Module diffpy.mpdf.mpdf3Dcalculator
class to perform 3D-mPDF calculations
Expand source code
#!/usr/bin/env python
##############################################################################
#
# diffpy.mpdf by Frandsen Group
# Benjamin A. Frandsen benfrandsen@byu.edu
# (c) 2022 Benjamin Allen Frandsen
# All rights reserved
#
# File coded by: Parker Hamilton and Benjamin Frandsen
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################
"""class to perform 3D-mPDF calculations"""
import copy
import numpy as np
from scipy.signal import convolve, correlate
from diffpy.mpdf.magutils import gauss, ups, vec_con, vec_ac
class MPDF3Dcalculator:
"""Create an MPDF3Dcalculator object to help calculate 3D-mPDF functions
This class is loosely modelled after the PDFcalculator cless in diffpy.
At minimum, tie requires a magnetic structure with atoms and spins and will
calculate the 3D-mPDF from that.
Args:
magstruc (MagStructure object): gives the information about the magnetic
structure. Must have arrays of atoms and spins
gaussPeakWidth (float): The width of the gaussian function that represents atoms
label (string): Optional label from the MPDF3Dcalculator
"""
def __init__(self, magstruc=None, gaussPeakWidth=0.5, label=""):
if magstruc is None:
self.magstruc = []
else:
self.magstruc = magstruc
self.gaussPeakWidth = gaussPeakWidth
self.label = label
self.Nx = None
self.Ny = None
self.Nz = None
self.dr = None
def __repr__(self):
if self.label == None:
return "3DMPDFcalculator() object"
else:
return self.label + ": 3DMPDFcalculator() object"
def calc(self, verbose=False, dr=None, originIdx=0):
"""Calculate the 3D magnetic PDF
Args:
verbose (boolean): indicates whether to output progress
dr (float): the grid spacing to use
originIdx (int): index of spin to be used as origin
if a correlation length is being applied
"""
if dr is not None:
self.dr = dr
self._makeRgrid()
s_arr = np.zeros((self.Nx,self.Ny,self.Nz,3))
if verbose :
print("Setting up point spins")
# Use the scaled spins if the correlation length has been set;
# otherwise, use the full magnitude spins
spins = self.magstruc.generateScaledSpins(originIdx)
for i in range(len(self.magstruc.atoms)):
idx = np.rint((self.magstruc.atoms[i] - self.rmin)/self.dr).astype(int)
s_arr[idx[0],idx[1],idx[2]] = spins[i]
if verbose:
print("Setting up filter grid")
filter_x = np.arange(-3,3+self.dr,self.dr)
X,Y,Z = np.meshgrid(filter_x,filter_x,filter_x,indexing='ij')
filter_grid = np.moveaxis([X,Y,Z],0,-1)
if verbose:
print("Making filters")
gaussian = gauss(filter_grid,s=self.gaussPeakWidth)
upsilon = ups(filter_grid)
if verbose:
print("Convolving spin array")
s_arr[:,:,:,0] = convolve(s_arr[:,:,:,0],gaussian,mode='same')*self.dr**3
s_arr[:,:,:,1] = convolve(s_arr[:,:,:,1],gaussian,mode='same')*self.dr**3
s_arr[:,:,:,2] = convolve(s_arr[:,:,:,2],gaussian,mode='same')*self.dr**3
if verbose:
print("Computing mpdf")
mag_ups = vec_con(s_arr,upsilon,self.dr)
if verbose:
print("comp1")
self.mpdf = vec_ac(s_arr,s_arr,self.dr,"full")
#comp1 = vec_ac(s_arr,s_arr,self.dr,"full")
if verbose:
print("comp2")
self.mpdf += -1/(np.pi**4)*correlate(mag_ups,mag_ups,mode="full")*self.dr**3
#comp2 = correlate(mag_ups,mag_ups,mode="full")*self.dr**3
if verbose:
print("mpdf")
#self.mpdf = comp1 - 1/(np.pi**4)*comp2
return
def _makeRgrid(self,dr = None,buf=0):
"""Set up bounds and intervals of the spatial grid to use
Args:
dr (float): the grid spacing to use
