def __init__(self, atoms, outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length() #*angstroms2bohr
b = B.length() #*angstroms2bohr
c = C.length() #*angstroms2bohr
# angles between the vectors
rad2deg = 360. / (2. * math.pi)
alpha = B.angle(C) * rad2deg
beta = A.angle(C) * rad2deg
gamma = A.angle(B) * rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += 'title \n'
input += '0 tolerance\n'
input += '2 lattice parameters in lengths and angles\n'
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a, b, c, alpha,
beta, gamma)
input += '1 3 basis vectors for unit cell\n'
input += '1.00 0.00 0.00\n'
input += '0.00 1.00 0.00\n'
input += '0.00 0.00 1.00\n'
input += '%i number of atoms\n' % len(atoms)
types = ''
for atom in atoms:
types += str(atom.get_atomic_number()) + ' '
input += types + '\n'
for i, atom in enumerate(atoms):
input += '%1.3f %1.3f %1.3f\n' % tuple(scaledpositions[i])
pin, pout = os.popen2('findsym')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile, 'w')
f.writelines(self.output)
f.close()
if os.path.exists('findsym.log'):
os.remove('findsym.log')
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += 'title \n'
input += '0 tolerance\n'
input += '2 lattice parameters in lengths and angles\n'
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 3 basis vectors for unit cell\n'
input += '1.00 0.00 0.00\n'
input += '0.00 1.00 0.00\n'
input += '0.00 0.00 1.00\n'
input += '%i number of atoms\n' % len(atoms)
types = ''
for atom in atoms:
types += str(atom.get_atomic_number()) + ' '
input += types + '\n'
for i,atom in enumerate(atoms):
input += '%1.3f %1.3f %1.3f\n' % tuple(scaledpositions[i])
pin,pout = os.popen2('findsym')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('findsym.log'):
os.remove('findsym.log')
def __init__(self, atoms, outfile=None):
'''outfile is where the results will be stored if you want
them. Otherwise they go into a tempfile that is deleted.'''
id, infile = tempfile.mkstemp()
if outfile is None:
od, ofile = tempfile.mkstemp()
else:
ofile = outfile
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length() #*angstroms2bohr
b = B.length() #*angstroms2bohr
c = C.length() #*angstroms2bohr
# angles between the vectors
rad2deg = 360. / (2. * math.pi)
alpha = B.angle(C) * rad2deg
beta = A.angle(C) * rad2deg
gamma = A.angle(B) * rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
f = open(infile, 'w')
f.write('P\n')
f.write('%1.4f %1.4f %1.4f %1.4f %1.4f %1.4f\n' %
(a, b, c, alpha, beta, gamma))
f.write('%i\n' % len(atoms))
for i, atom in enumerate(atoms):
f.write('%1.4f %1.4f %1.4f\n' % tuple(scaledpositions[i]))
f.write('%s\n\n' % chemicalsymbols[i])
f.close()
os.system('sgroup %s %s' % (infile, ofile))
f = open(ofile, 'r')
self.output = f.readlines()
f.close()
os.unlink(infile)
os.close(id)
if outfile is None:
os.unlink(ofile)
os.close(od) # you must close the file descriptor or
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 1 0.1 0.1\n'
for atom in atoms:
sym = atom.get_symbol()
group = 1
x,y,z = atom.get_position()
#format(a6,i2,6f9.5)
input += str(FortranLine((sym,
group,
x,y,z),
FortranFormat('a6,i2,3f9.5')))+'\n'
pin,pout = os.popen2('symmol')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('symmol.log'):
os.remove('symmol.log')
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
# scaledpositions = atoms.get_scaled_positions()
# chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 1 0.1 0.1\n'
for atom in atoms:
sym = atom.get_symbol()
group = 1
x,y,z = atom.get_position()
#format(a6,i2,6f9.5)
input += str(FortranLine((sym,
group,
x,y,z),
FortranFormat('a6,i2,3f9.5')))+'\n'
pin,pout = os.popen2('symmol')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('symmol.log'):
os.remove('symmol.log')
def _explicit_qvectors(self, qMin, qMax, indRange):
qVects = []
hkls = []
dimen = len(self.qDirections)
for ind in indRange:
qVect = Vector()
for i in range(dimen):
qVect += ind[i] * self.qDirections[i]
if qMin < qVect.length() <= qMax:
if not qVect in qVects:
qVects.append(qVect)
hkl = Vector([0, 0, 0])
for i in range(dimen):
hkl += ind[i] * self.hkl_dir[i]
hkls.append(hkl)
if len(qVects) >= self.qVectorsPerShell:
break
LogMessage(
'info', '%d explicit Q vectors generated for shell [%s,%s].' %
(len(qVects), qMin, qMax), ['file', 'console'])
return qVects, hkls
def __init__(self, *parameters):
"""
:param parameters: one of
1) three lattice vectors or
2) six numbers: the lengths of the three lattice
vectors (a, b, c) followed by the three
angles (alpha, beta, gamma).
