def mouseReleaseEvent(self, event):
button = event.button()
self.setCursor(Qt.arrowCursor)
if button == Qt.LeftButton:
try:
dx = event.x() - self.click1x
dy = event.y() - self.click1y
except AttributeError:
return
if dx != 0 or dy != 0:
normal = Vector(self.axis)
move = Vector(-dx*self.plane[:,0]+dy*self.plane[:,1])
axis = normal.cross(move) / \
N.minimum.reduce(N.fabs(self.plotbox_size))
rot = Rotation(axis.normal(), axis.length())
self.axis = rot(normal).array
self.plane[:,0] = rot(Vector(self.plane[:,0])).array
self.plane[:,1] = rot(Vector(self.plane[:,1])).array
elif button == Qt.MidButton:
try:
dx = event.x() - self.click2x
dy = event.y() - self.click2y
except AttributeError:
return
if dx != 0 or dy != 0:
self.translate = self.translate + N.array([dx, dy])
else:
try:
dy = event.y() - self.click3y
except AttributeError:
return
if dy != 0:
ratio = -dy/self.plotbox_size[1]
self.scale = self.scale * (1.+ratio)
self.update()
def releasehandler1(self, event):
self.configure(cursor='top_left_arrow')
self.update_idletasks()
try:
dx = event.x - self.click1x
dy = event.y - self.click1y
except AttributeError:
return
if dx != 0 or dy != 0:
normal = Vector(self.axis)
move = Vector(-dx*self.plane[:,0]+dy*self.plane[:,1])
axis = normal.cross(move) / \
Numeric.minimum.reduce(Numeric.fabs(self.plotbox_size))
rot = Rotation(axis.normal(), axis.length())
self.axis = rot(normal).array
self.plane[:,0] = rot(Vector(self.plane[:,0])).array
self.plane[:,1] = rot(Vector(self.plane[:,1])).array
self.clear(1)
self.redraw()
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 calc(self, atomIndexes, trajectory):
"""Calculates the contribution for one group.
@param bondIndex: the index of the group in |self.group| list.
@type bondIndex: integer.
@param trajectory: the trajectory.
@type trajectory: MMTK.Trajectory.Trajectory object
"""
atoms = [None] * 2
for at in trajectory.universe.atomList():
if at.index in atomIndexes:
atoms[atomIndexes.index(at.index)] = at
# The atoms forming the bond.
at1, at2 = atoms
at1Traj = trajectory.readParticleTrajectory(at1,
first=self.first,
last=self.last,
skip=self.skip)
at2Traj = trajectory.readParticleTrajectory(at2,
first=self.first,
last=self.last,
skip=self.skip)
costheta = N.zeros((self.nFrames, ), typecode=N.Float)
sinphi = N.zeros((self.nFrames, ), typecode=N.Float)
cosphi = N.zeros((self.nFrames, ), typecode=N.Float)
sintheta = N.zeros((self.nFrames, ), typecode=N.Float)
for comp in range(self.nFrames):
pVect = Vector(
trajectory.universe.distanceVector(at1Traj[comp],
at2Traj[comp]))
pVect = pVect.normal()
costheta[comp] = pVect * self.referenceDirection
sintheta[comp] = pVect.cross(self.referenceDirection).length()
cosphi[comp] = (pVect[0] / sintheta[comp])
sinphi[comp] = (pVect[1] / sintheta[comp])
tr2 = 3.0 * costheta**2 - 1.
cos2phi = 2.0 * cosphi**2 - 1.
sin2phi = 2.0 * sinphi * cosphi
cossintheta = costheta * sintheta
sintheta_sq = sintheta**2
# calcul de <P2(cos(theta))> en termes de somme de fonctions de correlation
# d'harmoniques spheriques (theoreme d'addition des harmoniques spheriques).
P2 = (0.25*correlation(tr2) + 3.00*correlation(cosphi*cossintheta) + \
3.00*correlation(sinphi*cossintheta) + 0.75*correlation(cos2phi*sintheta_sq) + \
0.75*correlation(sin2phi*sintheta_sq))
# calcul du parametre d'ordre S^2 (limite pour t->infini de <P2(cos(theta))>).
S2 = (0.75 * (N.sum(cos2phi*sintheta_sq)**2 + N.sum(sin2phi*sintheta_sq)**2) + \
3.00 * (N.sum(cosphi*cossintheta)**2 + N.sum(sinphi*cossintheta)**2) +
0.25 * N.sum(tr2)**2) / self.nFrames**2
return atomIndexes, (P2, S2)
