def test_can_execute(tmpdir):
"""Tests the can_execute method.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si",
positions=[[0, 0, 0]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
kwargs = {
"kpoints": {
"method": "mueller",
"mindistance": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
assert not calc.can_execute(target)
calc.write_input(atm, directory=target)
assert not calc.can_execute("def")
assert calc.can_execute(target)
def test_to_dict(tmpdir):
"""Tests the conversion of atoms to dictionaries.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("atoms_dict"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {"encut":400, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi, target, '.', 0, **kwargs)
atSi.set_calculator(calc)
atSi.group_uuid = "123456"
Sidict = atSi.to_dict()
assert "calc" in Sidict
assert "calc_kwargs" in Sidict
assert Sidict["calc_kwargs"]["encut"] == 400
assert Sidict["group_uuid"] == "123456"
assert "potcars" in Sidict["calc_kwargs"]
assert "kpoints" in Sidict["calc_kwargs"]
def test_extract(tmpdir):
"""Tests the extract method and cleanup method.
"""
from matdb.utility import symlink, relpath, touch
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si", positions=[[0, 0, 0]], cell=[1, 1, 1])
kwargs = {
"ibrion": 5,
"nsw": 1,
"kpoints": {
"method": "mueller",
"mindistance": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
calc.write_input(atm, target)
symlink(path.join(calc.folder, "OUTCAR"),
relpath("tests/files/VASP/OUTCAR_complete"))
symlink(path.join(calc.folder, "CONTCAR"),
path.join(calc.folder, "POSCAR"))
calc.extract(target)
assert hasattr(calc.atoms, calc.force_name)
assert hasattr(calc.atoms, calc.virial_name)
assert hasattr(calc.atoms, calc.energy_name)
assert calc.atoms.vasp_energy is not None
assert calc.atoms.vasp_virial is not None
assert calc.atoms.vasp_force is not None
touch(path.join(calc.folder, "CHG"))
calc.cleanup(target, clean_level="light")
assert not path.isfile(path.join(calc.folder, "CHG"))
touch(path.join(calc.folder, "CHGCAR"))
calc.cleanup(target)
assert not path.isfile(path.join(calc.folder, "CHGCAR"))
touch(path.join(calc.folder, "vasprun.xml"))
calc.cleanup(target, clean_level="aggressive")
assert not path.isfile(path.join(calc.folder, "OUTCAR"))
assert not path.isfile(path.join(calc.folder, "vasprun.xml"))
symlink(path.join(calc.folder, "CONTCAR"),
path.join(calc.folder, "POSCAR"))
symlink(path.join(calc.folder, "OUTCAR"),
relpath("tests/files/VASP/OUTCAR_incomplete"))
assert not calc.extract(target)
def test_write_input(tmpdir):
"""Tests the writing of the input files.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si",
positions=[[0, 0, 0]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
kwargs = {
"kpoints": {
"method": "mueller",
"mindistance": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
calc.write_input(atm, directory=target)
assert path.isfile(path.join(calc.folder, "POTCAR"))
assert path.isfile(path.join(calc.folder, "INCAR"))
assert path.isfile(path.join(calc.folder, "POSCAR"))
assert path.isfile(path.join(calc.folder, "KPOINTS"))
kwargs = {
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
calc.write_input(atm, directory=target)
assert path.isfile(path.join(calc.folder, "POTCAR"))
assert path.isfile(path.join(calc.folder, "INCAR"))
assert path.isfile(path.join(calc.folder, "POSCAR"))
assert path.isfile(path.join(calc.folder, "KPOINTS"))
calc.create()
assert path.isfile(path.join(calc.folder, "POTCAR"))
assert path.isfile(path.join(calc.folder, "INCAR"))
assert path.isfile(path.join(calc.folder, "POSCAR"))
assert path.isfile(path.join(calc.folder, "KPOINTS"))
def test_remote_read(tmpdir):
"""Tests the reading in of a atoms.h5 file from another directory."""
