pymatgen.analysis.diffusion.neb.tests.test_io module

class MVLCINEBEndPointSetTest(methodName='runTest')[source]

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.

endpoint = Structure Summary Lattice     abc : 8.815000056846058 8.815000056846058 9.131710473490111  angles : 61.14080369885537 61.14080369885537 59.9999995733517  volume : 510.2218449146199       A : -4.4075 -7.634014 -0.0       B : 4.4075 -7.634014 0.0       C : -0.0 -5.089343 7.582     pbc : True True True PeriodicSite: Na (0.0, 0.0, 0.0) [0.0, 0.0, 0.0] PeriodicSite: Zr (9.811e-17, -10.18, 0.4774) [0.6457, 0.6457, 0.06296] PeriodicSite: Zr (-2.422e-17, -5.089, 4.268) [0.1457, 0.1457, 0.563] PeriodicSite: Zr (-7.549e-17, -10.18, 7.105) [0.3543, 0.3543, 0.937] PeriodicSite: Zr (-9.811e-17, -15.27, 3.314) [0.8543, 0.8543, 0.437] PeriodicSite: P (-1.837, -7.634, 5.686) [0.4584, 0.0416, 0.75] PeriodicSite: P (3.122, -9.86, 5.686) [0.0416, 0.75, 0.75] PeriodicSite: P (-1.285, -13.04, 5.686) [0.75, 0.4584, 0.75] PeriodicSite: P (-3.122, -10.5, 1.895) [0.9584, 0.25, 0.25] PeriodicSite: P (1.285, -7.315, 1.895) [0.25, 0.5416, 0.25] PeriodicSite: P (1.837, -12.72, 1.895) [0.5416, 0.9584, 0.25] PeriodicSite: O (1.696, -15.14, 6.924) [0.495, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.8, 6.924) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.86, 6.924) [0.7121, 0.495, 0.9132] PeriodicSite: O (-3.451, -11.32, 3.133) [0.995, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.621, 3.133) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.712, -12.6, 3.133) [0.3797, 0.995, 0.4132] PeriodicSite: O (-1.696, -5.215, 0.6581) [0.505, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.558, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.495, 0.6581) [0.2879, 0.505, 0.0868] PeriodicSite: O (3.451, -9.039, 4.449) [0.005, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.74, 4.449) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.712, -7.76, 4.449) [0.6203, 0.005, 0.5868] PeriodicSite: O (0.9463, -11.46, 1.798) [0.564, 0.7787, 0.2372] PeriodicSite: O (-1.581, -10.36, 1.798) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.72, 1.798) [0.4201, 0.564, 0.2372] PeriodicSite: O (3.773, -11.26, 5.589) [0.064, 0.9201, 0.7372] PeriodicSite: O (-2.827, -12.9, 5.589) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.368, 5.589) [0.2787, 0.064, 0.7372] PeriodicSite: O (-0.9463, -8.9, 5.784) [0.436, 0.2213, 0.7628] PeriodicSite: O (1.581, -9.999, 5.784) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.64, 5.784) [0.5799, 0.436, 0.7628] PeriodicSite: O (-3.773, -9.093, 1.993) [0.936, 0.0799, 0.2628] PeriodicSite: O (2.827, -7.454, 1.993) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.99, 1.993) [0.7213, 0.936, 0.2628]
test_incar()[source]
test_incar_user_setting()[source]
class MVLCINEBSetTest(methodName='runTest')[source]

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.

