def rotateVectorAroundNormal(point, n, angle, turnAroundPoint = [0.0, 0.0, 0.0]): p = matrices.Matrix(4, 1,(point[0],point[1],point[2],1.0)) mul = matrices.Matrix(( [n[0]*n[0] + (n[1]*n[1] + n[2]*n[2])*math.cos(angle), n[0]*n[1]*(1.0-math.cos(angle)) - n[2]*math.sin(angle), n[0]*n[2]*(1.0-math.cos(angle)) + n[1]*math.sin(angle), 0.0], [n[0]*n[1]*(1.0 - math.cos(angle)) + n[2]*math.sin(angle), n[1]*n[1] + (n[0]*n[0] + n[2]*n[2])*math.cos(angle), n[1]*n[2]*(1.0-math.cos(angle)) - n[0]*math.sin(angle), 0.0], [n[0]*n[2]*(1.0 - math.cos(angle)) - n[1]*math.sin(angle), n[1]*n[2]*(1.0 - math.cos(angle)) - n[0]*math.sin(angle), n[2]*n[2] + (n[0]*n[0]+n[1]*n[1])*math.cos(angle), 0.0], [0.0, 0.0, 0.0, 1.0])) res = mul.multiply(p) return res[:3]
def generate_Sx_Sy_Sz_operators(atom_list, Sa_list, Sb_list, Sn_list):
"""Generates Sx, Sy and Sz operators"""
Sx_list = []
Sy_list = []
Sz_list = []
N = len(atom_list)
S = sp.Symbol('S', commutative=True)
for i in range(N):
rotmat = sp.Matrix(atom_list[i].spinRmatrix)
loc_vect = spm.Matrix([Sa_list[i], Sb_list[i], Sn_list[i]])
loc_vect = loc_vect.reshape(3, 1)
glo_vect = rotmat * loc_vect
Sx = sp.powsimp(glo_vect[0].expand())
Sy = sp.powsimp(glo_vect[1].expand())
Sz = sp.powsimp(glo_vect[2].expand())
Sx_list.append(Sx)
Sy_list.append(Sy)
Sz_list.append(Sz)
#Unit vector markers
kapxhat = sp.Symbol('kapxhat', commutative=False) #spm.Matrix([1,0,0])#
kapyhat = sp.Symbol('kapyhat', commutative=False) #spm.Matrix([0,1,0])#
kapzhat = sp.Symbol('kapzhat', commutative=False) #spm.Matrix([0,0,1])#
Sx_list.append(kapxhat)
Sy_list.append(kapyhat)
Sz_list.append(kapzhat)
print "Operators Generated: Sx, Sy, Sz"
return (Sx_list, Sy_list, Sz_list)
def inner_prod(vect1, vect2, ten=spm.Matrix([[1, 0, 0], [0, 1, 0], [0, 0,
1]])):
# For column vectors - make sure vectors match eachother as well as # of rows in tensor
if vect1.shape == vect2.shape == (3, 1) == (ten.lines, 1):
return (vect1.T * ten * vect2)[0]
# For row vectors - make sure vectors match eachother as well as # of cols in tensor
elif vect1.shape == vect2.shape == (1, 3) == (1, ten.cols):
return (vect1 * ten * vect2.T)[0]
# Everything else
else:
return None
def run_cross_section(interactionfile, spinfile):
start = clock()
# Generate Inputs
atom_list, jnums, jmats, N_atoms_uc = readFiles(interactionfile, spinfile)
atom1 = atom(pos=[0.00, 0, 0],
neighbors=[1],
interactions=[0],
int_cell=[0],
atomicNum=26,
valence=3)
atom2 = atom(pos=[0.25, 0, 0],
neighbors=[0, 2],
interactions=[0],
int_cell=[0],
atomicNum=26,
valence=3)
atom3 = atom(pos=[0.50, 0, 0],
neighbors=[1, 3],
interactions=[0],
int_cell=[0],
atomicNum=26,
valence=3)
atom4 = atom(pos=[0.75, 0, 0],
neighbors=[2],
interactions=[0],
int_cell=[0],
atomicNum=26,
valence=3)
# atom_list,N_atoms_uc = ([atom1, atom2, atom3, atom4],1)
N_atoms = len(atom_list)
print N_atoms
if 1:
kx = sp.Symbol('kx', real=True, commutative=True)
ky = sp.Symbol('ky', real=True, commutative=True)
kz = sp.Symbol('kz', real=True, commutative=True)
k = spm.Matrix([kx, ky, kz])
(b, bd) = generate_b_bd_operators(atom_list)