from matdb.atoms import Atoms
from matdb.utility import _set_config_paths, reporoot
from os import path
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("to_hdf5"))
globals_setup(target)
at = Atoms()
at.read(target=path.join(reporoot, "tests", "files", "test.h5"))
assert isinstance(at, Atoms)
def test_hdf5(tmpdir):
"""Tests whether an atoms object with calculated parameters can be saved to
JSON and then restored.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("to_hdf5"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {"kpoints":{"rmin":50}, "potcars": {"directory":"./tests/vasp",
"versions":{"Si": '05Jan2001'}}, "xc":"pbe"}
potSW = Vasp(atSi, target, str(tmpdir), 0, **kwargs)
atSi.set_calculator(potSW)
atSi.add_property("vasp_force", [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]])
atSi.add_param("vasp_energy", 25360.504084423999)
atSi.add_param("vasp_virial", [[ 33538.34327189, 11045.88697112, 11045.88697112],
[ 11045.88697112, 33538.34327189, 11045.88697112],
[ 11045.88697112, 11045.88697112, 33538.34327189]])
atSi.properties["rand"] = np.random.randint(0, 100, 8)
atSi.write(target=path.join(target,"temp.h5"))
atR = Atoms()
atR.read(target=path.join(target,"temp.h5"))
# check that the calculator got transfered properly.
assert type(atSi.calc) == type(atR.calc)
assert atSi.calc.args == atR.calc.args
assert atSi.calc.kwargs == atR.calc.kwargs
# check that the other properties got transfered properly.
assert atR.vasp_energy == atSi.vasp_energy
assert isinstance(atR, Atoms)
assert np.allclose(atR.vasp_force, atSi.vasp_force)
assert np.allclose(atR.vasp_virial, atSi.vasp_virial)
assert np.allclose(atR.properties["rand"], atSi.properties["rand"])
assert np.allclose(atR.positions, atSi.positions)
remove(path.join(target,"temp.h5"))
def test_read_atoms(tmpdir):
"""Tests the reading of atoms objects from files.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("read_atoms"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {"encut":400, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi, target, '.', 0, **kwargs)
atSi.set_calculator(calc)
atSi.set_calculator(calc)
atSi.add_property("vasp_force", [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]])
atSi.add_param("vasp_energy", 25360.504084423999)
atSi.add_param("vasp_virial", [[ 33538.34327189, 11045.88697112, 11045.88697112],
[ 11045.88697112, 33538.34327189, 11045.88697112],
[ 11045.88697112, 11045.88697112, 33538.34327189]])
atSi.group_uuid = "123456"
temp = path.join(target,"temp.h5")
atSi.write(temp)
atR = Atoms(temp)
assert atR.calc.name == "Vasp"
assert hasattr(atR.calc,"potcars")
assert atR.calc.kwargs["encut"] == 400
assert np.allclose(atR.positions,[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]])
def test_Atoms_attributes(tmpdir):
"""Tests the some of the attributes of an atoms object.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms
from matdb.utility import _set_config_paths, reporoot
from os import path
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("atom_attributes"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
at1 = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {"kpoints":{"rmin":50}, "potcars": {"directory":"./tests/vasp",
"versions":{"Si": '05Jan2001'}}, "xc":"pbe"}
potSW = Vasp(at1, target, str(tmpdir), 0, **kwargs)
at1.set_calculator(potSW)
at1.add_property("vasp_force", [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]])
at1.add_param("vasp_energy", 1234)
assert at1.get_energy() == 1234
at1.rm_param("vasp_energy")
assert not "vasp_energy" in at1.info["params"]
at1.rm_property("vasp_force")
assert not "vasp_force" in at1.info["properties"]
at1.params = {"vasp_energy": 1234}
assert at1.vasp_energy == 1234
at1.properties["vasp_force"] = [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]]
assert "vasp_force" in at1.info["properties"]
def test_to_dict():
"""Tests the to dict method.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", '.')
