def runTest(self):
neb_analysis1 = NEBAnalysis.from_dir(os.path.join
(test_dir, 'neb1', 'neb'))
neb_analysis1_from_dict = NEBAnalysis.from_dict(neb_analysis1.as_dict())
json_data = json.dumps(neb_analysis1.as_dict())
neb_dict = json.loads(json_data)
neb_analysis1_from_json_data = NEBAnalysis.from_dict(neb_dict)
self.assertArrayAlmostEqual(neb_analysis1.energies[0], -255.97992669000001)
self.assertArrayAlmostEqual(neb_analysis1.energies[3], -255.84261996000001)
self.assertArrayAlmostEqual(neb_analysis1.r, neb_analysis1_from_dict.r)
self.assertArrayAlmostEqual(neb_analysis1.energies, neb_analysis1_from_dict.energies)
self.assertArrayAlmostEqual(neb_analysis1.forces, neb_analysis1_from_dict.forces)
self.assertEqual(neb_analysis1.structures, neb_analysis1_from_dict.structures)
self.assertArrayAlmostEqual(neb_analysis1.r, neb_analysis1_from_json_data.r)
self.assertArrayAlmostEqual(neb_analysis1.energies, neb_analysis1_from_json_data.energies)
self.assertArrayAlmostEqual(neb_analysis1.forces, neb_analysis1_from_json_data.forces)
self.assertEqual(neb_analysis1.structures, neb_analysis1_from_json_data.structures)
self.assertArrayAlmostEqual(neb_analysis1.get_extrema()[1][0], (0.50023335723480078, 325.20043063935128))
neb_analysis1.setup_spline(spline_options={'saddle_point': 'zero_slope'})
self.assertArrayAlmostEqual(neb_analysis1.get_extrema()[1][0], (0.50023335723480078, 325.20003984140203))
with open(os.path.join(test_dir, 'neb2', 'neb_analysis2.json'),
'r') as f:
neb_analysis2_dict = json.load(f)
neb_analysis2 = NEBAnalysis.from_dict(neb_analysis2_dict)
self.assertArrayAlmostEqual(neb_analysis2.get_extrema()[1][0], (0.37255257367467326, 562.40825334519991))
neb_analysis2.setup_spline(spline_options={'saddle_point': 'zero_slope'})
self.assertArrayAlmostEqual(neb_analysis2.get_extrema()[1][0], (0.30371133723478794, 528.46229631648691))
def runTest(self):
neb_analysis = NEBAnalysis.from_dir(os.path.join(test_dir, 'neb'),
relaxation_dirs=(os.path.join(test_dir, 'start'),
os.path.join(test_dir, 'end')))
neb_analysis2 = NEBAnalysis.from_dict(neb_analysis.as_dict())
json_data = json.dumps(neb_analysis.as_dict())
neb_dict = json.loads(json_data)
neb_analysis3 = NEBAnalysis.from_dict(neb_dict)
self.assertArrayAlmostEqual(neb_analysis.r, neb_analysis2.r)
self.assertArrayAlmostEqual(neb_analysis.energies, neb_analysis2.energies)
self.assertArrayAlmostEqual(neb_analysis.forces, neb_analysis2.forces)
self.assertEqual(neb_analysis.structures, neb_analysis2.structures)
self.assertArrayAlmostEqual(neb_analysis.r, neb_analysis3.r)
self.assertArrayAlmostEqual(neb_analysis.energies, neb_analysis3.energies)
self.assertArrayAlmostEqual(neb_analysis.forces, neb_analysis3.forces)
self.assertEqual(neb_analysis.structures, neb_analysis3.structures)
self.assertAlmostEqual(neb_analysis.get_extrema()[1][0], (0.50023335723480078, 325.20043063935128))
