def test_prim_vec_from_angles_tetr():
energy_driver = None
template_file = None
#s = []
abc = []
angles = [90, 90, 90]
run = m.DftRun(energy_driver, template_file, abc, angles=angles)
correct_vec = np.array([[1,0,0],[0,1,0], [0,0,1]])
assert np.isclose(run._prim_vec_from_angles(), correct_vec).all()
def test_angles_prim_vec_both():
"""
raises value error if both angles and prim_vec are specified
"""
energy_driver = None
template_file = None
abc = []
with pytest.raises(ValueError):
m.DftRun(energy_driver, template_file, abc, angles=[90, 90, 90], prim_vec_unscaled=[] )
def test_preprocess_file_bad():
"""
entering bad name for energy driver raises value error
"""
energy_driver = 'bad_energy_driver_name'
template_file = None
pvu = []
abc = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
with pytest.raises(ValueError):
run._preprocess_file()
def test_angles_prim_vec_neither():
"""
raises value error if neither of angles and prim_vec are specified
"""
energy_driver = None
template_file = None
#abc_guess = []
#s = []
abc = []
with pytest.raises(ValueError):
m.DftRun(energy_driver, template_file, abc)
def test_get_energy_elk():
"""read total energy from elk correctly"""
with TemporaryDirectory() as tmp_dir:
energy_driver = 'elk'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'TOTENERGY.OUT.example'), 'TOTENERGY.OUT')
E = run.get_energy()
assert np.isclose(E, -7.51826352965)
def test_get_energy_espresso_none():
""" raises NoEnergyFromDFT if espresso output file doesn't show completion"""
with TemporaryDirectory() as tmp_dir:
with pytest.raises(m.NoEnergyFromDFT):
energy_driver = 'quantumespresso'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'espresso.out.noenergy'), 'log')
E = run.get_energy()
def test_get_energy_espresso():
"""read final energy from espresso output file correctly"""
with TemporaryDirectory() as tmp_dir:
energy_driver = 'quantumespresso'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'espresso.out.example'), 'log')
E = run.get_energy()
assert np.isclose(E, -4.18725738/2.)
def test_get_energy_socorro_relax():
""" gets FINAL energy from socorro diaryf if relaxation was performed """
with TemporaryDirectory() as tmp_dir:
energy_driver = 'socorro'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'diaryf.relax'), 'diaryf')
E = run.get_energy()
assert np.isclose(E, -360.361967002/2.)
def test_get_energy_socorro_none():
""" raises NoEnergyFromDFT if socorro doesn't complete """
with TemporaryDirectory() as tmp_dir:
with pytest.raises(m.NoEnergyFromDFT):
energy_driver = 'socorro'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'diaryf.noenergy'), 'diaryf')
E = run.get_energy()
def test_get_energy_socorro():
"""read cell enrgy from socorro correctly"""
with TemporaryDirectory() as tmp_dir:
energy_driver = 'socorro'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'diaryf.example'), 'diaryf')
E = run.get_energy()
assert np.isclose(E, -74.637868487/2.)
def test_abinit_get_energy_multiple():
"""When multiple etotal reported, returns correct etotal in Hartree"""
with TemporaryDirectory() as tmp_dir:
energy_driver='abinit'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'log.structurerelax.example'), 'log')
E = run.get_energy()
assert np.isclose(E, -7.3655263854)
def test_abinit_get_energy_single():
"""When only single etotal reported (typical case), returns etotal in Hartree"""
with TemporaryDirectory() as tmp_dir:
energy_driver='abinit'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'log.example'), 'log')
E = run.get_energy()
assert np.isclose(E, -6.1395717098)
def test_get_energy_bad():
"""
entering bad name for energy driver raises value error
"""
energy_driver = 'bad'
template_file = None
abc = []
pvu = [[1,1,0], [0,1,1], [1,0,1]]
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
with pytest.raises(ValueError):
run.get_energy()
def test_get_energy_espresso_relax():
""" gets FINAL energy from espresso if relaxation was performed """
with TemporaryDirectory() as tmp_dir:
energy_driver = 'quantumespresso'
template_file = None
abc = []
pvu = []
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
shutil.copy(os.path.join(input_dir, 'espresso.out.relax'), 'log')
E = run.get_energy()
assert np.isclose(E, -29.22370146/2.)
