def test_eos_fit_deriv():
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
eos = EosFit(volume=volume,
energy=energy,
splpoints=500)
# EosFit is a num.Fit1D subclass, so it has self.x and self.y
assert (volume == eos.x).all()
assert (energy == eos.y).all()
# this reference to self.spl causes self.spl to be defined (lazyprop)
xx = eos.spl.x
yy = eos.spl.y
assert len(xx) == len(yy) == 500
# spline thru fitted data, must be exactly like eos.spl
spl = num.Spline(xx, yy, k=5, s=None)
assert np.allclose(eos(xx), yy) # call _vinet, consistency of fitted data
assert np.allclose(eos(xx), spl(xx)) # consistency of splines
assert np.allclose(eos(xx), eos.spl(xx)) # consistency of splines
assert np.allclose(eos(xx, der=1), spl(xx, der=1)) # call _vinet_deriv1
assert np.allclose(eos(xx, der=2), spl(xx, der=2)) # call _vinet_deriv2
assert np.allclose(eos(xx, der=3), spl(xx, der=3)) # call eos.spl(xx, der=3)
def test_eos_fit_deriv():
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
eos = EosFit(volume=volume,
energy=energy,
splpoints=500)
# EosFit is a num.Fit1D subclass, so it has self.x and self.y
assert (volume == eos.x).all()
assert (energy == eos.y).all()
# this reference to self.spl causes self.spl to be defined (lazyprop)
xx = eos.spl.x
yy = eos.spl.y
assert len(xx) == len(yy) == 500
# spline thru fitted data, must be exactly like eos.spl
spl = num.Spline(xx, yy, k=5, s=None)
assert np.allclose(eos(xx), yy) # call _vinet, consistency of fitted data
assert np.allclose(eos(xx), spl(xx)) # consistency of splines
assert np.allclose(eos(xx), eos.spl(xx)) # consistency of splines
assert np.allclose(eos(xx, der=1), spl(xx, der=1)) # call _vinet_deriv1
assert np.allclose(eos(xx, der=2), spl(xx, der=2)) # call _vinet_deriv2
assert np.allclose(eos(xx, der=3), spl(xx, der=3)) # call eos.spl(xx, der=3)
def test_eos():
# load reference fitted with ElkEOSFit, data points [Bohr^3, Ha] -> [Ang^3, eV]
# EV input data [Bohr^3, Ry] -> [Ang^3, eV]
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
ref_ev = np.loadtxt("files/ev/EVPAI.OUT.gz")
ref_ev[:,0] *= Bohr3_to_Ang3
ref_ev[:,1] *= (Ha / eV)
ref_pv = np.loadtxt("files/ev/PVPAI.OUT.gz")
ref_pv[:,0] *= Bohr3_to_Ang3
ref_min = np.loadtxt("files/ev/min.txt")
ref_min[0] *= Bohr3_to_Ang3 # v0
ref_min[1] *= (Ry / eV) # e0
assert ref_ev.shape[0] == ref_pv.shape[0], ("reference data lengths "
"inconsistent")
ref = {}
ref['ev'] = ref_ev
ref['pv'] = ref_pv
ref['v0'], ref['e0'], ref['p0'], ref['b0'] = ref_min
# test new EosFit class, default func=Vinet()
eos = EosFit(volume=volume,
energy=energy)
assert np.allclose(eos.params['v0'], eos.spl.get_min())
assert np.allclose(eos.params['v0'], eos.get_min())
assert np.allclose(eos.params['e0'], eos(eos.params['v0']))
assert np.allclose(eos.params['b0']*eV_by_Ang3_to_GPa, eos.bulkmod(eos.params['v0']))
now = {}
now['v0'] = eos.params['v0']
now['e0'] = eos.params['e0']
now['b0'] = eos.params['b0'] * eV_by_Ang3_to_GPa
now['p0'] = eos.pressure(eos.params['v0'])
for key,val in now.items():
msg = "EosFit: key=%s, ref=%e, val=%e" %(key, ref[key], val)
