def simulate(k, tMax, tMin, tFactor, inFilePath, outFilePath, tol = 1e-12):
"""Runs the monte carlo simulation written in C.
k is the number of steps per temperature.
tFactor is the factor which is multiplied by the temperature to decrease it
at each temperature step.
i.e. .9 would be a good factor."""
atoms, jMatrices = readFile(inFilePath)#simple atom class defined in simple
spins = get_ground_state(k, tMax, tMin, tFactor, atoms, jMatrices)
write_to_file(outFilePath, atoms, spins)
def simulate(k, tMax, tMin, tFactor, inFilePath, outFilePath, tol=1e-12):
"""Runs the monte carlo simulation written in C.
k is the number of steps per temperature.
tFactor is the factor which is multiplied by the temperature to decrease it
at each temperature step.
i.e. .9 would be a good factor."""
atoms, jMatrices = readFile(
inFilePath) #simple atom class defined in simple
spins = get_ground_state(k, tMax, tMin, tFactor, atoms, jMatrices)
write_to_file(outFilePath, atoms, spins)
def simulate(k, tMax, tMin, tFactor, inFilePath, outFilePath, tol = 1e-7):
"""Runs the monte carlo simulation written in C.
k is the number of steps per temperature.
tFactor is the factor which is multiplied by the temperature to decrease it
at each temperature step.
i.e. .9 would be a good factor."""
print "Loading..."
atoms, jMatrices = readFile(inFilePath)#simple atom class defined in simple
if not jMatrices:
raise Exception("No Interactions were specified")
exceptionlist = [Exception('At least one jMatrix is empty') for mat in jMatrices if not mat.any()]
if exceptionlist:
raise exceptionlist[0]
spins = get_ground_state(k, tMax, tMin, tFactor, atoms, jMatrices, tol=tol)
write_to_file(outFilePath, atoms, spins)
def simulate(k, tMax, tMin, tFactor, inFilePath, outFilePath, tol=1e-7):
"""Runs the monte carlo simulation written in C.
k is the number of steps per temperature.
tFactor is the factor which is multiplied by the temperature to decrease it
at each temperature step.
i.e. .9 would be a good factor."""
print "Loading..."
atoms, jMatrices = readFile(
inFilePath) #simple atom class defined in simple
if not jMatrices:
raise Exception("No Interactions were specified")
exceptionlist = [
Exception('At least one jMatrix is empty') for mat in jMatrices
if not mat.any()
]
if exceptionlist:
raise exceptionlist[0]
spins = get_ground_state(k, tMax, tMin, tFactor, atoms, jMatrices, tol=tol)
write_to_file(outFilePath, atoms, spins)
print "Local Optimization Beginning..."
print "tolerance", tol
st = time.time()
# call minimizing function
m = fmin_l_bfgs_b(hamiltonian, p0, fprime = deriv, args = (Jij, spin_mags, anis), pgtol=tol, bounds = limits)
print time.time()-st, "seconds"
print "Optimization Complete"
# grab returned parameters
# thetas are the first half of the list, phis are the second half
pout=m[0]
theta=pout[0:len(pout)/2]
phi=pout[len(pout)/2::]
# recreate sx,sy,sz's
sx=spin_mags*sin(theta)*cos(phi)
sy=spin_mags*sin(theta)*sin(phi)
sz=spin_mags*cos(theta)
return np.array([sx,sy,sz]).T
if __name__ == '__main__':
#print optimizeSpins('C:\\export.txt', 'C:\\spins.txt', 'C:\\spins2.txt')
interfile = 'C:/Documents and Settings/wflynn/Desktop/yang_montecarlo.txt'
spinfile = 'c:/Documents and Settings/wflynn/Desktop/spins.txt'
atoms, mats = readFile(interfile)
#interfile='c:/montecarlo_ferro.txt'
#spinfile='c:/Spins_ferro.txt'
#readfile=interfile
tol = 1.0e-8
def getSpins(self, inFilePath):
atoms, jMatrices = readFile(inFilePath)
spins = Sim_Aux(self.k, self.tMax, self.tMin, self.tFactor, atoms, jMatrices)
opt_spins = opt_aux(atoms, jMatrices, spins, self.tol)
return (spins, opt_spins)
def createVideo(spinsToImageFunction, outFilePath, inFilePath):
"""This method is used to create snapshots of the monte carlo simulation.
