def cif2structure(filename, primitive=False, symprec=0.001):
"""
Read a given file as a cif file, convert it into a
ase atoms object and finally into a pychemia
structure
"""
aseatoms = ase.io.read(filename)
if primitive:
#lattice, scaled_positions, numbers = spglib.refine_cell(aseatoms, symprec)
#ref_atoms=ase.atoms(cell=lattice,scaled_positions=scaled_positions,numbers=numbers)
lattice, scaled_positions, numbers = spglib.find_primitive(aseatoms, symprec)
if lattice is not None and scaled_positions is not None and numbers is not None:
fin_atoms = ase.atoms.Atoms(cell=lattice, scaled_positions=scaled_positions, numbers=numbers, pbc=True)
else:
fin_atoms = aseatoms
else:
fin_atoms = aseatoms
ret = ase2pychemia(fin_atoms)
return ret
def spglib_get_primitive(struct, **kwds):
"""Find primitive structure for given :class:`~pwtools.crys.Structure`.
If `struct` is irreducible (is already a primitive cell), we return None,
else a Structure.
Uses pyspglib.
Parameters
----------
struct : Structure
**kwds : keywords
passed to ``spglib.find_primitive()``, e.g. `symprec` and
`angle_tolerance` last time I checked
Returns
-------
Structure or None
Notes
-----
spglib used to return (None,None,None) if no primitive cell can be found,
i.e. the given input Structure cannot be reduced, which can occur if (a) a
given Structure is already a primitive cell or (b) any other reason like a
too small value of `symprec`. Now [py]spglib >= 1.8.x seems to always
return data instead. We use :func:`is_same_struct` to determine if the
struct is irreducible. In that case we return None in order to keep the API
unchanged.
Also note that a primitive cell (e.g. with 2 atoms) can have a number of
different realizations. Therefore, you may not always get the primitive
cell which you would expect or get from other tools like Wien2K's sgroup.
Only things like `natoms` and the spacegroup can be safely compared.
"""
candidate = spglib2struct(spglib.find_primitive(struct.get_fake_ase_atoms(),
**kwds))
if is_same_struct(candidate, struct):
return None
else:
return candidate
def analyze_QHA_run(Calc, Tmin=1, Tmax=1500, Tsteps=100):
'''
Run the QHA analysis procedure on the set of volume calculation Calc.
This procedure produces an array with thermodynamic functions for
all calculated volumes and given temperature range (the zero temperature is always included).
Input
=====
Calc - List of calculation data
Tmin - Minimum temperature of the scan (K)
Tmax - Maximum temperature of the scan (K)
Tsteps - Number of temperature steps
bdir - base directory (subdirectories host and calculation are located below)
Output
======
qha - array of N x Tsteps x #params containing resulting data:
V, T, Etot, Fph, P*V, Cv, S, ...
for each calculation and each temperature step.
'''
phdos={}
qha=[]
for n,c in enumerate(Calc):
PCMUL=len(c.get_atomic_numbers())/len(spglib.find_primitive(c)[2])
# Read the calculated dos
clc=c.calc.results
phdos[n]=clc['phdos']
#Etot=c.get_potential_energy()
Etot=clc['etotal']*Rydberg
# Pressure returned in kbar we need to change it to eV/A^3 to get p*V in eV
# eV/A^3=160.2176487GPa
# kbar=0.1 GPa
# eV/A^3 = 1602.176487 kbar
P=clc['pressure']/1602.176487
#P=c.get_isotropic_pressure(c.get_stress())
# Scan the temperatures at this volume
# Unit cell (primitive) volume in Bohr^3 => (A^3)
#V=(calcQHA[idx][2]['A'])**3
#V=clc['volume']*(Bohr**3)
V=c.get_volume()/PCMUL
# get the ndf from the normalization of dos
dos=phdos[n]
ndf=round(simps(dos[1],dos[0]))
# frequencies/energies
# QE outputs dos in cm^-1, let's convert to sane units
# Let's convert to energy to include the hbar
nu=1e-3*cminv2meV*phdos[n][0]
dos=phdos[n][1]
# We need to cut the nu to positive range
no=array([[o,g] for o,g in zip(nu,dos) if o>0 ])
nu=no[:,0]
dos=no[:,1]
# correct the normalization for units, negative cut and numerical errors
dos=dos/simps(dos,nu)
# plot in meV
#plot(1e-3*nu,dos,label=n);
#legend()
#show()
# plot the integrand at 300K
#T=300
#plot(nu,dos*log(2*sinh(0.5*nu/(k_B*T))),label=idx)
# Zero-point energy - $\hbar\omega/2$ for each degree of freedom integrated over $\omega$
F0=ndf*simps(0.5*dos*nu,nu)
