Example #1
0
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)
Example #2
0
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)
Example #3
0
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)
Example #4
0
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)
Example #5
0
    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)
Example #7
0
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"
Example #8
0
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"
Example #9
0
    # 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