def setUpRigidBodies(self):
#set up one rigid body
from pele.potentials.rigid_bodies.molecule import Molecule
self.rb = Molecule()
for atomlist in self.permlist:
#make a rigid body from atomlist
for i in atomlist:
self.rb.insert_site( 0, self.XB0[i*3:i*3+3] )
class MinPermDistPotential(potential.potential):
"""
Find the rotation (in angle-axis representation) which maximizes the
permutation independent overlap between two structures.
This potential defines the energy as the overlap, here defined as
E = - sum_i sum_j exp( -|x_Ai - X_Bj|**2 / L**2 )
There are other options for the overlap which are not implemented. For
instance something with a slower decay than exp(-R**2).
"""
def __init__(self, XA, XB, L=0.2, permlist = []):
self.XA0 = np.copy(XA)
self.XB0 = np.copy(XB)
self.XB = np.copy(XB)
self.nsites = len(XA)/3
self.L2 = L*L
self.permlist = permlist
if len(self.permlist) == 0:
self.permlist = [range( self.nsites)]
try:
from overlap import overlap, overlap_gradient
self.overlap = overlap
self.overlap_gradient = overlap_gradient
except ImportError:
#self.overlap = overlap_fast
self.overlap = overlap_fast
self.overlap_gradient = overlap_gradient_slow
print "MinPermDistPotential> Using python energy calculation. Compile overlap.f90 to speed things up (a little)"
self.setUpRigidBodies()
def setUpRigidBodies(self):
#set up one rigid body
from pele.potentials.rigid_bodies.molecule import Molecule
self.rb = Molecule()
for atomlist in self.permlist:
#make a rigid body from atomlist
for i in atomlist:
self.rb.insert_site( 0, self.XB0[i*3:i*3+3] )
def getEnergy_no_rigid_body(self, AA ):
# Rotate XB0 according to angle axis AA
rot_mx = rot.aa2mx( AA )
for j in range(self.nsites):
i = 3*j
self.XB[i:i+3] = np.dot( rot_mx, self.XB0[i:i+3] )
#return distance between XB and XA0
E = 0.
for atomlist in self.permlist:
E -= self.overlap( self.XA0, self.XB, self.L2, atomlist, [self.nsites, len(atomlist)])
#if E < -10.5:
# print E, atomlist, [self.nsites, len(atomlist)], len(self.XA0), len(self.XB)
return E
def getEnergy(self, AA):
# Rotate rigid body according to angle axis AA
self.XB = self.rb.getxyz( aa = AA )
#get energy and gradient for each site
E = 0.
for atomlist in self.permlist:
E -= self.overlap( self.XA0, self.XB, self.L2, atomlist, [self.nsites, len(atomlist)])
return E
def getEnergyGradient(self, AA):
# Rotate XB0 according to angle axis AA
# Rotate rigid body according to angle axis AA
self.XB = self.rb.getxyz( aa = AA )
#get energy and gradient for each site
E = 0.
grad = np.zeros(len(self.XB))
for atomlist in self.permlist:
de, dg = self.overlap_gradient( self.XA0, self.XB, self.L2, atomlist, [self.nsites, len(atomlist)])
E -= de
grad -= dg
#convert site-gradients into angle -axis gradients
#first calculate the rotation matrix and derivatives
comgrad, aagrad = self.rb.getGradients(AA, grad, True)
return E, aagrad
def globalEnergyMin(self):
"""
return the lowest energy theoretically possible. This will happen if XB == XA
"""
E = 0.
for atomlist in self.permlist:
E -= self.overlap( self.XA0, self.XA0, self.L2, atomlist, [self.nsites, len(atomlist)])
return E