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {}
args = []
calc = Aflow(atSi, '$control$', '$control$', 0, *args, **kwargs)
out = {"folder":'$control$', "ran_seed":0, "contr_dir":'$control$',
"kwargs":{"entry":None}, "args":[]}
assert compare_nested_dicts(calc.to_dict(),out)
def test_Atoms_creation(tmpdir):
"""Tests the initialization of the atoms objcet.
"""
from matdb.atoms import Atoms
from ase.atoms import Atoms as aseAtoms
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
atR = Atoms(atSi)
assert atR==atSi
atSi = aseAtoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
atSi.info['nneightol'] = 10
atSi.info['cutoff'] = 5
atSi.info['cutoff_break'] = 10
atR = Atoms(atSi)
assert np.allclose(atR.positions,atSi.positions)
assert np.allclose(atR.cell,atSi.cell)
assert hasattr(atR,'nneightol')
assert hasattr(atR,'cutoff')
assert hasattr(atR,'cutoff_break')
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("make_atoms"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
atSi.write(target=path.join(target,"temp.xyz"))
atR = Atoms(path.join(target,"temp.xyz"))
assert np.allclose(atR.positions,atSi.positions)
assert np.allclose(atR.cell,atSi.cell)
remove(path.join(target,"temp.xyz"))
def test_can_extract(tmpdir):
"""Tests the can_extract method. We'll also test is_executing at the
same time.
"""
from matdb.utility import symlink, relpath
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si", positions=[[0, 0, 0]])
kwargs = {
"kpoints": {
"method": "mueller",
"mindistance": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
assert not calc.can_extract("def")
assert not calc.can_extract(target)
symlink(path.join(calc.folder, "OUTCAR"),
relpath("tests/files/VASP/OUTCAR_incomplete"))
assert not calc.can_extract(target)
assert calc.is_executing(target)
symlink(path.join(calc.folder, "OUTCAR"),
relpath("tests/files/VASP/OUTCAR_complete"))
assert calc.can_extract(target)
assert not calc.is_executing(target)
def test_build_calc():
"""Tests the setting of the calc builder."""
from matdb.calculators.utility import build_calc
from matdb.io import read
from matdb.calculators.utility import paths, set_paths
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", '.')
target = relpath("./tests/AgPd/matdb")
config = path.expanduser(path.abspath(target))
if path.isabs(config):
root, config = path.split(config)
else:
root, config = path.dirname(config), config
configyml = read(root, config)
set_paths(configyml)
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe"
}
}
res = build_calc("Vasp", None, **kwargs)
assert res.key == "vasp"
res = None
res = build_calc("Vasp", '.', **kwargs)
assert res.key == "vasp"
def test_ase_atoms_conversion(tmpdir):
"""Tests the conversion of an ase atoms objcet to a 'matdb.atoms.Atoms' object.
