def get_normalmodes(self, coords):
"""return the squared normal mode frequencies and eigenvectors
Notes
-----
This is usually used to compute the log product of the normal mode frequencies
which is used to determine the free energy of a minimum in the harmonic
superposition approximation.
Returns
-------
freqs : array
array of normal mode frequencies
vecs : 2d array
array of normal mode vectors. `vecs[:,i]` is the vector for
the the i'th frequency
See Also
--------
pele.thermodynamics, get_log_product_normalmode_freq, get_metric_tensor
"""
mt = self.get_metric_tensor(coords)
pot = self.get_potential()
hess = pot.getHessian(coords)
freqs, vecs = normalmodes(hess, mt)
return freqs, vecs
def get_normalmodes(self, coords):
"""return the squared normal mode frequencies and eigenvectors
Notes
-----
This is usually used to compute the log product of the normal mode frequencies
which is used to determine the free energy of a minimum in the harmonic
superposition approximation.
Returns
-------
freqs : array
array of normal mode frequencies
vecs : 2d array
array of normal mode vectors. `vecs[:,i]` is the vector for
the the i'th frequency
See Also
--------
pele.thermodynamics, get_log_product_normalmode_freq, get_metric_tensor
"""
mt = self.get_metric_tensor(coords)
pot = self.get_potential()
hess = pot.getHessian(coords)
freqs, vecs = normalmodes(hess, mt)
return freqs, vecs
def get_normalmodes(self, coords):
"""return the squared normal mode frequencies and eigenvectors
"""
mt = self.get_metric_tensor(coords)
pot = self.get_potential()
hess = pot.getHessian(coords)
freqs, vecs = normalmodes(hess, mt)
return freqs, vecs
def test_eigs():
from pele.transition_states import findLowestEigenVector
from pele.thermodynamics import normalmodes
system = HeisenbergSystem(field_disorder=3.1, disorder=True)
pot = system.get_potential()
x = system.get_random_configuration()
x = system.get_random_minimized_configuration().coords
ret = findLowestEigenVector(x, pot, orthogZeroEigs=None)
hess = pot.getHessian(x)
freq, modes = normalmodes(hess, metric=None)
print("lowest eig from hess", freq[0])
print("lowest eig from RR ", ret.eigenval)
def test_eigs():
from pele.transition_states import findLowestEigenVector
from pele.thermodynamics import normalmodes
system = HeisenbergSystem(field_disorder=3.1, disorder=True)
pot = system.get_potential()
x = system.get_random_configuration()
x = system.get_random_minimized_configuration().coords
ret = findLowestEigenVector(x, pot, orthogZeroEigs=None)
hess = pot.getHessian(x)
freq, modes = normalmodes(hess, metric=None)
print "lowest eig from hess", freq[0]
print "lowest eig from RR ", ret.eigenval
def _calculate_normalmodes(self):
"""
compute the normal modes
"""
if self._use_hessian_eigs():
pot = self.system.get_potential()
hess = pot.getHessian(self.coords)
freq, mode = normalmodes(hess, metric=None)
else:
freq, mode = self.system.get_normalmodes(self.coords)
mode=np.real(mode.transpose())
self.normalmodes = []
#self.normalmodes.append((fre[0], m.flatten()))
for f, m in zip(freq, mode):
self.normalmodes.append((f, m)) #np.dot(metric, m)))
