class RelaxationAnalyzerTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Li2O'),
check_for_POTCAR=False)
s1 = p.structure
p = Poscar.from_file(os.path.join(test_dir, 'CONTCAR.Li2O'),
check_for_POTCAR=False)
s2 = p.structure
self.analyzer = RelaxationAnalyzer(s1, s2)
def test_vol_and_para_changes(self):
for k, v in self.analyzer.get_percentage_lattice_parameter_changes().items():
self.assertAlmostEqual(-0.0092040921155279731, v)
latt_change = v
vol_change = self.analyzer.get_percentage_volume_change()
self.assertAlmostEqual(-0.0273589101391,
vol_change)
# This is a simple cubic cell, so the latt and vol change are simply
# Related. So let's test that.
self.assertAlmostEqual((1 + latt_change) ** 3 - 1, vol_change)
def test_get_percentage_bond_dist_changes(self):
for k, v in self.analyzer.get_percentage_bond_dist_changes().items():
for k2, v2 in v.items():
self.assertAlmostEqual(-0.009204092115527862, v2)
class RelaxationAnalyzerTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Li2O'),
check_for_POTCAR=False)
s1 = p.structure
p = Poscar.from_file(os.path.join(test_dir, 'CONTCAR.Li2O'),
check_for_POTCAR=False)
s2 = p.structure
self.analyzer = RelaxationAnalyzer(s1, s2)
def test_vol_and_para_changes(self):
for k, v in self.analyzer.get_percentage_lattice_parameter_changes().items():
self.assertAlmostEqual(-0.0092040921155279731, v)
latt_change = v
vol_change = self.analyzer.get_percentage_volume_change()
self.assertAlmostEqual(-0.0273589101391,
vol_change)
# This is a simple cubic cell, so the latt and vol change are simply
# Related. So let's test that.
self.assertAlmostEqual((1 + latt_change) ** 3 - 1, vol_change)
def test_get_percentage_bond_dist_changes(self):
for k, v in self.analyzer.get_percentage_bond_dist_changes().items():
for k2, v2 in v.items():
self.assertAlmostEqual(-0.009204092115527862, v2)
def get_percentage_bond_distance_change(self, n):
"""
Bond distance change after the introduction of interstitial.
Args:
n: index of interstitials
"""
def_struct = self._structs[n:n + 1][0] # copy
def_struct.remove(-1)
rv = RelaxationAnalyzer(self._blk_struct, def_struct)
return rv.get_percentage_bond_dist_changes()
def get_percentage_bond_distance_change(self, n):
"""
Bond distance change after the introduction of interstitial.
Args:
n: index of interstitials
"""
def_struct = self._structs[n:n + 1][0] # copy
def_struct.remove(-1)
rv = RelaxationAnalyzer(self._blk_struct, def_struct)
return rv.get_percentage_bond_dist_changes()
def get_percentage_bond_distance_change(self, n):
"""
Bond distance change after the introduction of interstitial
Args:
n: Symmetrically distinct interstitial index
"""
if not self._relax_struct:
self._relax_analysis()
blk_struct = self._relax_struct[0]
def_struct = self._relax_struct[n + 1:n + 2][0]
def_struct.remove(-1)
#print def_struct
rv = RelaxationAnalyzer(blk_struct, def_struct)
return rv.get_percentage_bond_dist_changes()
def get_percentage_bond_distance_change(self, n):
"""
Bond distance change after the introduction of interstitial
Args:
n: Symmetrically distinct interstitial index
"""
if not self._relax_struct:
self._relax_analysis()
blk_struct = self._relax_struct[0]
def_struct = self._relax_struct[n + 1:n + 2][0]
def_struct.remove(-1)
#print def_struct
rv = RelaxationAnalyzer(blk_struct, def_struct)
return rv.get_percentage_bond_dist_changes()
coordinate = Voronoi.get_coordination_number(1)
coordinate_sites = Voronoi.get_coordinated_sites(1)
Voronoi_Analyzer = VoronoiAnalyzer()
anay = Voronoi_Analyzer.analyze(s1, n=0)
strucs = [s1, s2]
anays = Voronoi_Analyzer.analyze_structures(strucs)
print("Voronoi_Analyzer.analyze(s1,n=0):", anay)
#plt = Voronoi_Analyzer.plot_vor_analysis(anays)
relax = RelaxationAnalyzer(s1, s2)
volume_change = relax.get_percentage_volume_change()
lattice_parameter_changes = relax.get_percentage_lattice_parameter_changes()
print('initial volume:', s1.volume)
print('final volume:', s2.volume)
print("percent_volume_change:", volume_change)
print("percent_lattice_change:", lattice_parameter_changes)
bond_dist = relax.get_percentage_bond_dist_changes(max_radius=6)
print("percent_bond_distance_change:", bond_dist)
connec = VoronoiConnectivity(s2)
#print("connec.get_connections():",connec.get_connections())
#A_222_dopant = [0]
A_222_dopant_neighbour = [[69, 73], [68, 72], [63, 65], [62, 64], [64, 65],
[62, 63], [72, 73], [68, 69]]
A_222_dopant_neighbour_MA_I_a = [[69, 73], [68, 72], [59, 61], [58, 60],
[60, 61], [58, 59], [68, 69], [72, 73]]
A_222_dopant_neighbour_MA_I_b = [[67, 71], [66, 70], [63, 65], [62, 64],
[70, 71], [66, 67], [62, 63], [64, 65]]
A_222_dopant_neighbour_MA_I_c = [[69, 73], [68, 72], [62, 64], [63, 65],
[72, 73], [68, 69], [64, 65], [62, 63]]
###Calculate dopant bond length
coordinate = Voronoi.get_coordination_number(1)
coordinate_sites = Voronoi.get_coordinated_sites(1)
Voronoi_Analyzer = VoronoiAnalyzer()
anay = Voronoi_Analyzer.analyze(s1,n=0)
strucs = [s1,s2]
anays = Voronoi_Analyzer.analyze_structures(strucs)
print("Voronoi_Analyzer.analyze(s1,n=0):",anay)
#plt = Voronoi_Analyzer.plot_vor_analysis(anays)
relax = RelaxationAnalyzer(s1,s2)
volume_change = relax.get_percentage_volume_change()
lattice_parameter_changes = relax.get_percentage_lattice_parameter_changes()
print('initial volume:',s1.volume)
print('final volume:',s2.volume)
print("percent_volume_change:",volume_change)
print("percent_lattice_change:",lattice_parameter_changes)
bond_dist = relax.get_percentage_bond_dist_changes()
connec = VoronoiConnectivity(s2)
B_233_dopant = [0]
B_233_dopant_neighbour = [144,153,162,165,180,181]
B_233_dopant_neighbour_Pb = [117,111,114,109,110]
B_233_dopant_neighbour_Pb_I =[[144,153,171,174,189,190],[147,156,165,168,183,184],[150,159,162,168,186,187],[145,154,163,166,181,182],[146,155,164,167,180,182]]
B_233 = zip(B_233_dopant_neighbour_Pb,B_233_dopant_neighbour_Pb_I)
### To determine the dopant and its neighbour I pair and bond distance
comb1 = []
for i in B_233_dopant:
for j in B_233_dopant_neighbour:
pair = []
pair.append(i)
