def test_Atoms_get_energy():
"""Tests get_energy method.
"""
from matdb.atoms import Atoms
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])
at1.add_param("vasp_energy", 4532)
assert at1.get_energy() == 4532
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_safeupdate():
"""Tests the safe_update method in utility.
"""
from matdb.atoms import Atoms
from matdb.utility import safe_update
al = Atoms("Si",positions=[[0,0,0]])
al.add_param("energy",None)
kv = {"positions":[[0.5,0.5,0.5]],"energy":10}
safe_update(al,kv)
assert np.allclose(al.positions,[[0,0,0]])
assert al.energy == 10
def test_AtomsList_sort():
"""Tests the method AtomsList.sort
"""
from matdb.atoms import Atoms, AtomsList
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})
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})
at3 = Atoms("CNi",positions=[[0,0,0],[0.5,0.5,0.5]], info={"rand":8})
at4 = Atoms("CoV",positions=[[0,0,0],[0.25,0.5,0.25]], info={"rand":8})
at1.add_param("vasp_energy", 25361.504084423999)
at2.add_param("vasp_energy", 25362.504084423999)
at3.add_param("vasp_energy", 25363.504084423999)
at4.add_param("vasp_energy", 25364.504084423999)
al1 = AtomsList([at4,at2,at1,at3])
#This is to test __getitem__
al2 = al1[0:2]
assert len(al2) == 2
al1.sort(key=len)
assert al1[0].get_chemical_formula() == "CoV"
assert al1[1].get_chemical_formula() == "CNi"
assert al1[2].get_chemical_formula() == "S6"
assert al1[3].get_chemical_formula() == "Si8"
al1.sort(attr="vasp_energy")
assert al1[0].get_chemical_formula() == "Si8"
assert al1[1].get_chemical_formula() == "S6"
assert al1[2].get_chemical_formula() == "CNi"
assert al1[3].get_chemical_formula() == "CoV"
al1.sort(attr="vasp_energy", reverse=True)
assert al1[0].get_chemical_formula() == "CoV"
assert al1[1].get_chemical_formula() == "CNi"
assert al1[2].get_chemical_formula() == "S6"
assert al1[3].get_chemical_formula() == "Si8"
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_split(Act):
"""Tests the split function.
"""
from matdb.atoms import Atoms, AtomsList
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})
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})
at3 = Atoms("CNi",
positions=[[0, 0, 0], [0.5, 0.5, 0.5]],
info={"rand": 8})
at4 = Atoms("CoV",
positions=[[0, 0, 0], [0.25, 0.5, 0.25]],
info={"rand": 8})
at1.add_param("vasp_energy", 25361.504084423999)
at2.add_param("vasp_energy", 25362.504084423999)
at3.add_param("vasp_energy", 25363.504084423999)
at4.add_param("vasp_energy", 25364.504084423999)
al = [at4, at2, at1, at3]
splits = {'A': 0.4, 'B': 0.2}
splitroot = path.join(Act.root, "split")
mkdir(splitroot)
file_targets = {
"train": Act.database.train_file,
"holdout": Act.database.holdout_file,
"super": Act.database.super_file
}
# the split directory should be empty
assert len(listdir(splitroot)) == 0
# split with an empty splits
split(al, {}, file_targets, splitroot, ran_seed=1, recalc=1)
# the split directory should still be empty
assert len(listdir(splitroot)) == 0
# split with an empty atom list
split([], splits, file_targets, splitroot, ran_seed=1, recalc=1)
# the split directory should have 2 entries
assert len(listdir(splitroot)) == 2
# split
split(al, splits, file_targets, splitroot, ran_seed=1)
# now we should have all the splitted files
assert path.exists(path.join(splitroot, Act.database.train_file('A')))
assert path.exists(path.join(splitroot, Act.database.holdout_file('A')))
assert path.exists(path.join(splitroot, Act.database.super_file('A')))
assert path.exists(path.join(splitroot, Act.database.train_file('B')))
assert path.exists(path.join(splitroot, Act.database.holdout_file('B')))
assert path.exists(path.join(splitroot, Act.database.super_file('B')))
# the split directory should have 2 entries
assert len(listdir(splitroot)) == 2
# split again with recalc
split(al, splits, file_targets, splitroot, ran_seed=1, recalc=1)
assert glob(
path.join(Act.database.root, "splits", "active", "A_*-train.h5"))
assert glob(
path.join(Act.database.root, "splits", "active", "A_*-holdout.h5"))
assert glob(
path.join(Act.database.root, "splits", "active", "A_*-super.h5"))
assert glob(
path.join(Act.database.root, "splits", "active", "B_*-train.h5"))
assert glob(
path.join(Act.database.root, "splits", "active", "B_*-holdout.h5"))
assert glob(
path.join(Act.database.root, "splits", "active", "B_*-super.h5"))
# the split directory should have 2 entries
assert len(listdir(splitroot)) == 2
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)