# list_print(b)
(a, ad) = generate_a_ad_operators(atom_list, k, b, bd)
list_print(a)
(Sp, Sm) = generate_Sp_Sm_operators(atom_list, a, ad)
list_print(Sp)
(Sa, Sb, Sn) = generate_Sa_Sb_Sn_operators(atom_list, Sp, Sm)
# list_print(Sa)
(Sx, Sy, Sz) = generate_Sx_Sy_Sz_operators(atom_list, Sa, Sb, Sn)
list_print(Sx)
print ''
#Ham = generate_Hamiltonian(N_atoms, atom_list, b, bd)
ops = generate_possible_combinations(atom_list, [Sx, Sy, Sz])
# list_print(ops)
ops = holstein(atom_list, ops)
# list_print(ops)
ops = apply_commutation(atom_list, ops)
# list_print(ops)
ops = replace_bdb(atom_list, ops)
# list_print(ops)
ops = reduce_options(atom_list, ops)
list_print(ops)
# Old Method
#cross_sect = generate_cross_section(atom_list, ops, 1, real, recip)
#print '\n', cross_sect
if 1:
aa = bb = cc = np.array([2.0 * np.pi], 'Float64')
alpha = beta = gamma = np.array([np.pi / 2.0], 'Float64')
vect1 = np.array([[1, 0, 0]])
vect2 = np.array([[0, 0, 1]])
lattice = Lattice(aa, bb, cc, alpha, beta, gamma,
Orientation(vect1, vect2))
data = {}
data['kx'] = 1.
data['ky'] = 0.
data['kz'] = 0.
direction = data
temperature = 100.0
min = 0
max = 2 * sp.pi
steps = 25
tau_list = []
for i in range(1):
tau_list.append(np.array([0, 0, 0], 'Float64'))
h_list = np.linspace(0, 2, 100)
k_list = np.zeros(h_list.shape)
l_list = np.zeros(h_list.shape)
w_list = np.linspace(-4, 4, 100)
efixed = 14.7 #meV
eief = True
eval_cross_section(interactionfile, spinfile, lattice, ops, tau_list,
h_list, k_list, l_list, w_list, data, temperature,
min, max, steps, eief, efixed)
end = clock()
print "\nFinished %i atoms in %.2f seconds" % (N_atoms, end - start)
def generate_cross_section(atom_list, arg, q, real_list, recip_list):
"""Generates the Cross-Section Formula for the one magnon case"""
N = len(atom_list)
gam = 1.913 #sp.Symbol('gamma', commutative = True)
r = sp.Symbol('r0', commutative=True)
h = 1. # 1.05457148*10**(-34) #sp.Symbol('hbar', commutative = True)
k = sp.Symbol('k', commutative=True)
kp = sp.Symbol('kp', commutative=True)
g = sp.Symbol('g', commutative=True)
F = sp.Function('F')
def FF(arg):
F = sp.Function('F')
if arg.shape == (3, 1) or arg.shape == (1, 3):
return sp.Symbol("%r" % (F(arg.tolist()), ), commutative=False)
kap = spm.Matrix([
sp.Symbol('kapx', commutative=False),
sp.Symbol('kapy', commutative=False),
sp.Symbol('kapz', commutative=False)
])
t = sp.Symbol('t', commutative=True)
w = sp.Symbol('w', commutative=True)
W = sp.Symbol('W', commutative=False)
kappa = sp.Symbol('kappa', commutative=False)
tau = sp.Symbol('tau', commutative=False)
# Wilds for sub_in method
A = sp.Wild('A', exclude=[0])
B = sp.Wild('B', exclude=[0])
C = sp.Wild('C')
D = sp.Wild('D')
front_constant = (gam * r)**2 / (2 * pi * h) * (kp / k) * N
front_func = (1. / 2.) * g #*F(k)
vanderwaals = exp(-2 * W)
temp2 = []
temp3 = []
temp4 = []
# Grabs the unit vectors from the back of the lists.
unit_vect = []
kapx = sp.Symbol('kapxhat', )
kapy = sp.Symbol('kapyhat', commutative=False)
kapz = sp.Symbol('kapzhat', commutative=False)
for i in range(len(arg)):
unit_vect.append(arg[i].pop())
