 10.58, 8.505) [0.5409, 0.8756, 0.8973] PeriodicSite: O (6.938, 0.2665, 0.9991) [0.6664, 0.02207, 0.1054] PeriodicSite: O (6.962, 0.2813, 5.739) [0.6687, 0.02329, 0.6056] PeriodicSite: O (6.942, 6.299, 0.9884) [0.6668, 0.5215, 0.1043] PeriodicSite: O (6.941, 6.283, 5.805) [0.6667, 0.5202, 0.6125] PeriodicSite: O (1.738, 2.739, 1.363) [0.1669, 0.2268, 0.1439] PeriodicSite: O (1.739, 2.746, 6.102) [0.167, 0.2274, 0.6438] PeriodicSite: O (1.729, 8.776, 1.362) [0.1661, 0.7266, 0.1437] PeriodicSite: O (1.728, 8.787, 6.117) [0.1659, 0.7275, 0.6454] PeriodicSite: O (3.459, 3.3, 3.737) [0.3322, 0.2732, 0.3942] PeriodicSite: O (3.461, 3.288, 8.468) [0.3324, 0.2722, 0.8934] PeriodicSite: O (3.389, 9.374, 3.797) [0.3255, 0.7761, 0.4006] PeriodicSite: O (3.444, 9.36, 8.482) [0.3308, 0.7749, 0.895] PeriodicSite: O (8.688, 5.775, 3.373) [0.8344, 0.4782, 0.3559] PeriodicSite: O (8.691, 5.764, 8.119) [0.8347, 0.4773, 0.8567] PeriodicSite: O (8.685, 11.81, 3.366) [0.8342, 0.9781, 0.3552] PeriodicSite: O (8.669, 11.8, 8.11) [0.8326, 0.9771, 0.8557] PeriodicSite: O (3.473, 5.773, 3.74) [0.3336, 0.4779, 0.3946] PeriodicSite: O (3.45, 5.758, 8.477) [0.3313, 0.4767, 0.8944] PeriodicSite: O (3.469, 11.82, 3.75) [0.3332, 0.9785, 0.3957] PeriodicSite: O (3.47, 11.83, 8.412) [0.3333, 0.9798, 0.8875] PeriodicSite: O (8.674, 3.3, 3.375) [0.8331, 0.2732, 0.3561] PeriodicSite: O (8.673, 3.293, 8.114) [0.833, 0.2726, 0.8562] PeriodicSite: O (8.682, 9.342, 3.377) [0.8339, 0.7734, 0.3563] PeriodicSite: O (8.684, 9.33, 8.099) [0.8341, 0.7725, 0.8546] PeriodicSite: O (6.952, 2.739, 1.002) [0.6678, 0.2268, 0.1058] PeriodicSite: O (6.951, 2.752, 5.749) [0.6676, 0.2278, 0.6066] PeriodicSite: O (7.022, 8.744, 0.9423) [0.6745, 0.7239, 0.09942] PeriodicSite: O (6.967, 8.757, 5.734) [0.6692, 0.7251, 0.605] PeriodicSite: O (1.724, 0.2638, 1.366) [0.1656, 0.02184, 0.1441] PeriodicSite: O (1.721, 0.2747, 6.097) [0.1653, 0.02274, 0.6433] PeriodicSite: O (1.726, 6.303, 1.372) [0.1658, 0.5219, 0.1448] PeriodicSite: O (1.743, 6.316, 6.107) [0.1674, 0.5229, 0.6443]