This is almost the same as simulate, but the outer loops
are controlled in python so that snapshots can be taken"""
timer = Timer()
#C code and dll should be put into a folder in close to this code
if sys.platform == 'win32':
print 'win32'
monteCarloDll = N.ctypeslib.load_library('monteCarlo', 'C:/spinwaves')
# elif sys.platform=='mac':
# monteCarloDll = N.ctypeslib.load_library('libpolarization2.so', '.')
# else:
# monteCarloDll = N.ctypeslib.load_library('libpolarization2.so', '.') #linux
atoms, jMatrices = readFile(inFilePath)
successCode = c_int(0)
atomListPointer = monteCarloDll.new_atom_list(c_int(len(atoms)),
ctypes.byref(successCode))
# print "Success Code: ", successCode
if successCode.value != 1:
raise Exception(
"Problem Allocating memory, simulation size may be too large")
#to keep pointers
matListList = []
nbr_ListList = []
#Create atom list in C
s1Class = c_float * 3
for i in range(len(atoms)):
# for i in range(5):
atom = atoms[i]
numInteractions = len(atom.interactions)
matListClass = c_int * numInteractions
nbrListClass = c_int * numInteractions
matList = matListClass()
neighbors = nbrListClass()
for j in range(numInteractions):
neighbors[j] = c_int(atom.interactions[j][0])
matList[j] = c_int(atom.interactions[j][1])
# print "interaction: " , atom.interactions[j][0], atom.interactions[j][1], " = " , neighbors[j], matList[j]
s1 = s1Class()
s1[0] = c_float(1)
s1[1] = c_float(0)
s1[2] = c_float(0)
anisotropyClass = c_float * 3
anisotropy = anisotropyClass()
anisotropy[0] = c_float(atom.anisotropy[0])
anisotropy[1] = c_float(atom.anisotropy[1])
anisotropy[2] = c_float(atom.anisotropy[2])
#to keep pointers
matListList.append(matList)
nbr_ListList.append(neighbors)
monteCarloDll.set_atom(atomListPointer, c_int(i), anisotropy, matList,
neighbors, c_int(numInteractions), s1)
print "atoms added"
timer.printTime()
#Create JMatrix List in C
matPointer = monteCarloDll.new_jMatrix_list(c_int(len(jMatrices)),
ctypes.byref(successCode))
if successCode.value != 1:
raise Exception(
"Problem Allocating memory, simulation size may be too large")
for i in range(len(jMatrices)):
j = jMatrices[i]
j11 = c_float(j[0][0])
j12 = c_float(j[0][1])
j13 = c_float(j[0][2])
j21 = c_float(j[1][0])
j22 = c_float(j[1][1])
j23 = c_float(j[1][2])
j31 = c_float(j[2][0])
j32 = c_float(j[2][1])
j33 = c_float(j[2][2])
monteCarloDll.add_matrix(matPointer, c_int(i), j11, j12, j13, j21, j22,
j23, j31, j32, j33)
#Until this point, code is almost the same as simulate(), now flipspins() must be called directly from python
totalMagX = 0
totalMagY = 0
totalMagZ = 0
magnetizations = [] #to make graph after
temperatures = []
T = 10 #tMax
imageNum = 0
spins = None
while T > .005: #tMin
for i in range(10):
for j in range(10):
monteCarloDll.flipSpins(
atomListPointer, c_int(len(atoms)), matPointer, c_float(T),
ctypes.byref(c_int(0))) #last parameter not used\
#output spins to file
spins = []
for i in range(len(atoms)):
spin = s1Class()
monteCarloDll.getSpin(atomListPointer, c_int(i),
ctypes.byref(spin))
spins.append(spin)
print "writing spins to file..."
