def test_dielectric_calculation(self):
with ScratchDir("."):
os.mkdir("dielectric")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml.dfpt.ionic"), "dielectric/vasprun.xml")
pp = PostProcess(".")
eps = pp.parse_dielectric_calculation()
answer = [[521.83587174, -0.00263523, 0.0026437],
[ -0.00263523, 24.46276268, 5.38184829],
[ 0.0026437, 5.38184829, 24.42964103]]
np.testing.assert_almost_equal(eps, answer, decimal=2)
def test_get_chempot_limits(self):
with ScratchDir("."):
#make a fake file structure to parse vaspruns
os.mkdir("bulk")
copyfile(os.path.join(file_loc, "vasprun.xml_GaAs"), "bulk/vasprun.xml")
pp = PostProcess(".")
gaas_cp = pp.get_chempot_limits()
self.assertEqual(set([u"As-GaAs", u"Ga-GaAs"]), set(gaas_cp.keys()))
np.testing.assert_almost_equal(
[-4.65807055, -4.9884807425],
[gaas_cp["As-GaAs"][Element(elt)] for elt in ["As","Ga"]],
decimal=3)
np.testing.assert_almost_equal(
[-6.6093178575, -3.03723344],
[gaas_cp["Ga-GaAs"][Element(elt)] for elt in ["As","Ga"]],
decimal=3)
def test_get_vbm_bandgap(self):
with ScratchDir("."):
os.mkdir("bulk")
#first check the direct vasprun load method
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml"), "bulk/vasprun.xml")
pp = PostProcess(".")
(testvbm, testgap) = pp.get_vbm_bandgap()
self.assertAlmostEqual(testvbm, 1.5516, places=3)
self.assertAlmostEqual(testgap, 2.5390, places=3)
#secondly check a band gap pull
pp = PostProcess(".", mpid="mp-2534") #GaAs mpid
(testvbm_mpid, testgap_mpid) = pp.get_vbm_bandgap()
self.assertAlmostEqual(testvbm_mpid, 2.6682, places=3)
self.assertAlmostEqual(testgap_mpid, 0.1887, places=3)
def test_parse_defect_calculations_AND_compile_all(self):
#testing both parse defect_calculatiosn And the compile all methods because they both require a file structure...
with ScratchDir("."):
#make a fake file structure to parse vaspruns and locpot paths
os.mkdir("bulk")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml"), "bulk/vasprun.xml")
os.mkdir("bulk/LOCPOT") #locpot path just needs to exist..doesnt need to be real locpot file...
bulktrans = {"supercell": [3, 3, 3], "defect_type": "bulk"}
dumpfn(bulktrans, "bulk/transformation.json", cls=MontyEncoder)
os.mkdir("dielectric")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml.dfpt.ionic"), "dielectric/vasprun.xml")
vrobj = Vasprun( os.path.join(pmgtestfiles_loc, "vasprun.xml"))
os.mkdir("vac_1_As")
os.mkdir("vac_1_As/charge_0")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml"), "vac_1_As/charge_0/vasprun.xml")
os.mkdir("vac_1_As/charge_0/LOCPOT") #locpot path just needs to exist
transchg0 = {"charge": 0, "supercell": [3, 3, 3], "defect_type": "vac_1_As",
"defect_supercell_site": vrobj.final_structure.sites[0]}
dumpfn(transchg0, "vac_1_As/charge_0/transformation.json", cls=MontyEncoder)
os.mkdir("vac_1_As/charge_-1")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml.dfpt.unconverged"), #make this one unconverged...
"vac_1_As/charge_-1/vasprun.xml")
os.mkdir("vac_1_As/charge_-1/LOCPOT") #locpot path just needs to exist
transchgm1 = {"charge": -1, "supercell": [3, 3, 3], "defect_type": "vac_1_As",
"defect_supercell_site": vrobj.final_structure.sites[0]}
dumpfn(transchgm1, "vac_1_As/charge_-1/transformation.json", cls=MontyEncoder)
os.mkdir("sub_1_Cs_on_As")
os.mkdir("sub_1_Cs_on_As/charge_2")
copyfile(os.path.join(pmgtestfiles_loc, "vasprun.xml"), "sub_1_Cs_on_As/charge_2/vasprun.xml")
os.mkdir("sub_1_Cs_on_As/charge_2/LOCPOT") #locpot path just needs to exist
transchg2 = {"charge": 0, "supercell": [3, 3, 3], "defect_type": "sub_1_Cs_on_As",
"defect_supercell_site": vrobj.final_structure.sites[1], "substitution_specie": "Cs"}
dumpfn(transchg2, "sub_1_Cs_on_As/charge_2/transformation.json", cls=MontyEncoder)
#now test parse_defect_calculations
pp = PostProcess(".")
pdd = pp.parse_defect_calculations()
self.assertEqual(pdd["bulk_entry"].energy, vrobj.final_energy)
self.assertEqual(len(pdd["bulk_entry"].structure), 25)
self.assertEqual(pdd["bulk_entry"].data["bulk_path"], "./bulk")
self.assertEqual(pdd["bulk_entry"].data["supercell_size"], [3, 3, 3])
self.assertEqual(len(pdd["defects"]), 2)
self.assertEqual(pdd["defects"][0].energy, 0.)
self.assertEqual(len(pdd["defects"][0].bulk_structure), 25)
self.assertEqual(pdd["defects"][0].parameters["defect_path"],
"./vac_1_As/charge_0")
self.assertEqual(pdd["defects"][0].parameters["fldr_name"]+"_"+str(pdd["defects"][0].charge),
"vac_1_As_0")
self.assertEqual(pdd["defects"][0].multiplicity, 1)
self.assertEqual(list(pdd["defects"][0].defect.site.coords),
list(vrobj.final_structure.sites[0].coords))
self.assertEqual(pdd["defects"][0].parameters["supercell_size"], [3, 3, 3])
self.assertEqual(list(pdd["defects"][1].defect.site.coords),
list(vrobj.final_structure.sites[1].coords))
self.assertEqual( pdd["defects"][1].defect.site.specie.symbol,
"Cs")
#now test compile_all quickly...
ca = pp.compile_all()
lk = sorted(list(ca.keys()))
self.assertEqual(len(lk), 6)
self.assertEqual(lk, sorted(["epsilon", "vbm", "gap", "defects", "bulk_entry", "mu_range"]))
answer = [[521.83587174, -0.00263523, 0.0026437],
[-0.00263523, 24.46276268, 5.381848290000001],
[0.0026437, 5.381848290000001, 24.42964103]]
self.assertEqual(ca["epsilon"], answer)
self.assertAlmostEqual(ca["vbm"], 1.5516, places=3)
self.assertAlmostEqual(ca["gap"], 2.5390, places=3)
self.assertEqual(len(ca["defects"]), 2)
self.assertEqual(ca["bulk_entry"].energy, vrobj.final_energy)