# Put in special case for the T=0. Just ZPV energy.
qhav=[[V,0,Etot,F0,0,0,0,0]]
qha.append(qhav)
print '# %s: V=%.2f A^3, Etot=%.3f eV, P=%6.1f GPa' % (n, V, Etot, P/GPa)
for T in linspace(Tmin,Tmax,Tsteps):
# Maradudin book formula - the only one important for thermal expansion
# The result is in eV, temperature in K
e=0.5*nu/(k_B*T)
Fph=ndf*T*k_B*simps(dos*log(2*sinh(e)),nu)
Cv=ndf*k_B*simps(e*e*dos/sinh(e)**2,nu)
S=k_B*(simps(2*dos*e/(exp(2*e)-1),nu)-simps(dos*(1-exp(-2*e)),nu))
# Alternative formula from QE
Sqe=k_B*simps(dos*(e/tanh(e)-log(2*sinh(e))),nu)
# Formulas lifted from the QHA code in QE - not correct with current units
#q=0.5*a3*nu/T
#E_int=simps(a1*dos*nu/tanh(q),nu)
#S0=simps(dos*(q/tanh(q)-log(2*sinh(q))),nu)
qhav.append([V, T, Etot, Fph, P*V, Cv, S, Sqe])
#print " %5.2f %12f %12f %12f" % (T, Cv, S, Sqe)
return array(qha)
def get_periodic_symmetry_operations(atoms, error_tolerance=0.01, debug=False):
from ase.utils import irotate
from ase.visualize import view
from pyspglib import spglib
#symmetry = spglib.get_symmetry(atoms, symprec=1e-5)
symmetry = spglib.get_symmetry(atoms, symprec=1e-2)
dataset = spglib.get_symmetry_dataset(atoms, symprec=1e-2)
result = []
if debug:
cell, scaled_positions, numbers = spglib.find_primitive(atoms,
symprec=1e-5)
a = Atoms(symbols='O4',
cell=cell,
scaled_positions=scaled_positions,
pbc=True)
#symmetry = spglib.get_symmetry(a, symprec=1e-2)
#dataset = spglib.get_symmetry_dataset(a, symprec=1e-2)
print dataset['equivalent_atoms']
print dataset['international']
print dataset['hall']
print dataset['wyckoffs']
print dataset['transformation_matrix']
print "Number of symmetry operations %i" % len(dataset['rotations'])
for i in range(dataset['rotations'].shape[0]):
new_atoms = atoms.copy()
test = atoms.copy()
rot = dataset['rotations'][i]
trans = dataset['translations'][i]
if debug:
x, y, z = irotate(rot)
#print x, y, z
print "------------------- %i -----------------------" % i
print "Rotation"
print rot
print "Translation"
print trans
new_pos = new_atoms.get_scaled_positions()
for l, pos in enumerate(new_atoms.get_scaled_positions()):
#print new_pos[l]
new_pos[l] = (numpy.dot(rot, pos))
new_pos[l] += trans
#print new_pos[l]
new_atoms.set_scaled_positions(new_pos)
equals = get_equals_periodic(atoms,
new_atoms,
error_tolerance=error_tolerance,
debug=debug)
if equals != None:
so = SymmetryOperation(str(i),
equals,
None,
vector=None,
magnitude=1,
rotation_matrix=rot,
translation_vector=trans)
#if debug:
# print so
result.append(so)
else:
print "Equivalent not found"
#view(test)
#view(new_atoms)
#raw_input()
return result
def write_cell_params(fh, a, p):
'''
Write the specification of the cell using a traditional A,B,C,
alpha, beta, gamma scheme. The symmetry and parameters are determined
from the atoms (a) object. The atoms object is translated into a
primitive unit cell but *not* converted. This is just an internal procedure.
If you wish to work with primitive unit cells in ASE, you need to make
a conversion yourself. The cell params are in angstrom.
Input
-----
fh file handle of the opened pw.in file
a atoms object
p parameters dictionary
Output
------
Primitive cell tuple of arrays: (lattice, atoms, atomic numbers)
'''
assert(p['use_symmetry'])
# Get a spacegroup name and number for the a
sg,sgn=spglib.get_spacegroup(a).split()
# Extract the number
sgn=int(sgn[1:-1])
# Extract the lattice type
ltyp=sg[0]
# Find a primitive unit cell for the system
# puc is a tuple of (lattice, atoms, atomic numbers)
puc=spglib.find_primitive(a)
cell=puc[0]
apos=puc[1]
anum=puc[2]
icell=a.get_cell()
A=norm(icell[0])
B=norm(icell[1])
C=norm(icell[2])
# Select appropriate ibrav
if sgn >= 195 :
# Cubic lattice
if ltyp=='P':
p['ibrav']=1 # Primitive
qepc=array([[1,0,0],[0,1,0],[0,0,1]])
elif ltyp=='F':
p['ibrav']=2 # FCC
qepc=array([[-1,0,1],[0,1,1],[-1,1,0]])/2.0
elif ltyp=='I':
p['ibrav']=3 # BCC
qepc=array([[1,1,1],[-1,1,1],[-1,-1,1]])/2.0
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
#a=sqrt(2)*norm(cell[0])
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
elif sgn >= 143 :
# Hexagonal and trigonal
if ltyp=='P' :
p['ibrav']=4 # Primitive
qepc=array([[1,0,0],[-1/2,sqrt(3)/2,0],[0,0,C/A]])
elif ltyp=='R' :
p['ibrav']=5 # Trigonal rhombohedral
raise NotImplementedError
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
fh.write(' C = %f,\n' % (C,))
elif sgn >= 75 :
raise NotImplementedError
elif sgn ==1 :
# P1 symmetry - no special primitive cell signal to the caller
p['ibrav']=0
return None
else :
raise NotImplementedError
cp=Atoms(cell=puc[0], scaled_positions=puc[1], numbers=puc[2], pbc=True)
qepc=Atoms(cell=qepc,
positions=cp.get_positions(),
numbers=cp.get_atomic_numbers(), pbc=True)
return qepc.get_cell(), qepc.get_scaled_positions(), qepc.get_atomic_numbers()
def analyze_QHA_run(Calc, Tmin=1, Tmax=1500, Tsteps=100):
'''
Run the QHA analysis procedure on the set of volume calculation Calc.