buf (float): the space to include on either side of the
spin distribution
"""
if dr is not None:
self.dr = dr
if self.dr is None:
self.dr = 0.2
pos = np.array([a for a in self.magstruc.atoms])
x_min = np.min(pos[:,0]) - buf
x_max = np.max(pos[:,0]) + buf
y_min = np.min(pos[:,1]) - buf
y_max = np.max(pos[:,1]) + buf
z_min = np.min(pos[:,2]) - buf
z_max = np.max(pos[:,2]) + buf
x = np.arange(x_min,x_max + self.dr, self.dr)
y = np.arange(y_min,y_max + self.dr, self.dr)
z = np.arange(z_min,z_max + self.dr, self.dr)
N_x = len(x)
N_y = len(y)
N_z = len(z)
x_max = np.max(x)
y_max = np.max(y)
z_max = np.max(z)
X,Y,Z = np.meshgrid(x,y,z,indexing='ij')
rgrid = np.moveaxis([X,Y,Z],0,-1)
self.Nx = N_x
self.Ny = N_y
self.Nz = N_z
self.rmin = np.array([x_min,y_min,z_min])
self.rmax = np.array([x_max,y_max,z_max])
return rgrid
def plot(self):
"""Plot the 3D-mPDF
ToDo: implement plotting, use Jacobs visualilze
"""
raise NotImplementedError()
def runChecks(self):
"""Runs bounds and compatibility checks for internal variables.
This should be called during __init__
ToDo: implement for troubleshooting
"""
raise NotImplementedError()
def rgrid(self):
"""Returns the spatial grid the 3D-mPDF is output on
Generates the spatial grid for the 3D-mPDF when needed by
the user
"""
if self.dr is None:
self._makeRgrid()
X = np.arange(-(self.Nx-1)*self.dr,stop = (self.Nx-1)*self.dr+self.dr/2,step = self.dr)
X[self.Nx-1] = 0
Y = np.arange(-(self.Ny-1)*self.dr,stop = (self.Ny-1)*self.dr+self.dr/2,step = self.dr)
Y[self.Ny-1] = 0
Z = np.arange(-(self.Nz-1)*self.dr,stop = (self.Nz-1)*self.dr+self.dr/2,step = self.dr)
Z[self.Nz-1] = 0
return X,Y,Z
def copy(self):
'''
Return a deep copy of the object
'''
return copy.deepcopy(self)Classes
class MPDF3Dcalculator (magstruc=None, gaussPeakWidth=0.5, label='')-
Create an MPDF3Dcalculator object to help calculate 3D-mPDF functions This class is loosely modelled after the PDFcalculator cless in diffpy. At minimum, tie requires a magnetic structure with atoms and spins and will calculate the 3D-mPDF from that.
Args
magstruc:MagStructure object- gives the information about the magnetic structure. Must have arrays of atoms and spins
gaussPeakWidth:float- The width of the gaussian function that represents atoms
label:string- Optional label from the MPDF3Dcalculator
Expand source code
class MPDF3Dcalculator: """Create an MPDF3Dcalculator object to help calculate 3D-mPDF functions This class is loosely modelled after the PDFcalculator cless in diffpy. At minimum, tie requires a magnetic structure with atoms and spins and will calculate the 3D-mPDF from that. Args: magstruc (MagStructure object): gives the information about the magnetic structure. Must have arrays of atoms and spins gaussPeakWidth (float): The width of the gaussian function that represents atoms label (string): Optional label from the MPDF3Dcalculator """ def __init__(self, magstruc=None, gaussPeakWidth=0.5, label=""): if magstruc is None: self.magstruc = [] else: self.magstruc = magstruc self.gaussPeakWidth = gaussPeakWidth self.label = label self.Nx = None self.Ny = None self.Nz = None self.dr = None def __repr__(self): if self.label == None: return "3DMPDFcalculator() object" else: return self.label + ": 3DMPDFcalculator() object" def calc(self, verbose=False, dr=None, originIdx=0): """Calculate the 3D magnetic PDF Args: verbose (boolean): indicates whether to output progress dr (float): the grid spacing to use originIdx (int): index of spin to be used as origin if a correlation length is being applied """ if dr is not None: self.dr = dr self._makeRgrid() s_arr = np.zeros((self.Nx,self.Ny,self.Nz,3)) if verbose : print("Setting up point spins") # Use the scaled spins if the correlation length has been set; # otherwise, use the full magnitude spins spins = self.magstruc.generateScaledSpins(originIdx) for i in range(len(self.magstruc.atoms)): idx = np.rint((self.magstruc.atoms[i] - self.rmin)/self.dr).astype(int) s_arr[idx[0],idx[1],idx[2]] = spins[i] if verbose: print("Setting up filter grid") filter_x = np.arange(-3,3+self.dr,self.dr) X,Y,Z = np.meshgrid(filter_x,filter_x,filter_x,indexing='ij') filter_grid = np.moveaxis([X,Y,Z],0,-1) if verbose: print("Making filters") gaussian = gauss(filter_grid,s=self.gaussPeakWidth) upsilon = ups(filter_grid) if verbose: print("Convolving spin array") s_arr[:,:,:,0] = convolve(s_arr[:,:,:,0],gaussian,mode='same')*self.dr**3 s_arr[:,:,:,1] = convolve(s_arr[:,:,:,1],gaussian,mode='same')*self.dr**3 s_arr[:,:,:,2] = convolve(s_arr[:,:,:,2],gaussian,mode='same')*self.dr**3 if verbose: print("Computing mpdf") mag_ups = vec_con(s_arr,upsilon,self.dr) if verbose: print("comp1") self.mpdf = vec_ac(s_arr,s_arr,self.dr,"full") #comp1 = vec_ac(s_arr,s_arr,self.dr,"full") if verbose: print("comp2") self.mpdf += -1/(np.pi**4)*correlate(mag_ups,mag_ups,mode="full")*self.dr**3 #comp2 = correlate(mag_ups,mag_ups,mode="full")*self.dr**3 if verbose: print("mpdf") #self.mpdf = comp1 - 1/(np.pi**4)*comp2 return def _makeRgrid(self,dr = None,buf=0): """Set up bounds and intervals of the spatial grid to use Args: dr (float): the grid spacing to use buf (float): the space to include on either side of the spin distribution """ if dr is not None: self.dr = dr if self.dr is None: self.dr = 0.2 pos = np.array([a for a in self.magstruc.atoms]) x_min = np.min(pos[:,0]) - buf x_max = np.max(pos[:,0]) + buf y_min = np.min(pos[:,1]) - buf y_max = np.max(pos[:,1]) + buf z_min = np.min(pos[:,2]) - buf z_max = np.max(pos[:,2]) + buf x = np.arange(x_min,x_max + self.dr, self.dr) y = np.arange(y_min,y_max + self.dr, self.dr) z = np.arange(z_min,z_max + self.dr, self.dr) N_x = len(x) N_y = len(y) N_z = len(z) x_max = np.max(x) y_max = np.max(y) z_max = np.max(z) X,Y,Z = np.meshgrid(x,y,z,indexing='ij') rgrid = np.moveaxis([X,Y,Z],0,-1) self.Nx = N_x self.Ny = N_y self.Nz = N_z self.rmin = np.array([x_min,y_min,z_min]) self.rmax = np.array([x_max,y_max,z_max]) return rgrid def plot(self): """Plot the 3D-mPDF ToDo: implement plotting, use Jacobs visualilze """ raise NotImplementedError() def runChecks(self): """Runs bounds and compatibility checks for internal variables. This should be called during __init__ ToDo: implement for troubleshooting """ raise NotImplementedError() def rgrid(self): """Returns the spatial grid the 3D-mPDF is output on Generates the spatial grid for the 3D-mPDF when needed by the user """ if self.dr is None: self._makeRgrid() X = np.arange(-(self.Nx-1)*self.dr,stop = (self.Nx-1)*self.dr+self.dr/2,step = self.dr) X[self.Nx-1] = 0 Y = np.arange(-(self.Ny-1)*self.dr,stop = (self.Ny-1)*self.dr+self.dr/2,step = self.dr) Y[self.Ny-1] = 0 Z = np.arange(-(self.Nz-1)*self.dr,stop = (self.Nz-1)*self.dr+self.dr/2,step = self.dr) Z[self.Nz-1] = 0 return X,Y,Z def copy(self): ''' Return a deep copy of the object ''' return copy.deepcopy(self)Methods
