def addBond(self, Atom1, Atom2, jMatrix = None):
"""Adds a bond and all symmettry equivalent bonds within the magnetic Cell
Performs every symmetry operation and every possible translation for each
symmetry operation to find all possible bonds"""
#Create Symmetry Bonds
xyz = Atom1.getPosition()
xyz2 = Atom2.getPosition()
for symop in self.space_Group.iter_symops():
# operate on coordinates in non-shifted spacegroup
pos1 = symop(xyz)
pos2 = symop(xyz2)
#Recording symops that map bond back to itself (for symmetry constraints)
if xyz[0] == pos1[0] and xyz2[0] == pos2[0]: #x component
if xyz[1] == pos1[1] and xyz2[1] == pos2[1]: #y component
if xyz[2] == pos1[2] and xyz2[2] == pos2[2]: #z component
self.bondConstraints.append(BondConstraint(xyz, xyz2, symop))
mask1 = numpy.logical_or(pos1 < 0.0, pos1 >= 1.0)
translation = numpy.floor(pos1[mask1]) #translates the first atom back to cell at (0,0,0)
pos1[mask1] -= translation
pos2[mask1] -= translation #Uses same translation to translate other atom
#translate new Bond to all cells
#Find the number of times to translate the bond in each direction so
#that it will will cover the whole magnetic cell but not go outside
if pos1[0]>pos2[0]:
Xiter = self.Na - pos1[0]
else:
Xiter = self.Na - pos2[0]
if pos1[1] > pos2[1]:
Yiter = self.Nb - pos1[1]
else:
Yiter = self.Nb - pos2[1]
if pos1[2] > pos2[2]:
Ziter = self.Nc - pos1[2]
else:
Ziter = self.Nc - pos2[2]
Xiter = int(Xiter) + 1
Yiter = int(Yiter) + 1
Ziter = int(Ziter) + 1
#iterate through each possible translation and check if there are atoms there that could
#be bonded; if so, add the bond
for i in range(0, Xiter): #translate in x direction (Na - Cell X position) times
for j in range(0, Yiter): #translate in y direction (Nb - Cell Y position) times
for k in range(0, Ziter): #translate in z direction (Nc - Cell Z position) times
translatedAtom1 = self.atomAtPosition((i + pos1[0],j + pos1[1],k + pos1[2]))
translatedAtom2 = self.atomAtPosition((i + pos2[0],j + pos2[1],k + pos2[2]))
if translatedAtom1 != None and translatedAtom2 != None:
newBond = Bond(translatedAtom1, translatedAtom2, jMatrix)
#make sure bond does not already exist
for currentBond in self.Bonds:
if newBond.sameBond(currentBond):
break
else: #if not, add the bond to the list of unique bonds
self.Bonds.append(newBond)
def addBond(self, atom1Num = None, atom1CellPos = None, atom2Num = None,
atom2CellPos = None, jMatrix = None, atom1 = None,
atom2 = None):
"""Adds an interaction between two atoms.
atom1Num is the unique number identifying the given atom in the unit cell.
atom1CellPos is a 3 integer tuple with the coordinates of the unit
cell containing atom1.
JMatrix is the 3x3 matrix describing the spin-spin interaction between
the atoms for the heisenberg hamiltonian.
If a bond with the same JMatrix that links the same two atoms already exists
nothing happens. If a bond linking the two atoms exists, but has a different
JMatrix, an Exception is raised.
"""
if atom1 == None:
cell1 = self.cellAtPosition((atom1CellPos[0], atom1CellPos[1], atom1CellPos[2]))
atom1 = cell1.atomWithID(atom1Num)
if atom2 == None:
cell2 = self.cellAtPosition((atom2CellPos[0], atom2CellPos[1], atom2CellPos[2]))
atom2 = cell2.atomWithID(atom2Num)
existingBond = self.getBond(atom1, atom2)
if existingBond != None:
if (existingBond.getJMatrix() != jMatrix).any():
#An exception will be raised if a different bond already exists
#that links these atoms.
raise Exception("A Bond already exists linking Atom1: " +
atom1.__str__()+" and Atom2: "+atom2.__str__())
else:#The bond exists, but it's the same bond
return
#def addBond(self, Atom1, Atom2, jMatrix = None):
#"""Adds a bond and all symmettry equivalent bonds within the magnetic Cell
#Performs every symmetry operation and every possible translation for each
#symmetry operation to find all possible bonds"""
#Create Symmetry Bonds
xyz = atom1.getPosition()
xyz2 = atom2.getPosition()
for symop in self.space_Group.iter_symops():
# operate on coordinates in non-shifted spacegroup
pos1 = symop(xyz)
pos2 = symop(xyz2)
#Recording symops that map bond back to itself (for symmetry constraints)
if xyz[0] == pos1[0] and xyz2[0] == pos2[0]: #x component
if xyz[1] == pos1[1] and xyz2[1] == pos2[1]: #y component
if xyz[2] == pos1[2] and xyz2[2] == pos2[2]: #z component
self.bondConstraints.append(BondConstraint(xyz, xyz2, symop))
mask1 = numpy.logical_or(pos1 < 0.0, pos1 >= 1.0)
translation = numpy.floor(pos1[mask1]) #translates the first atom back to cell at (0,0,0)
pos1[mask1] -= translation
pos2[mask1] -= translation #Uses same translation to translate other atom
#translate new Bond to all cells
#Find the number of times to translate the bond in each direction so
#that it will will cover the whole magnetic cell but not go outside
if pos1[0]>pos2[0]:
Xiter = self.Na - pos1[0]
else:
Xiter = self.Na - pos2[0]
if pos1[1] > pos2[1]:
Yiter = self.Nb - pos1[1]
else:
Yiter = self.Nb - pos2[1]
if pos1[2] > pos2[2]:
Ziter = self.Nc - pos1[2]
else:
Ziter = self.Nc - pos2[2]
Xiter = int(Xiter) + 1
Yiter = int(Yiter) + 1
Ziter = int(Ziter) + 1
#iterate through each possible translation and check if there are atoms there that could
#be bonded; if so, add the bond
for i in range(0, Xiter): #translate in x direction (Na - Cell X position) times
for j in range(0, Yiter): #translate in y direction (Nb - Cell Y position) times
for k in range(0, Ziter): #translate in z direction (Nc - Cell Z position) times
translatedAtom1 = self.atomAtPosition((i + pos1[0],j + pos1[1],k + pos1[2]))
translatedAtom2 = self.atomAtPosition((i + pos2[0],j + pos2[1],k + pos2[2]))
if translatedAtom1 != None and translatedAtom2 != None:
newBond = Bond(translatedAtom1, translatedAtom2, jMatrix)
#make sure bond does not already exist
for currentBond in self.Bonds:
if newBond.sameBond(currentBond):
break
else: #if not, add the bond to the list of unique bonds
self.Bonds.append(newBond)
def addBond(self,
atom1Num=None,
atom1CellPos=None,
atom2Num=None,
atom2CellPos=None,
jMatrix=None,
atom1=None,
atom2=None):
"""Adds an interaction between two atoms.
