def ball_move(inAtom,atomIndex):
"""takes an atom defined by atomIndex inside of inAtom
and moves it somewhere within the core of the atom randomly.
Atoms will almost always end up inside the sphere which
contains 85% of the atoms, centered at the center of mass."""
# we're going to be changing the position of atomIndex inside inAtom
# we'll take atom of index atomIndex and throw it somewhere inside the core
# make sure that you remove any crazy outliers before you do this
# or else it'll just make a bunch more outliers, which is a poor idea
try:
#get all the distances from the center of mass
inCOM = inAtom.get_center_of_mass()
inDistances = distanceCenter(inAtom)
#figure out the distance from the core to the 85th percentile
#we'll consider "the core" to be the sphere which contains 85% of the atoms
eightyFifthRadius = stats.scoreatpercentile(inDistances,85)
#pick a new distance from center somewhere inside that 85th percentile limit
randomNewRadius = random.normal(eightyFifthRadius/2, eightyFifthRadius/3 )
xFromCenter = random.uniform(0,randomNewRadius)
randomNewRadius = ((randomNewRadius**2) - (xFromCenter**2))**0.5
yFromCenter = random.uniform(0,randomNewRadius)
zFromCenter = ((randomNewRadius**2) - (yFromCenter**2))**0.5
newXPosition = inCOM[0] + plusOrMinus()*xFromCenter
newYPosition = inCOM[1] + plusOrMinus()*yFromCenter
newZPosition = inCOM[2] + plusOrMinus()*zFromCenter
positionArray = inAtom.get_positions()
positionArray[atomIndex] = (newXPosition,newYPosition,newZPosition)
inAtom.set_positions(positionArray)
return inAtom
except IndexError:
print "The index of the atom you wanted to move is too high or too low."
print "Please check your function call of ball_move(a,b)"
print "-Jeff"
def shell_move(inAtom,atomIndex):
# we're going to be changing the position of atomIndex inside inAtom
# make sure that you remove any crazy outliers before you do this
# or else it'll just make a bunch more outliers, which is a poor idea
# make sure atomIndex comes from range(len(inAtom.get_positions())) so we don't get out of bounds
try:
inCOM = inAtom.get_center_of_mass()
inDistances = distanceCenter(inAtom)
ninetyNinthRadius = stats.scoreatpercentile(inDistances,99)
ninetyFifthRadius = stats.scoreatpercentile(inDistances,95)
outerFourRadius = ninetyNinthRadius - ninetyFifthRadius
randomNewRadius = random.normal( (ninetyNinthRadius+ninetyFifthRadius)/2 , (ninetyNinthRadius - ninetyFifthRadius)/2 )
xFromCenter = random.uniform(0,randomNewRadius)
randomNewRadius = ((randomNewRadius**2) - (xFromCenter**2))**0.5
yFromCenter = random.uniform(0,randomNewRadius)
zFromCenter = ((randomNewRadius**2) - (yFromCenter**2))**0.5
newXPosition = inCOM[0] + plusOrMinus()*xFromCenter
newYPosition = inCOM[1] + plusOrMinus()*yFromCenter
newZPosition = inCOM[2] + plusOrMinus()*zFromCenter
positionArray = inAtom.get_positions()
positionArray[atomIndex] = (newXPosition,newYPosition,newZPosition)
inAtom.set_positions(positionArray)
return inAtom
except IndexError:
print "The index of the atom you wanted to move is too high or too low."
print "Please check your function call of shell_move(a,b)"
print "-Jeff"