"""
from matdb.atoms import Atoms as matAtoms
from ase.atoms import Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("from_ase"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
aR = matAtoms(atSi)
assert np.allclose(aR.positions, atSi.positions)
assert aR.calc == atSi.calc
def test_vasp_setup(tmpdir):
"""Tests Vasp calculator initialization.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si", positions=[[0, 0, 0]])
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"versions": {
"Si": '05Jan2001'
}
},
"xc": "pbe"
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
assert calc.potcars["xc"] == "pbe"
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
assert calc.kwargs["xc"] == "pbe"
stat = calc.set_static(kwargs)
assert "nsw" in stat and stat["nsw"] == 0
calc.asis = True
assert calc.read_convergence()
with pytest.raises(VersionError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe"
}
}
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
with pytest.raises(VersionError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '04Jan2001'
}
}
}
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
with pytest.raises(VersionError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '04Jan2001'
}
}
}
atm = Atoms("Al", positions=[[0, 0, 0]])
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
with pytest.raises(ValueError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp"
}
}
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
def test_AtomsList_creation(tmpdir):
"""Tests the creation of the AtomsList object.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms, AtomsList
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("make_AtomsList"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
kwargs = {"kpoints":{"rmin":50}, "potcars": {"directory":"./tests/vasp",
"versions":{"Si": '05Jan2001'}}, "xc":"pbe"}
at1 = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43],info={"rand":10})
potSW = Vasp(at1, target, str(tmpdir), 0, **kwargs)
at1.set_calculator(potSW)
at1.add_property("vasp_force", [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]])
at1.add_param("vasp_energy", 1234)
at2 = Atoms("S6",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75]],
cell=[6.43,5.43,4.43],info={"rand":10},calculator=potSW)
kwargs = {"kpoints":{"rmin":50}, "potcars": {"directory":"./tests/vasp",
"versions":{"S": '06Sep2000'}}, "xc":"pbe"}
potSW = Vasp(at2, target, str(tmpdir), 0, **kwargs)
at2.set_calculator(potSW)
at2.add_property("vasp_force", np.random.randint(0, 100, (6,3)))
at2.add_param("vasp_energy", 4321)
al1 = AtomsList([at1,at2])
assert len(al1) == 2
at1.write(target=path.join(target,"temp1.h5"))
at2.write(target=path.join(target,"temp2.h5"))
al2 = AtomsList([path.join(target,"temp1.h5"),path.join(target,"temp2.h5")])
assert len(al2) == 2
assert isinstance(al2[0],Atoms)
empty_list = AtomsList([])
assert len(empty_list) == 0
al3 = AtomsList(at1)
assert al3[0] == at1
al4 = AtomsList(path.join(target,"temp1.h5"))
assert len(al4) == 1
assert isinstance(al4[0],Atoms)
assert al4[0].vasp_energy == at1.vasp_energy
def test_atoms_to_cfg(tmpdir):
"""Tests the writing of an atoms object to cfg format.
"""
from matdb.io import atoms_to_cfg
from matdb.atoms import Atoms
from os import path, remove
from ase.calculators.singlepoint import SinglePointCalculator
from matdb.calculators import Vasp
from matdb.utility import _set_config_paths
atSi = Atoms("Si8",
positions=[[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0],
[0.75, 0.75, 0.25], [0.5, 0, 0.5],
[0.75, 0.25, 0.75], [0, 0.5, 0.5],
[0.25, 0.75, 0.75]],
cell=[5.43, 5.43, 5.43])
target = "train.cfg"
atoms_to_cfg(atSi, target)
assert path.isfile(target)
remove(target)
energy = 10.0
forces = [[1, 1, 1], [2, 2, 2], [3, 3, 3], [4, 4, 4], [5, 5, 5], [6, 6, 6],
[7, 7, 7], [8, 8, 8]]
virial = [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
atSi.calc = SinglePointCalculator(atSi,
energy=energy,
forces=np.array(forces),
stress=virial)
atSi.add_property("energy", energy)
atSi.add_property("virial", virial)
atSi.add_param("force", forces)
atoms_to_cfg(atSi, target)
assert path.isfile(target)
remove(target)
atSi = Atoms("Si8",
positions=[[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0],
[0.75, 0.75, 0.25], [0.5, 0, 0.5],
[0.75, 0.25, 0.75], [0, 0.5, 0.5],
[0.25, 0.75, 0.75]],
cell=[5.43, 5.43, 5.43])
type_map = {0: 1}
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"versions": {
"Si": "05Jan2001"
}
},
"xc": "pbe"
}
_set_config_paths("test", tmpdir)
atSi.calc = Vasp(atSi, str(tmpdir.join("Vasp")), str(tmpdir), 0, **kwargs)
atoms_to_cfg(atSi, target, type_map=type_map, config_id="test")
assert path.isfile(target)
remove(target)
def test_write_potcar(tmpdir):
"""Tests the writing of the POTCAR file.