This procedure produces an array with thermodynamic functions for
all calculated volumes and given temperature range (the zero temperature is always included).
Input
=====
Calc - List of calculation data
Tmin - Minimum temperature of the scan (K)
Tmax - Maximum temperature of the scan (K)
Tsteps - Number of temperature steps
bdir - base directory (subdirectories host and calculation are located below)
Output
======
qha - array of N x Tsteps x #params containing resulting data:
V, T, Etot, Fph, P*V, Cv, S, ...
for each calculation and each temperature step.
'''
phdos = {}
qha = []
for n, c in enumerate(Calc):
PCMUL = len(c.get_atomic_numbers()) / len(spglib.find_primitive(c)[2])
# Read the calculated dos
clc = c.calc.results
phdos[n] = clc['phdos']
#Etot=c.get_potential_energy()
Etot = clc['etotal'] * Rydberg
# Pressure returned in kbar we need to change it to eV/A^3 to get p*V in eV
# eV/A^3=160.2176487GPa
# kbar=0.1 GPa
# eV/A^3 = 1602.176487 kbar
P = clc['pressure'] / 1602.176487
#P=c.get_isotropic_pressure(c.get_stress())
# Scan the temperatures at this volume
# Unit cell (primitive) volume in Bohr^3 => (A^3)
#V=(calcQHA[idx][2]['A'])**3
#V=clc['volume']*(Bohr**3)
V = c.get_volume() / PCMUL
# get the ndf from the normalization of dos
dos = phdos[n]
ndf = round(simps(dos[1], dos[0]))
# frequencies/energies
# QE outputs dos in cm^-1, let's convert to sane units
# Let's convert to energy to include the hbar
nu = 1e-3 * cminv2meV * phdos[n][0]
dos = phdos[n][1]
# We need to cut the nu to positive range
no = array([[o, g] for o, g in zip(nu, dos) if o > 0])
nu = no[:, 0]
dos = no[:, 1]
# correct the normalization for units, negative cut and numerical errors
dos = dos / simps(dos, nu)
# plot in meV
#plot(1e-3*nu,dos,label=n);
#legend()
#show()
# plot the integrand at 300K
#T=300
#plot(nu,dos*log(2*sinh(0.5*nu/(k_B*T))),label=idx)
# Zero-point energy - $\hbar\omega/2$ for each degree of freedom integrated over $\omega$
F0 = ndf * simps(0.5 * dos * nu, nu)
# Put in special case for the T=0. Just ZPV energy.
qhav = [[V, 0, Etot, F0, 0, 0, 0, 0]]
qha.append(qhav)
print '# %s: V=%.2f A^3, Etot=%.3f eV, P=%6.1f GPa' % (n, V, Etot,
P / GPa)
for T in linspace(Tmin, Tmax, Tsteps):
# Maradudin book formula - the only one important for thermal expansion
# The result is in eV, temperature in K
e = 0.5 * nu / (k_B * T)
Fph = ndf * T * k_B * simps(dos * log(2 * sinh(e)), nu)
Cv = ndf * k_B * simps(e * e * dos / sinh(e)**2, nu)
S = k_B * (simps(2 * dos * e / (exp(2 * e) - 1), nu) -
simps(dos * (1 - exp(-2 * e)), nu))
# Alternative formula from QE
Sqe = k_B * simps(dos * (e / tanh(e) - log(2 * sinh(e))), nu)
# Formulas lifted from the QHA code in QE - not correct with current units
#q=0.5*a3*nu/T
#E_int=simps(a1*dos*nu/tanh(q),nu)
#S0=simps(dos*(q/tanh(q)-log(2*sinh(q))),nu)
qhav.append([V, T, Etot, Fph, P * V, Cv, S, Sqe])
#print " %5.2f %12f %12f %12f" % (T, Cv, S, Sqe)
return array(qha)