# for ele in unit_vect:
# ele = ele.subs(kapx,spm.Matrix([1,0,0]))
# ele = ele.subs(kapy,spm.Matrix([0,1,0]))
# ele = ele.subs(kapz,spm.Matrix([0,0,1]))
# This is were the heart of the calculation comes in.
# First the exponentials are turned into delta functions:
for i in range(len(arg)):
for j in range(N):
arg[i][j] = sp.powsimp(arg[i][j], deep=True, combine='all')
arg[i][j] = arg[i][j] * exp(-I * w * t) * exp(
I * inner_prod(spm.Matrix(atom_list[j].pos).T, kap))
arg[i][j] = sp.powsimp(arg[i][j], deep=True, combine='all')
arg[i][j] = sub_in(arg[i][j], exp(I * t * A + I * t * B + C),
sp.DiracDelta(A * t + B * t +
C / I)) #*sp.DiracDelta(C))
arg[i][j] = sub_in(
arg[i][j], sp.DiracDelta(A * t + B * t + C),
sp.DiracDelta(A * h + B * h) * sp.DiracDelta(C + tau))
arg[i][j] = sub_in(arg[i][j], sp.DiracDelta(-A - B),
sp.DiracDelta(A + B))
print arg[i][j]
print "Applied: Delta Function Conversion"
# for ele in arg:
# for subele in ele:
# temp2.append(subele)
# temp3.append(sum(temp2))
#
# for i in range(len(temp3)):
# temp4.append(unit_vect[i] * temp3[i])
for k in range(len(arg)):
temp4.append(arg[k][q])
dif = (front_func**2 * front_constant * vanderwaals * sum(temp4)
) #.expand()#sp.simplify(sum(temp4))).expand()
print "Complete: Cross-section Calculation"
return dif
import sympy as sy
import sympy.matrices as syma
d = 2
rho = sy.Symbol("rho")
rhouvec = [sy.Symbol("rho" + chr(ord("u") + i)) for i in range(d)]
uvec = [rhou_i / rho for rhou_i in rhouvec]
E = sy.Symbol("E")
p = sy.Symbol("p")
gamma = sy.Symbol("gamma")
p_solved = sy.solve(
-E + p / (gamma - 1) + rho / 2 * sum(uvec[i]**2 for i in range(d)), p)[0]
print p_solved
flux_rho = syma.Matrix(1, d, [rho * uvec[i] for i in range(d)])
flux_E = syma.Matrix(1, d, [(E + p_solved) * uvec[i] for i in range(d)])
flux_rho_u = syma.Matrix(1, d, [(E + p_solved) * uvec[i] for i in range(d)])
print flux_E
def P(tp, pi, ti):
p0 = smm.Matrix([1, 0, 0])
R_i = R(0, -ti, -pi) * R_z(tp)
return R_i * p0
def R_z(alpha):
return smm.Matrix([[sm.cos(alpha), -sm.sin(alpha), 0],
[sm.sin(alpha), sm.cos(alpha), 0], [0, 0, 1]])
def R_y(alpha):
return smm.Matrix([[sm.cos(alpha), 0, sm.sin(alpha)], [0, 1, 0],
[-sm.sin(alpha), 0, sm.cos(alpha)]])
def R_x(alpha):
return smm.Matrix([[1, 0, 0], [0, sm.cos(alpha), -sm.sin(alpha)],
[0, sm.sin(alpha), sm.cos(alpha)]])
import mpmath import sys import numpy as np import matplotlib.pyplot as plt init_printing(use_unicode=True, wrap_line=False) sys.modules['sympy.mpmath'] = mpmath component = 'VH' a, b, c, d, p, t = sm.symbols(r'a b c d \phi \theta') # symbol matrices # si A_1 = smm.Matrix([[a, 0, 0], [0, a, 0], [0, 0, a]]) E1 = smm.Matrix([[b, 0, 0], [0, b, 0], [0, 0, -2 * b]]) E2 = smm.Matrix([[-sm.sqrt(3) * b, 0, 0], [0, sm.sqrt(3) * b, 0], [0, 0, 0]]) T_2x = smm.Matrix([[0, 0, 0], [0, 0, d], [0, d, 0]]) T_2y = smm.Matrix([[0, 0, d], [0, 0, 0], [d, 0, 0]]) T_2z = smm.Matrix([[0, d, 0], [d, 0, 0], [0, 0, 0]]) # grf/hbn A1g = smm.Matrix([[a, 0, 0], [0, a, 0], [0, 0, b]]) E2g1 = smm.Matrix([[0, -d, 0], [-d, 0, 0], [0, 0, 0]])