"""
from matdb.utility import _set_config_paths
from hashlib import sha1
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("Si",
positions=[[0, 0, 0]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
calc._write_potcar()
this_potcar = str(
sha1("{0}{1}".format("Si", "05Jan2001").encode()).hexdigest())
assert path.isfile(path.join(calc.contr_dir, "POTCARS", this_potcar))
assert path.isfile(path.join(calc.folder, "POTCAR"))
remove(path.join(calc.contr_dir, "POTCARS", this_potcar))
kwargs = {
"kpoints": {
"method": "mueller",
"mindistance": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
calc._write_potcar()
assert path.isfile(path.join(calc.contr_dir, "POTCARS", this_potcar))
calc._write_potcar()
assert path.isfile(path.join(calc.folder, "POTCAR"))
# check POTCAR reuse
calc = Vasp(atm, target, str(tmpdir), 0, **kwargs)
with pytest.raises(SpeciesError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
symlink(
path.join(calc.contr_dir, "POTCARS", calc.this_potcar),
path.join(reporoot, "tests", "vasp", "potpaw_PBE", "Ag", "POTCAR"))
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
with pytest.raises(VersionError):
kwargs = {
"kpoints": {
"rmin": 50
},
"potcars": {
"directory": "./tests/vasp",
"xc": "pbe",
"versions": {
"Si": '05Jan2001'
}
}
}
symlink(
path.join(calc.contr_dir, "POTCARS", calc.this_potcar),
path.join(reporoot, "tests", "vasp", "potpaw_PBE", "Si_sv_GW",
"POTCAR"))
atm = Atoms("Si",
positions=[[0, 0, 0]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
calc = Vasp(atm, '.', str(tmpdir), 0, **kwargs)
def test_to_dict(tmpdir):
"""Tests the calculator to_dict method.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Vasp"))
globals_setup(target)
atm = Atoms("AgPd",
positions=[[0, 0, 0], [0.25, 0.25, 0.25]],
cell=[1, 1, 1])
kwargs = {
"ibrion": 5,
"xc": "pbe",
"nsw": 1,
"kpoints": {
"method": "mueller",
"mindistance": 30
},
"potcars": {
"directory": '156def0ed29f1a908d5a7b4eae006c672e7b0ff1',
"xc": "pbe",
"versions": {
"Ag": '09Dec2005',
"Pd": '04Jan2005'
},
"setups": {
"Ag": "_pv"
}
},
"exec_path": None
}
calc = Vasp(atm, '$control$/Vasp', '$control$', 0, **kwargs)
calc_dict = calc.to_dict()
kwargs1 = {
"ibrion": 5,
"xc": "pbe",
"nsw": 1,
"kpoints": {
"method": "mueller",
"mindistance": 30
},
"potcars": {
"directory": '156def0ed29f1a908d5a7b4eae006c672e7b0ff1',
"xc": "pbe",
"versions": {
"Ag": '09Dec2005',
"Pd": '04Jan2005'
},
"setups": {
"Ag": "_pv"
}
}
}
kwargs2 = {
"ibrion": 5,
"xc": "pbe",
"nsw": 1,
"kpoints": {
"method": "mueller",
"mindistance": 30
},
"potcars": {
"directory": '03526af4c062e11236b794c0b260a2571cfe12d6',
"xc": "pbe",
"versions": {
"Ag": '09Dec2005',
"Pd": '04Jan2005'
},
"setups": {
"Ag": "_pv"
}
}
}
out1 = {
"folder": '$control$/Vasp',
"ran_seed": 0,
"contr_dir": '$control$',
"kwargs": kwargs1,
"args": ()
} #, "version": "vasp.4.6.35"}
out2 = {
"folder": '$control$/Vasp',
"ran_seed": 0,
"contr_dir": '$control$',
"kwargs": kwargs2,
"args": ()
} #, "version": "vasp.4.6.35"}
# "version" appears in calc_dict on local device
if "version" in calc_dict:
out1["version"] = calc_dict["version"]
out2["version"] = calc_dict["version"]