assert np.allclose(val, ref[key], atol=1e-7), msg
# Test legacy ElkEOSFit / ExternEOS.
# 'exe' must be on your $PATH.
exe = 'eos.x'
app = common.backtick("which %s" %exe).strip()
if app == '':
tools.skip("cannot find '%s' on PATH, skipping test" %exe)
else:
eos_store = {}
type_arr = type(np.array([1.0,2.0]))
for bv_method in ['ev', 'pv']:
print("bv_method: %s" %bv_method)
# natoms = 1, no normalization
eos = ElkEOSFit(energy=energy,
volume=volume,
natoms=1,
etype=1,
npoints=300,
dir=testdir,
bv_method=bv_method)
eos.fit()
now = {}
now['ev'] = eos.ev
now['pv'] = eos.pv
now.update(eos.get_min())
# compare to reference
for key, val in ref.items():
print("ElkEOSFit: testing:", key)
if type(val) == type_arr:
np.testing.assert_array_almost_equal(now[key], ref[key])
else:
np.testing.assert_almost_equal(now[key], ref[key],
decimal=3)
eos_store[bv_method] = eos
# internal check: are the splines correct?
for name in ['ev', 'pv', 'bv']:
# API
getter = getattr(eos, 'get_spl_' + name)
assert getattr(eos, 'spl_' + name) == getter()
# (N,2) arrays self.{ev,pv,bv}
data = getattr(eos, name)
vv = data[:,0]
yy = data[:,1]
# self.spl_{ev,pv,bv}
spl = getattr(eos, 'spl_' + name)
np.testing.assert_array_almost_equal(yy, spl(vv))
# Other attrs for which we do not have external ref data. Test only
# among the two bv_methods 'ev' and 'pv'.
print("bv")
np.testing.assert_array_almost_equal(eos_store['ev'].bv,
eos_store['pv'].bv,
decimal=2)
def test_eos():
# load reference fitted with ElkEOSFit, data points [Bohr^3, Ha] -> [Ang^3, eV]
# EV input data [Bohr^3, Ry] -> [Ang^3, eV]
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
ref_ev = np.loadtxt("files/ev/EVPAI.OUT.gz")
ref_ev[:,0] *= Bohr3_to_Ang3
ref_ev[:,1] *= (Ha / eV)
ref_pv = np.loadtxt("files/ev/PVPAI.OUT.gz")
ref_pv[:,0] *= Bohr3_to_Ang3
ref_min = np.loadtxt("files/ev/min.txt")
ref_min[0] *= Bohr3_to_Ang3 # v0
ref_min[1] *= (Ry / eV) # e0
assert ref_ev.shape[0] == ref_pv.shape[0], ("reference data lengths "
"inconsistent")
ref = {}
ref['ev'] = ref_ev
ref['pv'] = ref_pv
ref['v0'], ref['e0'], ref['p0'], ref['b0'] = ref_min
# test new EosFit class, default func=Vinet()
eos = EosFit(volume=volume,
energy=energy)
assert np.allclose(eos.params['v0'], eos.spl.get_min())
assert np.allclose(eos.params['v0'], eos.get_min())
assert np.allclose(eos.params['e0'], eos(eos.params['v0']))
assert np.allclose(eos.params['b0']*eV_by_Ang3_to_GPa, eos.bulkmod(eos.params['v0']))
now = {}
now['v0'] = eos.params['v0']
now['e0'] = eos.params['e0']
now['b0'] = eos.params['b0'] * eV_by_Ang3_to_GPa
now['p0'] = eos.pressure(eos.params['v0'])
for key,val in now.iteritems():
msg = "EosFit: key=%s, ref=%e, val=%e" %(key, ref[key], val)
assert np.allclose(val, ref[key], atol=1e-7), msg
# Test legacy ElkEOSFit / ExternEOS.
# 'exe' must be on your $PATH.
exe = 'eos.x'
app = common.backtick("which %s" %exe).strip()
if app == '':
tools.skip("cannot find '%s' on PATH, skipping test" %exe)
else:
eos_store = {}
type_arr = type(np.array([1.0,2.0]))
for bv_method in ['ev', 'pv']:
print "bv_method: %s" %bv_method
# natoms = 1, no normalization
eos = ElkEOSFit(energy=energy,
volume=volume,
natoms=1,
etype=1,
npoints=300,
dir=testdir,
bv_method=bv_method)
eos.fit()
now = {}
now['ev'] = eos.ev
now['pv'] = eos.pv
now.update(eos.get_min())
# compare to reference
for key, val in ref.iteritems():
print "ElkEOSFit: testing:", key
if type(val) == type_arr:
np.testing.assert_array_almost_equal(now[key], ref[key])
else:
np.testing.assert_almost_equal(now[key], ref[key],
decimal=3)
eos_store[bv_method] = eos
# internal check: are the splines correct?
for name in ['ev', 'pv', 'bv']:
# API
getter = getattr(eos, 'get_spl_' + name)
assert getattr(eos, 'spl_' + name) == getter()
# (N,2) arrays self.{ev,pv,bv}
data = getattr(eos, name)
vv = data[:,0]
yy = data[:,1]
# self.spl_{ev,pv,bv}
spl = getattr(eos, 'spl_' + name)
np.testing.assert_array_almost_equal(yy, spl(vv))
# Other attrs for which we do not have external ref data. Test only
# among the two bv_methods 'ev' and 'pv'.
print "bv"
np.testing.assert_array_almost_equal(eos_store['ev'].bv,
eos_store['pv'].bv,
decimal=2)