init_struct = Structure Summary Lattice     abc : 10.411723299877 12.0783517723596 9.47759961582329  angles : 90.0 90.0 90.0  volume : 1191.8693444977544       A : 10.411723299877 0.0 0.0       B : 0.0 12.0783517723596 0.0       C : 0.0 0.0 9.47759961582329     pbc : True True True PeriodicSite: Li (5.187, 8.921, 2.417) [0.4982, 0.7386, 0.255] PeriodicSite: Li (5.206, 12.08, 2.369) [0.5, 1.0, 0.25] PeriodicSite: Li (5.206, 12.08, 7.108) [0.5, 1.0, 0.75] PeriodicSite: Li (5.206, 6.039, 7.108) [0.5, 0.5, 0.75] PeriodicSite: Li (10.41, 3.032, 0.007788) [0.9997, 0.251, 0.0008217] PeriodicSite: Li (0.002969, 3.023, 4.739) [0.0002851, 0.2503, 0.5] PeriodicSite: Li (10.41, 9.055, 4.493e-05) [0.9997, 0.7497, 4.741e-06] PeriodicSite: Li (0.002765, 9.046, 4.731) [0.0002656, 0.749, 0.4992] PeriodicSite: Li (5.224, 3.158, 2.322) [0.5018, 0.2614, 0.245] PeriodicSite: Li (5.182, 3.031, 7.084) [0.4977, 0.2509, 0.7475] PeriodicSite: Li (5.23, 9.047, 7.132) [0.5023, 0.7491, 0.7525] PeriodicSite: Li (0.0003644, 0.0009345, 0.005748) [3.5e-05, 7.737e-05, 0.0006065] PeriodicSite: Li (10.41, 12.08, 4.733) [1.0, 0.9999, 0.4994] PeriodicSite: Li (10.41, 6.039, 0.003601) [0.9995, 0.5, 0.00038] PeriodicSite: Li (0.005541, 6.039, 4.735) [0.0005322, 0.5, 0.4996] PeriodicSite: Fe (8.142, 1.509, 2.487) [0.782, 0.1249, 0.2624] PeriodicSite: Fe (8.141, 1.513, 7.228) [0.7819, 0.1253, 0.7627] PeriodicSite: Fe (8.101, 7.529, 2.472) [0.7781, 0.6233, 0.2608] PeriodicSite: Fe (8.137, 7.552, 7.234) [0.7816, 0.6253, 0.7633] PeriodicSite: Fe (2.947, 1.518, 4.614) [0.283, 0.1257, 0.4868] PeriodicSite: Fe (2.938, 1.517, 9.355) [0.2822, 0.1256, 0.9871] PeriodicSite: Fe (2.956, 7.52, 4.607) [0.2839, 0.6226, 0.4861] PeriodicSite: Fe (2.959, 7.533, 9.38) [0.2842, 0.6237, 0.9897] PeriodicSite: Fe (2.311, 4.549, 2.267) [0.2219, 0.3767, 0.2392] PeriodicSite: Fe (2.274, 4.526, 6.982) [0.2184, 0.3747, 0.7367] PeriodicSite: Fe (2.27, 10.57, 2.252) [0.218, 0.8751, 0.2376] PeriodicSite: Fe (2.271, 10.56, 6.988) [0.2181, 0.8747, 0.7373] PeriodicSite: Fe (7.455, 4.558, 0.1314) [0.7161, 0.3774, 0.01386] PeriodicSite: Fe (7.453, 4.546, 4.836) [0.7158, 0.3763, 0.5103] PeriodicSite: Fe (7.465, 10.56, 0.1251) [0.717, 0.8743, 0.0132] PeriodicSite: Fe (7.473, 10.56, 4.861) [0.7178, 0.8744, 0.5129] PeriodicSite: P (6.198, 1.511, 0.3753) [0.5953, 0.1251, 0.0396] PeriodicSite: P (6.211, 1.505, 5.111) [0.5966, 0.1246, 0.5393] PeriodicSite: P (6.196, 7.55, 0.3633) [0.5951, 0.6251, 0.03833] PeriodicSite: P (6.22, 7.584, 5.119) [0.5974, 0.6279, 0.5401] PeriodicSite: P (0.9888, 1.515, 1.99) [0.09497, 0.1255, 