atom1Num is the unique number identifying the given atom in the unit cell.
atom1CellPos is a 3 integer tuple with the coordinates of the unit
cell containing atom1.
JMatrix is the 3x3 matrix describing the spin-spin interaction between
the atoms for the heisenberg hamiltonian.
If a bond with the same JMatrix that links the same two atoms already exists
nothing happens. If a bond linking the two atoms exists, but has a different
JMatrix, an Exception is raised.
"""
if atom1 == None:
cell1 = self.cellAtPosition(
(atom1CellPos[0], atom1CellPos[1], atom1CellPos[2]))
atom1 = cell1.atomWithID(atom1Num)
if atom2 == None:
cell2 = self.cellAtPosition(
(atom2CellPos[0], atom2CellPos[1], atom2CellPos[2]))
atom2 = cell2.atomWithID(atom2Num)
existingBond = self.getBond(atom1, atom2)
if existingBond != None:
if (existingBond.getJMatrix() != jMatrix).any():
#An exception will be raised if a different bond already exists
#that links these atoms.
raise Exception("A Bond already exists linking Atom1: " +
atom1.__str__() + " and Atom2: " +
atom2.__str__())
else: #The bond exists, but it's the same bond
return
#def addBond(self, Atom1, Atom2, jMatrix = None):
#"""Adds a bond and all symmettry equivalent bonds within the magnetic Cell
#Performs every symmetry operation and every possible translation for each
#symmetry operation to find all possible bonds"""
#Create Symmetry Bonds
xyz = atom1.getPosition()
xyz2 = atom2.getPosition()
for symop in self.space_Group.iter_symops():
# operate on coordinates in non-shifted spacegroup
pos1 = symop(xyz)
pos2 = symop(xyz2)
#Recording symops that map bond back to itself (for symmetry constraints)
if xyz[0] == pos1[0] and xyz2[0] == pos2[0]: #x component
if xyz[1] == pos1[1] and xyz2[1] == pos2[1]: #y component
if xyz[2] == pos1[2] and xyz2[2] == pos2[2]: #z component
self.bondConstraints.append(
BondConstraint(xyz, xyz2, symop))
mask1 = numpy.logical_or(pos1 < 0.0, pos1 >= 1.0)
translation = numpy.floor(
pos1[mask1]
) #translates the first atom back to cell at (0,0,0)
pos1[mask1] -= translation
pos2[
mask1] -= translation #Uses same translation to translate other atom
#translate new Bond to all cells
#Find the number of times to translate the bond in each direction so
#that it will will cover the whole magnetic cell but not go outside
if pos1[0] > pos2[0]:
Xiter = self.Na - pos1[0]
else:
Xiter = self.Na - pos2[0]
if pos1[1] > pos2[1]:
Yiter = self.Nb - pos1[1]
else:
Yiter = self.Nb - pos2[1]
if pos1[2] > pos2[2]:
Ziter = self.Nc - pos1[2]
else:
Ziter = self.Nc - pos2[2]
Xiter = int(Xiter) + 1
Yiter = int(Yiter) + 1
Ziter = int(Ziter) + 1
#iterate through each possible translation and check if there are atoms there that could
#be bonded; if so, add the bond
for i in range(
0, Xiter
): #translate in x direction (Na - Cell X position) times
for j in range(
0, Yiter
): #translate in y direction (Nb - Cell Y position) times
for k in range(
0, Ziter
): #translate in z direction (Nc - Cell Z position) times
translatedAtom1 = self.atomAtPosition(
(i + pos1[0], j + pos1[1], k + pos1[2]))
translatedAtom2 = self.atomAtPosition(
(i + pos2[0], j + pos2[1], k + pos2[2]))
if translatedAtom1 != None and translatedAtom2 != None:
newBond = Bond(translatedAtom1, translatedAtom2,
jMatrix)
#make sure bond does not already exist
for currentBond in self.Bonds:
if newBond.sameBond(currentBond):
break
else: #if not, add the bond to the list of unique bonds
self.Bonds.append(newBond)