"""
if len(parameters) == 6:
self.a, self.b, self.c, self.alpha, self.beta, self.gamma = \
parameters
e1 = Vector(self.a, 0, 0)
e2 = self.b * Vector(N.cos(self.gamma), N.sin(self.gamma), 0.)
e3_x = N.cos(self.beta)
e3_y = (N.cos(self.alpha)-N.cos(self.beta)*N.cos(self.gamma)) \
/ N.sin(self.gamma)
e3_z = N.sqrt(1. - e3_x**2 - e3_y**2)
e3 = self.c * Vector(e3_x, e3_y, e3_z)
self.basis = (e1, e2, e3)
elif len(parameters) == 3:
assert isVector(parameters[0])
assert isVector(parameters[1])
assert isVector(parameters[2])
self.basis = list(parameters)
e1, e2, e3 = self.basis
self.a = e1.length()
self.b = e2.length()
self.c = e3.length()
self.alpha = N.arccos(e2 * e3 / (self.b * self.c))
self.beta = N.arccos(e1 * e3 / (self.a * self.c))
self.gamma = N.arccos(e1 * e2 / (self.a * self.b))
else:
raise ValueError("Parameter list incorrect")
r = LA.inverse(N.transpose([e1, e2, e3]))
self.reciprocal_basis = [Vector(r[0]), Vector(r[1]), Vector(r[2])]
import numpy as np from Scientific.Geometry import Vector A = Vector([1,1,1]) #Scientfic a = np.array([1,1,1]) #numpy B = Vector([0.0,1.0,0.0]) print '|A| = ',A.length() #Scientific Python way print '|a| = ',np.sum(a**2)**0.5 #numpy way print '|a| = ',np.linalg.norm(a) #numpy way 2 print 'ScientificPython angle = ',A.angle(B) #in radians print 'numpy angle = ',np.arccos(np.dot(a/np.linalg.norm(a),B/np.linalg.norm(B))) #cross products print 'Scientific A .cross. B = ',A.cross(B) print 'numpy A .cross. B = ',np.cross(A,B) #you can use Vectors in numpy
def pretty_print(self):
'''
__str__ function to print the calculator with a nice summary, e.g. jaspsum
'''
# special case for neb calculations
if self.int_params['images'] is not None:
# we have an neb.
s = []
s.append(': -----------------------------')
s.append(' VASP NEB calculation from %s' % os.getcwd())
try:
images, energies = self.get_neb()
for i,e in enumerate(energies):
s += ['image {0}: {1: 1.3f}'.format(i,e)]
except (VaspQueued):
s += ['Job is in queue']
return '\n'.join(s)
s = []
s.append(': -----------------------------')
s.append(' VASP calculation from %s' % os.getcwd())
if hasattr(self,'converged'):
s.append(' converged: %s' % self.converged)
try:
atoms = self.get_atoms()
uc = atoms.get_cell()
try:
self.converged = self.read_convergence()
except IOError:
# eg no outcar
self.converged = False
if not self.converged:
try:
print self.read_relaxed()
except IOError:
print False
if self.converged:
energy = atoms.get_potential_energy()
forces = atoms.get_forces()
else:
energy = np.nan
forces = [np.array([np.nan, np.nan, np.nan]) for atom in atoms]
if self.converged:
if hasattr(self,'stress'):
stress = self.stress
else:
stress = None
else:
stress = None
# get a,b,c,alpha,beta, gamma
from Scientific.Geometry import Vector
A = Vector(uc[0,:])
B = Vector(uc[1,:])
C = Vector(uc[2,:])
a = A.length()
b = B.length()
c = C.length()
alpha = B.angle(C)*180/np.pi
beta = A.angle(C)*180/np.pi
gamma = B.angle(C)*180/np.pi
volume = atoms.get_volume()
s.append(' Energy = %f eV' % energy)
s.append('\n Unit cell vectors (angstroms)')
s.append(' x y z length')
s.append(' a0 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[0][0],
uc[0][1],
uc[0][2],
A.length()))
s.append(' a1 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[1][0],
uc[1][1],
uc[1][2],
B.length()))