structures = [Structure Summary Lattice     abc : 8.815000056846058 8.815000056846058 9.131710473490111  angles : 61.14080369885537 61.14080369885537 59.9999995733517  volume : 510.2218449146199       A : -4.4075 -7.634014 -0.0       B : 4.4075 -7.634014 0.0       C : -0.0 -5.089343 7.582     pbc : True True True PeriodicSite: Na (0.0, 0.0, 0.0) [0.0, 0.0, 0.0] PeriodicSite: Zr (9.811e-17, -10.18, 0.4774) [0.6457, 0.6457, 0.06296] PeriodicSite: Zr (-2.422e-17, -5.089, 4.268) [0.1457, 0.1457, 0.563] PeriodicSite: Zr (-7.549e-17, -10.18, 7.105) [0.3543, 0.3543, 0.937] PeriodicSite: Zr (-9.811e-17, -15.27, 3.314) [0.8543, 0.8543, 0.437] PeriodicSite: P (-1.837, -7.634, 5.686) [0.4584, 0.0416, 0.75] PeriodicSite: P (3.122, -9.86, 5.686) [0.0416, 0.75, 0.75] PeriodicSite: P (-1.285, -13.04, 5.686) [0.75, 0.4584, 0.75] PeriodicSite: P (-3.122, -10.5, 1.895) [0.9584, 0.25, 0.25] PeriodicSite: P (1.285, -7.315, 1.895) [0.25, 0.5416, 0.25] PeriodicSite: P (1.837, -12.72, 1.895) [0.5416, 0.9584, 0.25] PeriodicSite: O (1.696, -15.14, 6.924) [0.495, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.8, 6.924) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.86, 6.924) [0.7121, 0.495, 0.9132] PeriodicSite: O (-3.451, -11.32, 3.133) [0.995, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.621, 3.133) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.712, -12.6, 3.133) [0.3797, 0.995, 0.4132] PeriodicSite: O (-1.696, -5.215, 0.6581) [0.505, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.558, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.495, 0.6581) [0.2879, 0.505, 0.0868] PeriodicSite: O (3.451, -9.039, 4.449) [0.005, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.74, 4.449) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.712, -7.76, 4.449) [0.6203, 0.005, 0.5868] PeriodicSite: O (0.9463, -11.46, 1.798) [0.564, 0.7787, 0.2372] PeriodicSite: O (-1.581, -10.36, 1.798) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.72, 1.798) [0.4201, 0.564, 0.2372] PeriodicSite: O (3.773, -11.26, 5.589) [0.064, 0.9201, 0.7372] PeriodicSite: O (-2.827, -12.9, 5.589) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.368, 5.589) [0.2787, 0.064, 0.7372] PeriodicSite: O (-0.9463, -8.9, 5.784) [0.436, 0.2213, 0.7628] PeriodicSite: O (1.581, -9.999, 5.784) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.64, 5.784) [0.5799, 0.436, 0.7628] PeriodicSite: O (-3.773, -9.093, 1.993) [0.936, 0.0799, 0.2628] PeriodicSite: O (2.827, -7.454, 1.993) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.99, 1.993) [0.7213, 0.936, 0.2628], Structure Summary Lattice     abc : 8.815000056846058 8.815000056846058 9.131710473490111  angles : 61.14080369885537 61.14080369885537 59.9999995733517  volume : 510.2218449146199       A : -4.4075 -7.634014 -0.0       B : 4.4075 -7.634014 0.0       C : -0.0 -5.089343 7.582     pbc : True True True PeriodicSite: Na (0.0, -5.089, 1.895) [0.25, 0.25, 0.25] PeriodicSite: Zr (1.35e-16, -10.18, 0.4774) [0.6457, 0.6457, 0.06296] PeriodicSite: Zr (1.269e-17, -5.089, 4.268) [0.1457, 0.1457, 0.563] PeriodicSite: Zr (1.096e-16, -10.18, 7.105) [0.3543, 0.3543, 0.937] PeriodicSite: Zr (-1.35e-16, -15.27, 3.314) [0.8543, 0.8543, 0.437] PeriodicSite: P (-1.837, -7.634, 5.686) [0.4584, 0.0416, 0.75] PeriodicSite: P (3.122, -9.86, 5.686) [0.0416, 0.75, 0.75] PeriodicSite: P (-1.285, -13.04, 5.686) [0.75, 0.4584, 0.75] PeriodicSite: P (-3.122, -10.5, 1.895) [0.9584, 0.25, 0.25] PeriodicSite: P (1.285, -7.315, 1.895) [0.25, 0.5416, 0.25] PeriodicSite: P (1.837, -12.72, 1.895) [0.5416, 0.9584, 0.25] PeriodicSite: O (1.696, -15.14, 6.924) [0.495, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.8, 6.924) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.86, 6.924) [0.7121, 0.495, 0.9132] PeriodicSite: O (-3.451, -11.32, 3.133) [0.995, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.621, 