timer.printTime()
#output the spins to a file
outFile = open(outFilePath, 'w')
outFile.write(
"#Atom_Number Position_X Position_Y Position_Z Spin_X Spin_Y Spin_Z\n"
)
for i in range(len(atoms)):
atom = atoms[i]
Posx = str(atom.pos[0])
Posy = str(atom.pos[1])
Posz = str(atom.pos[2])
spin = spins[i]
Spinx = str(spin[0])
Spiny = str(spin[1])
Spinz = str(spin[2])
atomStr = str(
i
) + " " + Posx + " " + Posy + " " + Posz + " " + Spinx + " " + Spiny + " " + Spinz + "\n"
outFile.write(atomStr)
outFile.close()
#draw the spins
spinsToImageFunction(outFilePath, imageNum)
imageNum += 1
for spin in spins:
totalMagX += spin[0]
totalMagY += spin[1]
totalMagZ += spin[2]
magnetizations.append(
(totalMagX**2 + totalMagY**2 + totalMagZ**2)**(.5))
# print "magnetization:", magnetizations[len(magnetizations)-1]
temperatures.append(T)
totalMagX = 0
totalMagY = 0
totalMagZ = 0
T = T * .9 #tFactor
monteCarloDll.del_jMat(matPointer)
monteCarloDll.del_atom(atomListPointer)
#drawing magnetization graphs
#find max value
max = 0
min = 0
for num in magnetizations:
if num > max:
max = num
elif num < min:
min = num
#draw magnetization vs. temp
# pylab.plot(temperatures, magnetizations, 'ro')
# pylab.axis([temperatures[len(temperatures)-1], temperatures[0], min, max])
# pylab.show()
#draw magnetization vs. iteration number
# pylab.plot(range(len(magnetizations)), magnetizations, 'ro')
# pylab.axis([len(temperatures)-1, 0, min, max])
# savefig('secondfig.png')
# pylab.show()
timer.printTime()
print "done"
def createVideo(spinsToImageFunction, outFilePath, inFilePath):
"""This method is used to create snapshots of the monte carlo simulation.
This is almost the same as simulate, but the outer loops
are controlled in python so that snapshots can be taken"""
timer = Timer()
#C code and dll should be put into a folder in close to this code
if sys.platform=='win32':
print 'win32'
monteCarloDll = N.ctypeslib.load_library('monteCarlo', 'C:/spinwaves')
# elif sys.platform=='mac':
# monteCarloDll = N.ctypeslib.load_library('libpolarization2.so', '.')
# else:
# monteCarloDll = N.ctypeslib.load_library('libpolarization2.so', '.') #linux
atoms, jMatrices = readFile(inFilePath)
successCode = c_int(0)
atomListPointer = monteCarloDll.new_atom_list(c_int(len(atoms)), ctypes.byref(successCode))
# print "Success Code: ", successCode
if successCode.value != 1:
raise Exception("Problem Allocating memory, simulation size may be too large")
#to keep pointers
matListList = []
nbr_ListList = []
#Create atom list in C
s1Class = c_float * 3
for i in range(len(atoms)):
# for i in range(5):
atom = atoms[i]
numInteractions = len(atom.interactions)
matListClass = c_int * numInteractions
nbrListClass = c_int * numInteractions
matList = matListClass()
neighbors = nbrListClass()
for j in range(numInteractions):
neighbors[j] = c_int(atom.interactions[j][0])
matList[j] = c_int(atom.interactions[j][1])
# print "interaction: " , atom.interactions[j][0], atom.interactions[j][1], " = " , neighbors[j], matList[j]
s1 = s1Class()
s1[0] = c_float(1)
s1[1] = c_float(0)
s1[2] = c_float(0)
anisotropyClass = c_float * 3
anisotropy = anisotropyClass()
anisotropy[0] = c_float(atom.anisotropy[0])
anisotropy[1] = c_float(atom.anisotropy[1])
anisotropy[2] = c_float(atom.anisotropy[2])
#to keep pointers
matListList.append(matList)
nbr_ListList.append(neighbors)
monteCarloDll.set_atom(atomListPointer, c_int(i), anisotropy, matList, neighbors, c_int(numInteractions), s1)
print "atoms added"
timer.printTime()
#Create JMatrix List in C
matPointer = monteCarloDll.new_jMatrix_list(c_int(len(jMatrices)), ctypes.byref(successCode))
if successCode.value != 1:
raise Exception("Problem Allocating memory, simulation size may be too large")
for i in range(len(jMatrices)):
j = jMatrices[i]
j11 = c_float(j[0][0])
j12 = c_float(j[0][1])
j13 = c_float(j[0][2])
j21 = c_float(j[1][0])
j22 = c_float(j[1][1])
j23 = c_float(j[1][2])
j31 = c_float(j[2][0])
j32 = c_float(j[2][1])
j33 = c_float(j[2][2])
monteCarloDll.add_matrix(matPointer, c_int(i),j11, j12, j13, j21, j22, j23, j31, j32, j33)
#Until this point, code is almost the same as simulate(), now flipspins() must be called directly from python
totalMagX = 0
totalMagY = 0
totalMagZ = 0
magnetizations = []#to make graph after
temperatures = []
T = 10#tMax
imageNum = 0
spins = None
while T > .005:#tMin
for i in range(10):
for j in range(10):
monteCarloDll.flipSpins(atomListPointer, c_int(len(atoms)), matPointer, c_float(T), ctypes.byref(c_int(0)))#last parameter not used\
#output spins to file
spins = []
for i in range(len(atoms)):
spin = s1Class()
monteCarloDll.getSpin(atomListPointer, c_int(i), ctypes.byref(spin))
spins.append(spin)
print "writing spins to file..."
