def test_vasp_poscar_setup_no_poscar(self):
compare_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_perfect"))
myvc = VaspChecker(name="childdir", structure=compare_pos.structure)
self.assertFalse(os.path.isfile(os.path.join(testdir, "childdir", "POSCAR")))
myvc._vasp_poscar_setup()
mypos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "childdir", "POSCAR"))
self.assertEqual(mypos.structure, compare_pos.structure)
def test_vasp_poscar_setup_no_poscar(self):
compare_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_perfect"))
myvc = VaspChecker(name="childdir", structure=compare_pos.structure)
self.assertFalse(
os.path.isfile(os.path.join(testdir, "childdir", "POSCAR")))
myvc._vasp_poscar_setup()
mypos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "childdir", "POSCAR"))
self.assertEqual(mypos.structure, compare_pos.structure)
def test_add_selective_dynamics(self):
mystruc = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_Al")).structure
myvc = VaspChecker(name="childdir", structure=mystruc)
myvc._vasp_poscar_setup()
sdarr = np.zeros([4, 3], bool)
sdarr[0][0] = True
sdarr[1][1] = True
sdarr[2][2] = True
sdarr[3][0] = True
sdarr[3][1] = True
myvc.add_selective_dynamics_to_structure_file(sdarr)
after_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "childdir", "POSCAR"))
compare_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_Al_sd"))
self.assertEqual(after_pos.structure, compare_pos.structure)
self.assertEqual(after_pos.selective_dynamics, compare_pos.selective_dynamics)
def test_vasp_incar_setup(self):
my_structure = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_LNO").structure
kdict = dict()
kdict["mast_xc"] = "pw91"
kdict["mast_pp_setup"] = {"La": "La", "Ni": "Ni_pv", "O": "O_s"}
kdict["IBRION"] = 3
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
mypos = myvc._vasp_poscar_setup()
mypot = myvc._vasp_potcar_setup(mypos)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_notags"))
self.assertEqual(myincar, incar_compare)
#
kdict["ENCUT"] = 100
kdict["mast_multiplyencut"] = 1.1
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_encut"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("ENCUT")
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_multiply_110"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("mast_multiplyencut")
kdict["mast_charge"] = -2
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_charge_neg"))
self.assertEqual(myincar, incar_compare)
#
kdict["mast_charge"] = 2
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_charge_pos"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("mast_charge")
kdict["mast_setmagmom"] = "3 5 2"
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_setmagmom"))
self.assertEqual(myincar, incar_compare)
#
kdict[
"mast_setmagmom"
] = "-1 -2 3 1 2 3 1 2 7 8 7 8 7 8 7 8 5 4 3 2 1 1 2 3 4 5 -5 -4 -3 -2 -1 1 2 3 4 5 4 4 4 -4"
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(os.path.join(testdir, "files", "INCAR_setmagmom_indiv"))
self.assertEqual(myincar, incar_compare)
def test_vasp_poscar_setup_mast_coordinates(self):
kdict = dict()
kdict["mast_coordinates"] = ["structure/POSCAR_coordinates"] # note that the input is a list of strings
myvc = VaspChecker(name="childdir", program_keys=kdict)
perf_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_perfect"))
perf_pos.write_file(os.path.join(testdir, "childdir", "POSCAR"))
coord_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_coordinates"))
grafted_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_grafted"))
mypos = myvc._vasp_poscar_setup()
self.assertEqual(mypos.structure, grafted_pos.structure)
def test_add_selective_dynamics(self):
mystruc = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_Al")).structure
myvc = VaspChecker(name="childdir", structure=mystruc)
myvc._vasp_poscar_setup()
sdarr = np.zeros([4, 3], bool)
sdarr[0][0] = True
sdarr[1][1] = True
sdarr[2][2] = True
sdarr[3][0] = True
sdarr[3][1] = True
myvc.add_selective_dynamics_to_structure_file(sdarr)
after_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "childdir", "POSCAR"))
compare_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_Al_sd"))
self.assertEqual(after_pos.structure, compare_pos.structure)
self.assertEqual(after_pos.selective_dynamics,
compare_pos.selective_dynamics)
def test_vasp_poscar_setup_mast_coordinates(self):
kdict = dict()
kdict['mast_coordinates'] = [
"structure/POSCAR_coordinates"
] #note that the input is a list of strings
myvc = VaspChecker(name="childdir", program_keys=kdict)
perf_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_perfect"))
perf_pos.write_file(os.path.join(testdir, "childdir", "POSCAR"))
coord_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_coordinates"))
grafted_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_grafted"))
mypos = myvc._vasp_poscar_setup()
self.assertEqual(mypos.structure, grafted_pos.structure)
def test_vasp_incar_setup(self):
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"structure/POSCAR_LNO").structure
kdict = dict()
kdict['mast_xc'] = "pw91"
kdict['mast_pp_setup'] = {'La': 'La', 'Ni': 'Ni_pv', 'O': 'O_s'}
kdict['IBRION'] = 3
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
mypos = myvc._vasp_poscar_setup()
mypot = myvc._vasp_potcar_setup(mypos)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_notags"))
self.assertEqual(myincar, incar_compare)
#
kdict['ENCUT'] = 100
kdict['mast_multiplyencut'] = 1.1
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_encut"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("ENCUT")
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_multiply_110"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("mast_multiplyencut")
kdict["mast_charge"] = -2
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_charge_neg"))
self.assertEqual(myincar, incar_compare)
#
kdict["mast_charge"] = 2
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_charge_pos"))
self.assertEqual(myincar, incar_compare)
#
kdict.pop("mast_charge")
kdict["mast_setmagmom"] = "3 5 2"
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_setmagmom"))
self.assertEqual(myincar, incar_compare)
#
kdict[
"mast_setmagmom"] = "-1 -2 3 1 2 3 1 2 7 8 7 8 7 8 7 8 5 4 3 2 1 1 2 3 4 5 -5 -4 -3 -2 -1 1 2 3 4 5 4 4 4 -4"
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc._vasp_incar_setup(mypot, mypos)
myincar = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "childdir", "INCAR"))
incar_compare = pymatgen.io.vaspio.Incar.from_file(
os.path.join(testdir, "files", "INCAR_setmagmom_indiv"))
self.assertEqual(myincar, incar_compare)