assert compare_nested_dicts(calc_dict, out1) or compare_nested_dicts(
calc_dict, out2)
calc_dict = calc.to_dict()
out1 = {
"folder": '$control$/Vasp',
"ran_seed": 0,
"contr_dir": '$control$',
"kwargs": kwargs1,
"args": (),
"version": ""
}
out2 = {
"folder": '$control$/Vasp',
"ran_seed": 0,
"contr_dir": '$control$',
"kwargs": kwargs2,
"args": (),
"version": ""
}
assert compare_nested_dicts(calc_dict, out1) or compare_nested_dicts(
calc_dict, out2)
def test_reading_multiple_files(tmpdir):
"""Tests the reading in of multiple atoms objects to an AtomsList.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms, AtomsList
from matdb.io import save_dict_to_h5
import h5py
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("read_atoms2"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
kwargs = {"encut":400, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi, target, '.', 0, **kwargs)
atSi.set_calculator(calc)
temp = path.join(target,"temp.h5")
atSi.write(temp)
atSi2 = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[6.43,6.43,6.43])
kwargs = {"encut":600, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi2, target, '.', 0, **kwargs)
atSi2.set_calculator(calc)
temp2 = path.join(target,"temp2.h5")
atSi2.write(temp2)
atRL = AtomsList([temp,temp2])
assert len(atRL) == 2
assert atRL[0].calc.kwargs["encut"] != atRL[1].calc.kwargs["encut"]
assert atRL[1].calc.kwargs["encut"] in [400,600]
assert atRL[0].calc.kwargs["encut"] in [400,600]
atom_dict = {"atom_1":temp, "atom_2": temp2}
temp3 = path.join(target,"temp3.h5")
with h5py.File(temp3,"w") as hf:
save_dict_to_h5(hf,atom_dict,'/')
atRL = AtomsList(temp3)
assert len(atRL) == 2
assert atRL[0].calc.kwargs["encut"] != atRL[1].calc.kwargs["encut"]
assert atRL[1].calc.kwargs["encut"] in [400,600]
assert atRL[0].calc.kwargs["encut"] in [400,600]
def test_to_dict(tmpdir):
"""Tests the calculator to_dict method.
"""
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("Qe"))
globals_setup(target)
atm = Atoms("AlPd", positions=[[0, 0, 0], [0.5, 0.5, 0.5]])
kwargs = {
"potcars": {
"directory": "./tests/qe",
"potentials": {
"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF",
"Pd": "Pd_ONCV_PBE-1.0.upf"
},
"versions": {
"Al": ["2.0.1", ".5.1"],
"Pd": ["2.0.1", "2.1.1"]
}
},
"kpoints": {
"method": "kspacing",
"spacing": 0.1,
"offset": 1
},
"input_data": {
"control": {
"calculation": "relax",
"prefix": "test"
}
}
}
calc = Qe(atm, '$control$/Qe', '$control$', 0, **kwargs)
symlink(path.join(calc.folder, "test.xml"),
relpath("tests/qe/complete.xml"))
calc.extract(target)
calc_dict = calc.to_dict()
kwargs = {
"potcars": {
"directory": "156def0ed29f1a908d5a7b4eae006c672e7b0ff1",
"potentials": {
"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF",
"Pd": "Pd_ONCV_PBE-1.0.upf"
},
"versions": {
"Al": ["2.0.1", ".5.1"],
"Pd": ["2.0.1", "2.1.1"]
}
},
"kpoints": {
"method": "kspacing",
"spacing": 0.1,
"offset": 1
},
"input_data": {
"control": {
"calculation": "relax",
"prefix": "test"
},
'tprnfor': True,
'tstress': True
}
}
out = {
"folder": '$control$/Qe',
"ran_seed": 0,
"contr_dir": '$control$',
"kwargs": kwargs,
"args": (),
"version": "6.2 (svn rev. 14038)"
}
assert compare_nested_dicts(calc_dict, out)
