def test_to_pmg_structure(varied_test_struc):
pmgstruc = pytest.importorskip("pymatgen.core.structure")
new_struc = Structure.to_pmg_structure(varied_test_struc)
assert len(varied_test_struc) == len(varied_test_struc)
assert np.equal(new_struc.cart_coords, varied_test_struc.positions).all()
assert (new_struc.atomic_numbers == varied_test_struc.coded_species).all()
def edit_dft_input_positions(output_name: str, structure: Structure):
"""
Writes a VASP POSCAR file from structure with the name poscar .
WARNING: Destructively replaces the file with the name specified by poscar
:param poscar: Name of file
:param structure: structure to write to file
"""
if os.path.isfile(output_name):
shutil.copyfile(output_name, output_name + ".bak")
poscar = Poscar(structure.to_pmg_structure())
poscar.write_file(output_name)
return output_name
def edit_dft_input_positions(poscar: str, structure: Structure):
"""
Writes a VASP POSCAR file from structure with the name poscar .
WARNING: Destructively replaces the file with the name specified by poscar
:param poscar: Name of file
:param structure: structure to write to file
"""
if os.path.isfile(poscar):
shutil.copyfile(poscar, poscar + '.bak')
f = open(poscar, 'w')
f.write(
Poscar(
structure.to_pmg_structure()).get_string(significant_figures=15))
f.close()
return poscar
def test_to_pmg_structure(varied_test_struc):
new_struc = Structure.to_pmg_structure(varied_test_struc)
assert len(varied_test_struc) == len(varied_test_struc)
assert np.equal(new_struc.cart_coords, varied_test_struc.positions).all()
assert (new_struc.atomic_numbers == varied_test_struc.coded_species).all()