def test_preprocess_file_espresso_rprim():
"""
calling _preprocess_file for espresso correctly writes scale and lattice constants to
espresso input file
"""
with TemporaryDirectory() as tmp_dir:
correct_file = os.path.join(input_dir, 'espresso.in.correct')
energy_driver = 'quantumespresso'
template_file = os.path.join(input_dir, 'espresso.in.template.example')
abc = [1.5, 3, 6]
pvu = [[1,1,0], [0,1,1], [1,0,1]]
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
run._preprocess_file()
# compare written espresso input file with correct input file
with open(correct_file) as f1, open('espresso.in') as f2:
assert f1.readlines() == f2.readlines()
def test_preprocess_file_abinit_rprim():
"""
calling _preprocess_file with for abinit correctly writes acell and lattice vectors to file
not very robust since different number format would cause a fail
"""
with TemporaryDirectory() as tmp_dir:
correct_file = os.path.join(input_dir, 'abinit.in.correct.2')
energy_driver = 'abinit'
template_file = os.path.join(input_dir, 'abinit.in.template.example')
abc = [1.5,3,6]
pvu = [[1,1,0], [0,1,1], [1,0,1]]
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
run._preprocess_file()
# compare written abinit file with correct input file
with open(correct_file) as f1, open('abinit.in') as f2:
assert f1.readlines() == f2.readlines()
def test_preprocess_file_socorro_rprim():
"""
calling _preprocess_file for socorro correctly writes scale and lattice constants to socorro crystal file
not very robust since different number format would cause a fail
"""
with TemporaryDirectory() as tmp_dir:
correct_file = os.path.join(input_dir, 'crystal.correct')
energy_driver = 'socorro'
template_file = os.path.join(input_dir, 'crystal.template.example')
abc = [1.5, 3, 6]
pvu = [[1,1,0], [0,1,1], [1,0,1]]
run = m.DftRun(energy_driver, template_file, abc, prim_vec_unscaled=pvu)
run._preprocess_file()
# compare written socorro crystal file with correct input file
with open(correct_file) as f1, open('crystal') as f2:
assert f1.readlines() == f2.readlines()
def test_preprocess_file_abinit_angdeg():
"""
calling _preprocess_file with for abinit correctly writes lattice constants and angles to abinit input file.
not very robust since different number format would cause a fail
"""
with TemporaryDirectory() as tmp_dir:
energy_driver = 'abinit'
template_file = os.path.join(input_dir, 'abinit.in.template.example')
correct_file = os.path.join(input_dir, 'abinit.in.correct')
ang = [90, 90, 120]
abc = [1.5, 3.0, 4.5]
run = m.DftRun(energy_driver, template_file, abc, angles=ang)
run._preprocess_file()
# compare written abinit file with correct input file
with open(correct_file) as f1, open('abinit.in') as f2:
assert f1.readlines() == f2.readlines()
def test_calc_unit_cell_volume_2():
abc = [8,10,12]
pvu = [[2,0,0], [0,3,0], [0,0,1]]
run = m.DftRun(None, None, abc, prim_vec_unscaled=pvu)
assert np.isclose(run._calc_unit_cell_volume(), 5760.)
def test_calc_unit_cell_volume_3():
abc = [12,15,18]
pvu = [[1,1,0], [0,1,1], [1,0,1]]
run = m.DftRun(None, None, abc, prim_vec_unscaled=pvu)
assert np.isclose(run._calc_unit_cell_volume(), 6480.)
def test_calc_unit_cell_volume_6():
abc = [2,2,10]
angles = [90,90,120]
run = m.DftRun(None, None, abc, angles=angles)
assert np.isclose(run._calc_unit_cell_volume(), 20*np.sqrt(3))
def test_calc_unit_cell_volume_5():
abc = [3,6,9]
angles = [90,90,90]
run = m.DftRun(None, None, abc, angles=angles)
assert np.isclose(run._calc_unit_cell_volume(), 162.)