s.append(' a2 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[2][0],
uc[2][1],
uc[2][2],
C.length()))
s.append(' a,b,c,alpha,beta,gamma (deg): %1.3f %1.3f %1.3f %1.1f %1.1f %1.1f' % (a,
b,
c,
alpha,
beta,gamma))
s.append(' Unit cell volume = {0:1.3f} Ang^3'.format(volume))
if stress is not None:
s.append(' Stress (GPa):xx, yy, zz, yz, xz, xy')
s.append(' % 1.3f % 1.3f % 1.3f % 1.3f % 1.3f % 1.3f' % tuple(stress))
else:
s += [' Stress was not computed']
constraints = None
if hasattr(atoms, 'constraints'):
from ase.constraints import FixAtoms, FixScaled
constraints = [[None, None, None] for atom in atoms]
for constraint in atoms.constraints:
if isinstance(constraint, FixAtoms):
for i, constrained in enumerate(constraint.index):
if constrained:
constraints[i] = [True, True, True]
if isinstance(constraint, FixScaled):
constraints[constraint.a] = constraint.mask.tolist()
if constraints is None:
s.append(' Atom# sym position [x,y,z] tag rmsForce')
else:
s.append(' Atom# sym position [x,y,z] tag rmsForce constraints')
for i,atom in enumerate(atoms):
rms_f = np.sum(forces[i]**2)**0.5
ts = ' {0:^4d} {1:^4s} [{2:<9.3f}{3:^9.3f}{4:9.3f}] {5:^6d}{6:1.2f}'.format(i,
atom.symbol,
atom.x,
atom.y,
atom.z,
atom.tag,
rms_f)
# VASP has the opposite convention of constrained
# Think: F = frozen
if constraints is not None:
ts += ' {0} {1} {2}'.format('F' if constraints[i][0] is True else 'T',
'F' if constraints[i][1] is True else 'T',
'F' if constraints[i][2] is True else 'T')
s.append(ts)
s.append('--------------------------------------------------')
if self.get_spin_polarized() and self.converged:
s.append('Spin polarized: Magnetic moment = %1.2f' % self.get_magnetic_moment(atoms))
except AttributeError:
# no atoms
pass
if os.path.exists('INCAR'):
# print all parameters that are set
self.read_incar()
ppp_list = self.get_pseudopotentials()
else:
ppp_list=[(None, None, None)]
s += ['\nINCAR Parameters:']
s += ['-----------------']
for d in [self.int_params,
self.float_params,
self.exp_params,
self.bool_params,
self.list_params,
self.dict_params,
self.string_params,
self.special_params,
self.input_params]:
for key in d:
if key is 'magmom':
np.set_printoptions(precision=3)
value = textwrap.fill(str(d[key]),
width=56,
subsequent_indent=' '*17)
s.append(' %12s: %s' % (key, value))
elif d[key] is not None:
value = textwrap.fill(str(d[key]),
width=56,
subsequent_indent=' '*17)
s.append(' %12s: %s' % (key, value))
s += ['\nPseudopotentials used:']
s += ['----------------------']
for sym,ppp,hash in ppp_list:
s += ['{0}: {1} (git-hash: {2})'.format(sym,ppp,hash)]
# if ibrion in [5,6,7,8] print frequencies
if self.int_params['ibrion'] in [5,6,7,8]:
freq,modes = self.get_vibrational_modes()
s += ['\nVibrational frequencies']
s += ['mode frequency']
s += ['------------------']
for i,f in enumerate(freq):
if isinstance(f, float):
s += ['{0:4d}{1: 10.3f} eV'.format(i,f)]
elif isinstance(f, complex):
s += ['{0:4d}{1: 10.3f} eV'.format(i,-f.real)]
return '\n'.join(s)
x, V0, e0, B = analyze_eos()
except TypeError:
x, V0, e0, B = None, None, None, None
magmom = atoms.get_magnetic_moment()
# now we want to write out a row of
data = [id1, composition, spacegroup, natoms, formation_energy, B, magmom]
for i, d in enumerate(data):
sh0.write(NROWS0, i, d)