3.133) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.712, -12.6, 3.133) [0.3797, 0.995, 0.4132] PeriodicSite: O (-1.696, -5.215, 0.6581) [0.505, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.558, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.495, 0.6581) [0.2879, 0.505, 0.0868] PeriodicSite: O (3.451, -9.039, 4.449) [0.005, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.74, 4.449) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.712, -7.76, 4.449) [0.6203, 0.005, 0.5868] PeriodicSite: O (0.9463, -11.46, 1.798) [0.564, 0.7787, 0.2372] PeriodicSite: O (-1.581, -10.36, 1.798) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.72, 1.798) [0.4201, 0.564, 0.2372] PeriodicSite: O (3.773, -11.26, 5.589) [0.064, 0.9201, 0.7372] PeriodicSite: O (-2.827, -12.9, 5.589) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.368, 5.589) [0.2787, 0.064, 0.7372] PeriodicSite: O (-0.9463, -8.9, 5.784) [0.436, 0.2213, 0.7628] PeriodicSite: O (1.581, -9.999, 5.784) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.64, 5.784) [0.5799, 0.436, 0.7628] PeriodicSite: O (-3.773, -9.093, 1.993) [0.936, 0.0799, 0.2628] PeriodicSite: O (2.827, -7.454, 1.993) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.99, 1.993) [0.7213, 0.936, 0.2628], Structure Summary Lattice     abc : 8.815000056846058 8.815000056846058 9.131710473490111  angles : 61.14080369885537 61.14080369885537 59.9999995733517  volume : 510.2218449146199       A : -4.4075 -7.634014 -0.0       B : 4.4075 -7.634014 0.0       C : -0.0 -5.089343 7.582     pbc : True True True PeriodicSite: Na (0.0, -10.18, 3.791) [0.5, 0.5, 0.5] PeriodicSite: Zr (9.811e-17, -10.18, 0.4774) [0.6457, 0.6457, 0.06296] PeriodicSite: Zr (-2.422e-17, -5.089, 4.268) [0.1457, 0.1457, 0.563] PeriodicSite: Zr (-7.549e-17, -10.18, 7.105) [0.3543, 0.3543, 0.937] PeriodicSite: Zr (-9.811e-17, -15.27, 3.314) [0.8543, 0.8543, 0.437] PeriodicSite: P (-1.837, -7.634, 5.686) [0.4584, 0.0416, 0.75] PeriodicSite: P (3.122, -9.86, 5.686) [0.0416, 0.75, 0.75] PeriodicSite: P (-1.285, -13.04, 5.686) [0.75, 0.4584, 0.75] PeriodicSite: P (-3.122, -10.5, 1.895) [0.9584, 0.25, 0.25] PeriodicSite: P (1.285, -7.315, 1.895) [0.25, 0.5416, 0.25] PeriodicSite: P (1.837, -12.72, 1.895) [0.5416, 0.9584, 0.25] PeriodicSite: O (1.696, -15.14, 6.924) [0.495, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.8, 6.924) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.86, 6.924) [0.7121, 0.495, 0.9132] PeriodicSite: O (-3.451, -11.32, 3.133) [0.995, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.621, 3.133) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.712, -12.6, 3.133) [0.3797, 0.995, 0.4132] PeriodicSite: O (-1.696, -5.215, 0.6581) [0.505, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.558, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.495, 0.6581) [0.2879, 0.505, 0.0868] PeriodicSite: O (3.451, -9.039, 4.449) [0.005, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.74, 4.449) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.712, -7.76, 4.449) [0.6203, 0.005, 0.5868] PeriodicSite: O (0.9463, -11.46, 1.798) [0.564, 0.7787, 0.2372] PeriodicSite: O (-1.581, -10.36, 1.798) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.72, 1.798) [0.4201, 0.564, 0.2372] PeriodicSite: O (3.773, -11.26, 5.589) [0.064, 0.9201, 0.7372] PeriodicSite: O (-2.827, -12.9, 5.589) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.368, 5.589) [0.2787, 0.064, 0.7372] PeriodicSite: O (-0.9463, -8.9, 5.784) [0.436, 0.2213, 0.7628] PeriodicSite: O (1.581, -9.999, 5.784) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.64, 5.784) [0.5799, 0.436, 0.7628] PeriodicSite: O (-3.773, -9.093, 1.993) [0.936, 0.0799, 0.2628] PeriodicSite: O (2.827, -7.454, 1.993) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.99, 1.993) [0.7213, 0.936, 0.2628]]
test_incar()[source]
test_incar_user_setting()[source]
class UtilityTest(methodName='runTest')[source]

