def test_from_pmg_structure():
pmg_struc = pmgstruc.Structure(lattice= np.eye(3),
species=['H'],
coords=[[.25, .5, 0]],
site_properties={
'force': [np.array((1., 1., 1.))],
'std':[np.array((1., 1., 1.))]},
coords_are_cartesian=True)
new_struc = Structure.from_pmg_structure(pmg_struc)
assert len(new_struc) == 1
assert np.equal(new_struc.positions, np.array([.25, .5, 0])).all()
assert new_struc.coded_species == [1]
assert new_struc.species_labels[0] == 'H'
assert np.equal(new_struc.forces, np.array([1., 1., 1.])).all()
pmg_struc = pmgstruc.Structure(lattice= np.diag([1.2,0.8,1.5]),
species=['H'],
coords=[[.25, .5, 0]],
site_properties={
'force': [np.array((1., 1., 1.))],
'std':[np.array((1., 1., 1.))]},
coords_are_cartesian=True)
new_struc = Structure.from_pmg_structure(pmg_struc)
assert len(new_struc) == 1
assert np.equal(new_struc.positions, np.array([.25, .5, 0])).all()
assert new_struc.coded_species == [1]
assert new_struc.species_labels[0] == 'H'
assert np.equal(new_struc.forces, np.array([1., 1., 1.])).all()
def parse_dft_input(input: str):
"""
Returns the positions, species, and cell of a POSCAR file.
Outputs are specced for OTF module.
:param input: POSCAR file input
:return:
"""
pmg_structure = Poscar.from_file(input).structure
flare_structure = Structure.from_pmg_structure(pmg_structure)
positions = flare_structure.positions
species = flare_structure.species_labels
cell = flare_structure.cell
# TODO Allow for custom masses in POSCAR
elements = set(species)
# conversion from amu to md units
mass_dict = {
elt: Element(elt).atomic_mass * 0.000103642695727
for elt in elements
}
return positions, species, cell, mass_dict
def test_from_pmg_structure():
pmgstruc = pytest.importorskip("pymatgen.core.structure")
pmg_struc = pmgstruc.Structure(
lattice=np.eye(3),
species=["H"],
coords=[[0.25, 0.5, 0]],
site_properties={
"force": [np.array((1.0, 1.0, 1.0))],
"std": [np.array((1.0, 1.0, 1.0))],
},
coords_are_cartesian=True,
)
new_struc = Structure.from_pmg_structure(pmg_struc)
assert len(new_struc) == 1
assert np.equal(new_struc.positions, np.array([0.25, 0.5, 0])).all()
assert new_struc.coded_species == [1]
assert new_struc.species_labels[0] == "H"
assert np.equal(new_struc.forces, np.array([1.0, 1.0, 1.0])).all()
pmg_struc = pmgstruc.Structure(
lattice=np.diag([1.2, 0.8, 1.5]),
species=["H"],
coords=[[0.25, 0.5, 0]],
site_properties={
"force": [np.array((1.0, 1.0, 1.0))],
"std": [np.array((1.0, 1.0, 1.0))],
},
coords_are_cartesian=True,
)
new_struc = Structure.from_pmg_structure(pmg_struc)
assert len(new_struc) == 1
assert np.equal(new_struc.positions, np.array([0.25, 0.5, 0])).all()
assert new_struc.coded_species == [1]
assert new_struc.species_labels[0] == "H"
assert np.equal(new_struc.forces, np.array([1.0, 1.0, 1.0])).all()
def md_trajectory_from_vasprun(vasprun, ionic_step_skips=1, vasprun_kwargs: dict = {}):
"""
Returns a list of flare Structure objects decorated with forces, stress,
and total energy from a MD trajectory performed in VASP.
:param vasprun: pymatgen Vasprun object or vasprun filename
:param ionic_step_skips: if True, only samples the configuration every
ionic_skip_steps steps.
"""
vasprun = check_vasprun(vasprun, vasprun_kwargs)
struc_lst = []
for step in vasprun.ionic_steps[::ionic_step_skips]:
structure = Structure.from_pmg_structure(step["structure"])
structure.energy = step["electronic_steps"][-1]["e_0_energy"]
# TODO should choose e_wo_entrp or e_fr_energy?
structure.forces = np.array(step.get("forces"))
structure.stress = np.array(step.get("stress"))
struc_lst.append(structure)
return struc_lst
def dft_input_to_structure(poscar: str):
"""
Parse the DFT input in a directory.
:param vasp_input: directory of vasp input
"""
return Structure.from_pmg_structure(Poscar.from_file(poscar).structure)