0.2099] PeriodicSite: P (0.9865, 1.506, 6.728) [0.09474, 0.1247, 0.7099] PeriodicSite: P (0.9815, 7.554, 1.992) [0.09427, 0.6254, 0.2102] PeriodicSite: P (0.9909, 7.552, 6.737) [0.09517, 0.6252, 0.7109] PeriodicSite: P (4.216, 4.528, 4.375) [0.4049, 0.3749, 0.4617] PeriodicSite: P (4.192, 4.495, 9.098) [0.4026, 0.3721, 0.9599] PeriodicSite: P (4.214, 10.57, 4.364) [0.4047, 0.8749, 0.4604] PeriodicSite: P (4.2, 10.57, 9.105) [0.4034, 0.8754, 0.9607] PeriodicSite: P (9.43, 4.524, 2.747) [0.9057, 0.3746, 0.2898] PeriodicSite: P (9.421, 4.526, 7.479) [0.9048, 0.3747, 0.7891] PeriodicSite: P (9.423, 10.56, 2.749) [0.905, 0.8745, 0.2901] PeriodicSite: P (9.425, 10.57, 7.488) [0.9053, 0.8753, 0.7901] PeriodicSite: O (6.222, 1.492, 3.577) [0.5976, 0.1236, 0.3775] PeriodicSite: O (6.21, 1.505, 8.315) [0.5965, 0.1246, 0.8774] PeriodicSite: O (6.274, 7.658, 3.601) [0.6026, 0.634, 0.3799] PeriodicSite: O (6.211, 7.552, 8.293) [0.5965, 0.6252, 0.8751] PeriodicSite: O (0.9903, 1.507, 3.526) [0.09511, 0.1248, 0.372] PeriodicSite: O (0.9896, 1.508, 8.264) [0.09505, 0.1248, 0.872] PeriodicSite: O (0.99, 7.55, 3.529) [0.09508, 0.6251, 0.3723] PeriodicSite: O (0.9927, 7.558, 8.273) [0.09534, 0.6258, 0.8729] PeriodicSite: O (4.137, 4.42, 1.138) [0.3974, 0.366, 0.1201] PeriodicSite: O (4.201, 4.527, 5.923) [0.4035, 0.3748, 0.6249] PeriodicSite: O (4.189, 10.59, 1.161) [0.4024, 0.8764, 0.1225] PeriodicSite: O (4.202, 10.57, 5.901) [0.4035, 0.8754, 0.6226] PeriodicSite: O (9.422, 4.528, 1.21) [0.9049, 0.3749, 0.1277] PeriodicSite: O (9.419, 4.52, 5.943) [0.9047, 0.3742, 0.6271] PeriodicSite: O (9.421, 10.57, 1.213) [0.9049, 0.8752, 0.128] PeriodicSite: O (9.422, 10.57, 5.952) [0.905, 0.8752, 0.628] PeriodicSite: O (9.968, 1.505, 1.378) [0.9574, 0.1246, 0.1454] PeriodicSite: O (9.966, 1.497, 6.12) [0.9572, 0.1239, 0.6457] PeriodicSite: O (9.962, 7.555, 1.383) [0.9568, 0.6255, 0.1459] PeriodicSite: O (9.972, 7.557, 6.124) [0.9577, 0.6257, 0.6462] PeriodicSite: O (4.766, 1.5, 0.9756) [0.4577, 0.1242, 0.1029] PeriodicSite: O (4.778, 1.506, 5.719) [0.4589, 0.1247, 0.6034] PeriodicSite: O (4.763, 7.596, 0.9216) [0.4574, 0.6289, 0.09724] PeriodicSite: O (4.779, 7.556, 5.71) [0.459, 0.6256, 0.6024] PeriodicSite: O (0.4493, 4.523, 3.356) [0.04315, 0.3745, 0.3541] PeriodicSite: O (0.44, 4.521, 8.092) [0.04226, 0.3743, 0.8538] PeriodicSite: O (0.4436, 10.57, 3.36) [0.0426, 0.8754, 0.3546] PeriodicSite: O (0.4459, 10.58, 8.097) [0.04283, 0.8761, 0.8543] PeriodicSite: O (5.649, 4.483, 3.817) [0.5426, 0.3711, 0.4028] PeriodicSite: O (5.633, 4.522, 8.507) [0.541, 0.3744, 0.8976] PeriodicSite: O (5.646, 10.58, 3.763) [0.5423, 0.8758, 0.3971] PeriodicSite: O (5.633, 10.57, 8.497) [0.5411, 0.8753, 0.8966] PeriodicSite: O (6.951, 0.2785, 1.003) [0.6676, 0.02306, 0.1058] PeriodicSite: O (6.95, 0.266, 5.748) [0.6675, 0.02202, 0.6065] PeriodicSite: O (7.022, 6.354, 0.9424) [0.6744, 0.5261, 0.09944] PeriodicSite: O (6.966, 6.34, 5.733) [0.669, 0.5249, 0.6049] PeriodicSite: O (1.725, 2.756, 1.366) [0.1657, 0.2281, 0.1441] PeriodicSite: O (1.721, 2.745, 6.097) [0.1653, 0.2272, 0.6433] PeriodicSite: O (1.726, 8.795, 1.372) [0.1657, 0.7282, 0.1447] PeriodicSite: O (1.743, 8.782, 6.106) [0.1674, 0.7271, 0.6442] PeriodicSite: O (3.469, 3.278, 3.752) [0.3332, 0.2714, 0.3959] PeriodicSite: O (3.47, 3.264, 8.411) [0.3333, 0.2702, 0.8875] PeriodicSite: O (3.472, 9.327, 3.74) [0.3335, 0.7722, 0.3946] PeriodicSite: O (3.448, 9.342, 8.477) [0.3312, 0.7734, 0.8944] PeriodicSite: O (8.683, 5.756, 3.377) [0.8339, 0.4765, 0.3563] PeriodicSite: O (8.683, 5.767, 8.099) [0.834, 0.4775, 0.8545] PeriodicSite: O (8.674, 11.8, 3.375) [0.8331, 0.9768, 0.3561] PeriodicSite: O (8.673, 11.81, 8.114) [0.833, 0.9774, 0.8561] PeriodicSite: O (3.39, 5.725, 3.796) [0.3256, 0.474, 0.4006] PeriodicSite: O (3.446, 5.739, 8.484) [0.331, 0.4751, 0.8951] PeriodicSite: O (3.461, 11.8, 3.736) [0.3324, 0.9769, 0.3942] PeriodicSite: O (3.462, 11.81, 8.468) [0.3325, 0.978, 0.8935] PeriodicSite: O (8.686, 3.283, 3.367) [0.8343, 0.2718, 0.3553] PeriodicSite: O (8.669, 3.296, 8.111) [0.8326, 0.2729, 0.8558] PeriodicSite: O (8.687, 9.323, 3.373) [0.8343, 0.7719, 0.3559] PeriodicSite: O (8.691, 9.334, 8.119) [0.8347, 0.7728, 0.8567] PeriodicSite: O (6.94, 2.751, 0.9992) [0.6665, 0.2278, 0.1054] PeriodicSite: O (6.963, 2.736, 5.739) [0.6688, 0.2266, 0.6056] PeriodicSite: O (6.942, 8.8, 0.9868) [0.6668, 0.7286, 0.1041] PeriodicSite: O (6.942, 8.815, 5.805) [0.6667, 0.7298, 0.6125] PeriodicSite: O (1.738, 0.2801, 1.364) [0.1669, 0.02319, 0.1439] PeriodicSite: O (1.739, 0.2732, 6.102) [0.167, 0.02262, 0.6439] PeriodicSite: O (1.729, 6.322, 1.362) [0.1661, 0.5235, 0.1437] PeriodicSite: O (1.729, 6.311, 6.117) [0.166, 0.5225, 0.6455]

test_idpp()

test_idpp_from_ep()

test_idpp_from_ep_diff_latt()

class MigrationHopTest(methodName='runTest')

Bases: PymatgenTest

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.

setUp()

Hook method for setting up the test fixture before exercising it.

test_get_sc_structures()

test_get_sc_structures_vacmode()

test_get_start_end_structs_from_hop()

test_get_start_end_structs_from_hop_vac()

test_msonable()

get_path(path_str, dirname='./')