def calc(self, verbose=False, dr=None, originIdx=0)-
Calculate the 3D magnetic PDF
Args
verbose:boolean- indicates whether to output progress
dr:float- the grid spacing to use
originIdx:int- index of spin to be used as origin if a correlation length is being applied
Expand source code
def calc(self, verbose=False, dr=None, originIdx=0): """Calculate the 3D magnetic PDF Args: verbose (boolean): indicates whether to output progress dr (float): the grid spacing to use originIdx (int): index of spin to be used as origin if a correlation length is being applied """ if dr is not None: self.dr = dr self._makeRgrid() s_arr = np.zeros((self.Nx,self.Ny,self.Nz,3)) if verbose : print("Setting up point spins") # Use the scaled spins if the correlation length has been set; # otherwise, use the full magnitude spins spins = self.magstruc.generateScaledSpins(originIdx) for i in range(len(self.magstruc.atoms)): idx = np.rint((self.magstruc.atoms[i] - self.rmin)/self.dr).astype(int) s_arr[idx[0],idx[1],idx[2]] = spins[i] if verbose: print("Setting up filter grid") filter_x = np.arange(-3,3+self.dr,self.dr) X,Y,Z = np.meshgrid(filter_x,filter_x,filter_x,indexing='ij') filter_grid = np.moveaxis([X,Y,Z],0,-1) if verbose: print("Making filters") gaussian = gauss(filter_grid,s=self.gaussPeakWidth) upsilon = ups(filter_grid) if verbose: print("Convolving spin array") s_arr[:,:,:,0] = convolve(s_arr[:,:,:,0],gaussian,mode='same')*self.dr**3 s_arr[:,:,:,1] = convolve(s_arr[:,:,:,1],gaussian,mode='same')*self.dr**3 s_arr[:,:,:,2] = convolve(s_arr[:,:,:,2],gaussian,mode='same')*self.dr**3 if verbose: print("Computing mpdf") mag_ups = vec_con(s_arr,upsilon,self.dr) if verbose: print("comp1") self.mpdf = vec_ac(s_arr,s_arr,self.dr,"full") #comp1 = vec_ac(s_arr,s_arr,self.dr,"full") if verbose: print("comp2") self.mpdf += -1/(np.pi**4)*correlate(mag_ups,mag_ups,mode="full")*self.dr**3 #comp2 = correlate(mag_ups,mag_ups,mode="full")*self.dr**3 if verbose: print("mpdf") #self.mpdf = comp1 - 1/(np.pi**4)*comp2 return def copy(self)-
Return a deep copy of the object
Expand source code
def copy(self): ''' Return a deep copy of the object ''' return copy.deepcopy(self) def plot(self)-
Plot the 3D-mPDF ToDo: implement plotting, use Jacobs visualilze
Expand source code
def plot(self): """Plot the 3D-mPDF ToDo: implement plotting, use Jacobs visualilze """ raise NotImplementedError() def rgrid(self)-
Returns the spatial grid the 3D-mPDF is output on Generates the spatial grid for the 3D-mPDF when needed by the user
Expand source code
def rgrid(self): """Returns the spatial grid the 3D-mPDF is output on Generates the spatial grid for the 3D-mPDF when needed by the user """ if self.dr is None: self._makeRgrid() X = np.arange(-(self.Nx-1)*self.dr,stop = (self.Nx-1)*self.dr+self.dr/2,step = self.dr) X[self.Nx-1] = 0 Y = np.arange(-(self.Ny-1)*self.dr,stop = (self.Ny-1)*self.dr+self.dr/2,step = self.dr) Y[self.Ny-1] = 0 Z = np.arange(-(self.Nz-1)*self.dr,stop = (self.Nz-1)*self.dr+self.dr/2,step = self.dr) Z[self.Nz-1] = 0 return X,Y,Z def runChecks(self)-
Runs bounds and compatibility checks for internal variables. This should be called during init
ToDo: implement for troubleshooting
Expand source code
def runChecks(self): """Runs bounds and compatibility checks for internal variables. This should be called during __init__ ToDo: implement for troubleshooting """ raise NotImplementedError()