Bases: TestCase

Unit test for outside methods in io.py

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.

structure = Structure Summary Lattice     abc : 8.815000056846058 8.815000056846058 9.131710473490111  angles : 61.14080369885537 61.14080369885537 59.9999995733517  volume : 510.2218449146199       A : -4.4075 -7.634014 -0.0       B : 4.4075 -7.634014 0.0       C : -0.0 -5.089343 7.582     pbc : True True True PeriodicSite: Na (0.0, 0.0, 0.0) [0.0, 0.0, 0.0] PeriodicSite: Na (0.0, -10.18, 3.791) [0.5, 0.5, 0.5] PeriodicSite: Zr (9.811e-17, -10.18, 0.4774) [0.6457, 0.6457, 0.06296] PeriodicSite: Zr (-2.422e-17, -5.089, 4.268) [0.1457, 0.1457, 0.563] PeriodicSite: Zr (-7.549e-17, -10.18, 7.105) [0.3543, 0.3543, 0.937] PeriodicSite: Zr (-9.811e-17, -15.27, 3.314) [0.8543, 0.8543, 0.437] PeriodicSite: P (-1.837, -7.634, 5.686) [0.4584, 0.0416, 0.75] PeriodicSite: P (3.122, -9.86, 5.686) [0.0416, 0.75, 0.75] PeriodicSite: P (-1.285, -13.04, 5.686) [0.75, 0.4584, 0.75] PeriodicSite: P (-3.122, -10.5, 1.895) [0.9584, 0.25, 0.25] PeriodicSite: P (1.285, -7.315, 1.895) [0.25, 0.5416, 0.25] PeriodicSite: P (1.837, -12.72, 1.895) [0.5416, 0.9584, 0.25] PeriodicSite: O (1.696, -15.14, 6.924) [0.495, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.8, 6.924) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.86, 6.924) [0.7121, 0.495, 0.9132] PeriodicSite: O (-3.451, -11.32, 3.133) [0.995, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.621, 3.133) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.712, -12.6, 3.133) [0.3797, 0.995, 0.4132] PeriodicSite: O (-1.696, -5.215, 0.6581) [0.505, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.558, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.495, 0.6581) [0.2879, 0.505, 0.0868] PeriodicSite: O (3.451, -9.039, 4.449) [0.005, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.74, 4.449) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.712, -7.76, 4.449) [0.6203, 0.005, 0.5868] PeriodicSite: O (0.9463, -11.46, 1.798) [0.564, 0.7787, 0.2372] PeriodicSite: O (-1.581, -10.36, 1.798) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.72, 1.798) [0.4201, 0.564, 0.2372] PeriodicSite: O (3.773, -11.26, 5.589) [0.064, 0.9201, 0.7372] PeriodicSite: O (-2.827, -12.9, 5.589) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.368, 5.589) [0.2787, 0.064, 0.7372] PeriodicSite: O (-0.9463, -8.9, 5.784) [0.436, 0.2213, 0.7628] PeriodicSite: O (1.581, -9.999, 5.784) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.64, 5.784) [0.5799, 0.436, 0.7628] PeriodicSite: O (-3.773, -9.093, 1.993) [0.936, 0.0799, 0.2628] PeriodicSite: O (2.827, -7.454, 1.993) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.99, 1.993) [0.7213, 0.936, 0.2628]
test_get_endpoint_dist()[source]
test_get_endpoints_from_index()[source]
get_path(path_str, dirname='./')[source]