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 check_relaxation(mat, new_style_mat):
final_structure = Structure.from_dict(new_style_mat["structure"])
warnings = []
# Check relaxation for just the initial structure to optimized structure
init_struc = new_style_mat["initial_structure"]
orig_crystal = Structure.from_dict(init_struc)
try:
analyzer = RelaxationAnalyzer(orig_crystal, final_structure)
latt_para_percentage_changes = (
analyzer.get_percentage_lattice_parameter_changes()
)
for l in ["a", "b", "c"]:
change = latt_para_percentage_changes[l] * 100
if change < latt_para_interval[0] or change > latt_para_interval[1]:
warnings.append(
"Large change in a lattice parameter during relaxation."
)
change = analyzer.get_percentage_volume_change() * 100
if change < vol_interval[0] or change > vol_interval[1]:
warnings.append("Large change in volume during relaxation.")
except Exception as ex:
# print icsd_crystal.formula
# print final_structure.formula
print(
"Relaxation analyzer failed for Material:{} due to {}".format(
mat["task_id"], traceback.print_exc()
)
)
mat["warnings"] = list(set(warnings))
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 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 setUp(self):
p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR,
"POSCAR.Li2O"),
check_for_POTCAR=False)
s1 = p.structure
p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR,
"CONTCAR.Li2O"),
check_for_POTCAR=False)
s2 = p.structure
self.analyzer = RelaxationAnalyzer(s1, s2)
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_lattice_parameter_change(self, n):
"""
Lattice parameter 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_lattice_parameter_changes()
def get_percentage_volume_change(self, n):
"""
Volume change after the introduction of interstitial
Args:
n: index of interstitials
"""
def_struct = self._structs[n:n + 1][0]
def_struct.remove(-1)
rv = RelaxationAnalyzer(self._blk_struct, def_struct)
return rv.get_percentage_volume_change()
def get_percentage_lattice_parameter_change(self, n):
"""
Lattice parameter 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_lattice_parameter_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_volume_change(self, n):
"""
Volume change after the introduction of interstitial
Args:
n: index of interstitials
"""
def_struct = self._structs[n:n + 1][0]
def_struct.remove(-1)
rv = RelaxationAnalyzer(self._blk_struct, def_struct)
return rv.get_percentage_volume_change()
def get_percentage_lattice_parameter_change(self, n):
"""
Lattice parameter 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)
rv = RelaxationAnalyzer(blk_struct, def_struct)
return rv.get_percentage_lattice_parameter_changes()
def get_percentage_lattice_parameter_change(self, n):
"""
Lattice parameter 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)
rv = RelaxationAnalyzer(blk_struct, def_struct)
return rv.get_percentage_lattice_parameter_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()
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 add_icsd(mat, icsds):
relevant_icsd = [
icsd for icsd in icsds if icsd["icsd_id"] in mat.get("icsd_ids", [])
]
results = []
for icsd in relevant_icsd:
result = {"warnings": []}
tags = [
icsd[t] for t in ["chem_name", "min_name"] if t in icsd and icsd[t]
]
result["exp"] = {'pressure': icsd["pressure"], 'tags': tags}
if icsd.get('pressure', 0) > 1:
result["warnings"].append("High pressure experimental phase.")
results.append(result)
if len(results) == 0:
results.append({
"warnings":
["Structure has been removed in the 2012 version of ICSD."],
"exp": {}
})
if mat["icsd_ids"]:
results[0]["exp_lattice"] = mat["snl"]["lattice"]
# Check relaxation
orig_crystal = Structure.from_dict(mat["snl"])
final_structure = Structure.from_dict(mat["structure"])
try:
analyzer = RelaxationAnalyzer(orig_crystal, final_structure)
latt_para_percentage_changes = analyzer.get_percentage_lattice_parameter_changes(
)
for l in ["a", "b", "c"]:
change = latt_para_percentage_changes[l] * 100
if change < latt_para_interval[0] or change > latt_para_interval[1]:
results[0]["warnings"].append(
"Large change in {} lattice parameter during relaxation.".
format(l))
change = analyzer.get_percentage_volume_change() * 100
if change < vol_interval[0] or change > vol_interval[1]:
results[0]["warnings"].append(
"Large change in volume during relaxation.")
except Exception as ex:
# print icsd_crystal.formula
# print final_structure.formula
print("Relaxation analyzer failed for Material:{} due to {}".format(
mat["task_id"], traceback.print_exc()))
# Merge all the results
if len(results) > 1:
results_union = {"exp": {"tags": []}, "warnings": []}
tags = []
warnings = []
for i in results:
if i.get("exp_lattice"):
results_union["exp_lattice"] = i["exp_lattice"]
if i.get("exp"):
if i["exp"].get("tags"):
tags.extend(i["exp"]["tags"])
if i.get("warnings"):
warnings.extend(i["warnings"])
if tags:
results_union["exp"]["tags"] = [i for i in set(tags)]
if warnings:
high_pressure_count = 0
for w in warnings:
if w == "High pressure experimental phase.":
high_pressure_count += 1
results_union["warnings"] = [i for i in set(warnings)]
if high_pressure_count != 0 and high_pressure_count != len(
mat.get("icsd_ids", [])):
results_union["warnings"].remove(
"High pressure experimental phase.")
results = results_union
else:
results = results[0]
if results.get("exp_lattice"):
mat["exp_lattice"] = results["exp_lattice"]
mat["exp"] = results["exp"]
mat["warnings"] = results["warnings"]
spacegroup2.get_space_group_number())
Voronoi = VoronoiCoordFinder(s2, target=None)
site = s2.num_sites
#print("s2[0]:",s2.sites)
print("s2_cart_coords[0]", s2.cart_coords[0])
#print("s2_distance_(0,1)",s2.get_distance(0,1))
polyhedra = Voronoi.get_voronoi_polyhedra(1)
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],
def get_relaxation_analyzer(self):
"""
Return a pymatgen :class:`RelaxationAnalyzer` object to analyze the relaxation in a calculation.
"""
return RelaxationAnalyzer(self.initial_structure, self.final_structure)
