Python Structure Examples

Example #1

File: test_handlers.py Project: shyamd/custodian

    def test_static_run_correction(self):
        shutil.copy("OSZICAR.empty", "OSZICAR")
        s1 = Structure.from_file("POSCAR")
        incar = Incar.from_file("INCAR")

        # Test for NSW 0
        incar.update({"NSW": 0})
        incar.write_file("INCAR")
        h = VaspErrorHandler("vasp.out")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d['errors'], ['zpotrf'])
        s2 = Structure.from_file("POSCAR")
        self.assertAlmostEqual(s2.volume, s1.volume, 3)
        self.assertEqual(Incar.from_file("INCAR")["ISYM"], 0)

        # Test for ISIF 0-2
        incar.update({"NSW":99, "ISIF":2})
        incar.write_file("INCAR")
        h = VaspErrorHandler("vasp.out")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d['errors'], ['zpotrf'])
        s2 = Structure.from_file("POSCAR")
        self.assertAlmostEqual(s2.volume, s1.volume, 3)
        self.assertEqual(Incar.from_file("INCAR")["ISYM"], 0)

Example #2

    def test_static_run_correction(self):
        shutil.copy("OSZICAR.empty", "OSZICAR")
        s1 = Structure.from_file("POSCAR")
        incar = Incar.from_file("INCAR")

        # Test for NSW 0
        incar.update({"NSW": 0})
        incar.write_file("INCAR")
        h = VaspErrorHandler("vasp.out")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d['errors'], ['zpotrf'])
        s2 = Structure.from_file("POSCAR")
        self.assertAlmostEqual(s2.volume, s1.volume, 3)
        self.assertEqual(Incar.from_file("INCAR")["ISYM"], 0)

        # Test for ISIF 0-2
        incar.update({"NSW":99, "ISIF":2})
        incar.write_file("INCAR")
        h = VaspErrorHandler("vasp.out")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d['errors'], ['zpotrf'])
        s2 = Structure.from_file("POSCAR")
        self.assertAlmostEqual(s2.volume, s1.volume, 3)
        self.assertEqual(Incar.from_file("INCAR")["ISYM"], 0)

Example #3

File: test_handlers.py Project: shyamd/custodian

 def test_first_step(self):
     shutil.copy("OSZICAR.empty", "OSZICAR")
     s1 = Structure.from_file("POSCAR")
     h = VaspErrorHandler("vasp.out")
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d['errors'], ['zpotrf'])
     s2 = Structure.from_file("POSCAR")
     self.assertAlmostEqual(s2.volume, s1.volume * 1.2 ** 3, 3)

Example #4

 def test_first_step(self):
     shutil.copy("OSZICAR.empty", "OSZICAR")
     s1 = Structure.from_file("POSCAR")
     h = VaspErrorHandler("vasp.out")
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d['errors'], ['zpotrf'])
     s2 = Structure.from_file("POSCAR")
     self.assertAlmostEqual(s2.volume, s1.volume * 1.2 ** 3, 3)

Example #5

File: test_handlers.py Project: shyamd/custodian

 def test_potim_correction(self):
     shutil.copy("OSZICAR.one_step", "OSZICAR")
     s1 = Structure.from_file("POSCAR")
     h = VaspErrorHandler("vasp.out")
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d['errors'], ['zpotrf'])
     s2 = Structure.from_file("POSCAR")
     self.assertAlmostEqual(s2.volume, s1.volume, 3)
     self.assertAlmostEqual(Incar.from_file("INCAR")['POTIM'], 0.25)

Example #6

 def test_potim_correction(self):
     shutil.copy("OSZICAR.one_step", "OSZICAR")
     s1 = Structure.from_file("POSCAR")
     h = VaspErrorHandler("vasp.out")
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d['errors'], ['zpotrf'])
     s2 = Structure.from_file("POSCAR")
     self.assertAlmostEqual(s2.volume, s1.volume, 3)
     self.assertAlmostEqual(Incar.from_file("INCAR")['POTIM'], 0.25)

Example #7

File: polarByDiff.py Project: woal777/vasp

import numpy as np
from pymatgen.io.vasp import Structure, Outcar

s: Structure = Structure.from_file('POSCAR')
out = Outcar('OUTCAR')
pDown: Structure = Structure.from_file('POSCAR')
pOrigin: Structure = Structure.from_file('test_POSCAR/POSCAR')
e = 1.60217646e-19
v = s.volume
pol = np.zeros(3)
b = out.born

for i in range(len(b)):
    pol += np.dot(b[i], pDown.cart_coords[i] - pOrigin.cart_coords[i])

print(pol * e / v * 1e+22)  # uC/cm^2

Example #8

    'GGA_COMPAT': '.False.',
    'ISMEAR': 0,
    'SIGMA': 0.05,
    'GGA': 'PE',
    'ENCUT': '280.00 eV',
    'MAGMOM': '6*0.0',
    'NBANDS': 24,
}

larray = array([[0,.5,.5],
                [.5,0,.5],
                [.5,.5,0]])
lattice = Lattice(larray * 6.058)
species = ['In', 'As']
coords = [[0,0,0],[.25,.25,.25]]
structure = Structure(lattice, species, coords, coords_are_cartesian=False)
poscar = Poscar(structure, 'fcc InAs').as_dict()

#~ potcar = Potcar.from_file(sys.argv[2]).as_dict()
from os.path import abspath
potcar = abspath(sys.argv[2])

kpoints = {
    'comment': 'fcc InAs - selfconsistent',
    'generation_style': 'Gamma',
    'kpoints': [[8,8,8]],
    'usershift': [0,0,0],
}

code = Code.get_from_string('vasp')
calc = code.new_calc()

Example #9

from pymatgen.io.vasp import Structure
from pymatgen.core.sites import PeriodicSite


p: Structure = Structure.from_file('POSCAR')
i: PeriodicSite = None

for i in p.sites:
    if 0.16 < i.c < 0.37 or 0.53 < i.c < 0.77:
        i._properties = {'selective_dynamics': [True] * 3}
    else:
        i._properties = {'selective_dynamics': [False] * 3}
p.to('POSCAR', 'POSCAR')