timer.printTime()
#output the spins to a file
outFile = open(outFilePath, 'w')
outFile.write("#Atom_Number Position_X Position_Y Position_Z Spin_X Spin_Y Spin_Z\n")
for i in range(len(atoms)):
atom = atoms[i]
Posx = str(atom.pos[0])
Posy = str(atom.pos[1])
Posz = str(atom.pos[2])
spin = spins[i]
Spinx = str(spin[0])
Spiny = str(spin[1])
Spinz = str(spin[2])
atomStr = str(i) + " " + Posx + " " + Posy + " " + Posz + " " + Spinx + " " + Spiny + " " + Spinz + "\n"
outFile.write(atomStr)
outFile.close()
#draw the spins
spinsToImageFunction(outFilePath, imageNum)
imageNum += 1
for spin in spins:
totalMagX += spin[0]
totalMagY += spin[1]
totalMagZ += spin[2]
magnetizations.append( (totalMagX**2 + totalMagY**2 + totalMagZ**2)**(.5) )
print "magnetization:", magnetizations[len(magnetizations)-1]
temperatures.append(T)
totalMagX = 0
totalMagY = 0
totalMagZ = 0
T = T*.9#tFactor
monteCarloDll.del_jMat(matPointer)
monteCarloDll.del_atom(atomListPointer)
#drawing magnetization graphs
#find max value
max = 0
min = 0
for num in magnetizations:
if num > max:
max = num
elif num < min:
min = num
#draw magnetization vs. temp
# pylab.plot(temperatures, magnetizations, 'ro')
# pylab.axis([temperatures[len(temperatures)-1], temperatures[0], min, max])
# pylab.show()
#draw magnetization vs. iteration number
# pylab.plot(range(len(magnetizations)), magnetizations, 'ro')
# pylab.axis([len(temperatures)-1, 0, min, max])
# savefig('secondfig.png')
# pylab.show()
timer.printTime()
print "done"
# call minimizing function
m = fmin_l_bfgs_b(hamiltonian,
p0,
fprime=deriv,
args=(Jij, spin_mags, anis),
pgtol=tol,
bounds=limits)
print time.time() - st, "seconds"
print "Optimization Complete"
# grab returned parameters
# thetas are the first half of the list, phis are the second half
pout = m[0]
theta = pout[0:len(pout) / 2]
phi = pout[len(pout) / 2::]
# recreate sx,sy,sz's
sx = spin_mags * sin(theta) * cos(phi)
sy = spin_mags * sin(theta) * sin(phi)
sz = spin_mags * cos(theta)
return np.array([sx, sy, sz]).T
if __name__ == '__main__':
#print optimizeSpins('C:\\export.txt', 'C:\\spins.txt', 'C:\\spins2.txt')
interfile = 'C:/Documents and Settings/wflynn/Desktop/yang_montecarlo.txt'
spinfile = 'c:/Documents and Settings/wflynn/Desktop/spins.txt'
atoms, mats = readFile(interfile)
#interfile='c:/montecarlo_ferro.txt'
#spinfile='c:/Spins_ferro.txt'
#readfile=interfile
tol = 1.0e-8