# now for sheet 1 - unit cell parameters
uc = atoms.get_cell()
A = Vector(uc[0, :])
B = Vector(uc[1, :])
C = Vector(uc[2, :])
a = A.length()
b = B.length()
c = C.length()
alpha = B.angle(C) * 180.0 / np.pi
beta = A.angle(C) * 180.0 / np.pi
gamma = B.angle(C) * 180.0 / np.pi
volume = atoms.get_volume()
stress = atoms.get_stress()
if stress is not None:
sxx, syy, szz, sxy, syz, sxz = stress
else:
sxx, syy, szz, sxy, syz, sxz = [None, None, None, None, None, None]
data = [id1, a, b, c, alpha, beta, gamma, volume, sxx, syy, szz, sxy, syz, sxz]
for i, d in enumerate(data):
magmom = atoms.get_magnetic_moment()
# now we want to write out a row of
data = [
id1, composition, spacegroup, natoms, formation_energy, B,
magmom
]
for i, d in enumerate(data):
sh0.write(NROWS0, i, d)
# now for sheet 1 - unit cell parameters
uc = atoms.get_cell()
A = Vector(uc[0, :])
B = Vector(uc[1, :])
C = Vector(uc[2, :])
a = A.length()
b = B.length()
c = C.length()
alpha = B.angle(C) * 180. / np.pi
beta = A.angle(C) * 180. / np.pi
gamma = B.angle(C) * 180. / np.pi
volume = atoms.get_volume()
stress = atoms.get_stress()
if stress is not None:
sxx, syy, szz, sxy, syz, sxz = stress
else:
sxx, syy, szz, sxy, syz, sxz = [
None, None, None, None, None, None
]
# http://books.google.com/books?id=nJHSqEseuIUC&lpg=PA118&ots=YA9TBldoVH
# &dq=reciprocal%20metric%20tensor&pg=PA119#v=onepage
# &q=reciprocal%20metric%20tensor&f=false
'''Finally, many text books on crystallography use long algebraic
formulas for computing the d-spacing with sin and cos, vector lengths,
and angles. Below we compute these and use them in the general
triclinic structure formula which applies to all the structures.
'''
from Scientific.Geometry import Vector
import math
unitcell = ag.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors in radians
alpha = B.angle(C)
beta = A.angle(C)
gamma = A.angle(B)
print('')
print('a b c alpha beta gamma')
print('{0:1.3f} {1:1.3f} {2:1.3f} {3:1.3f} {4:1.3f} {5:1.3f}\n'.format(a,b,c, alpha,beta,gamma))
h, k, l = (1, 1, 1)
from math import sin, cos
id2 = ((h**2 / a**2 * sin(alpha)**2
+ k**2 / b**2 * sin(beta)**2
+ l**2 / c**2 * sin(gamma)**2
+ 2 * k * l / b / c * (cos(beta) * cos(gamma) - cos(alpha))
# http://books.google.com/books?id=nJHSqEseuIUC&lpg=PA118&ots=YA9TBldoVH
# &dq=reciprocal%20metric%20tensor&pg=PA119#v=onepage
# &q=reciprocal%20metric%20tensor&f=false
'''Finally, many text books on crystallography use long algebraic
formulas for computing the d-spacing with sin and cos, vector lengths,
and angles. Below we compute these and use them in the general
triclinic structure formula which applies to all the structures.
'''
from Scientific.Geometry import Vector
import math
unitcell = ag.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length() #*angstroms2bohr
b = B.length() #*angstroms2bohr
c = C.length() #*angstroms2bohr
# angles between the vectors in radians
alpha = B.angle(C)
beta = A.angle(C)
gamma = A.angle(B)
print
print 'a b c alpha beta gamma'
print '{0:1.3f} {1:1.3f} {2:1.3f} {3:1.3f} {4:1.3f} {5:1.3f}\n'.format(
a, b, c, alpha, beta, gamma)
h, k, l = (1, 1, 1)
from math import sin, cos
id2 = ((h**2 / a**2 * sin(alpha)**2 + k**2 / b**2 * sin(beta)**2 +
l**2 / c**2 * sin(gamma)**2 + 2 * k * l / b / c *
(cos(beta) * cos(gamma) - cos(alpha)) + 2 * h * l / a / c *
