def ligandDistances(ciffile):
cif = cef.CifFile(ciffile)
for asuc in cif.asymunitcell:
if asuc[1].strip('3+') in ['Sm','Pm','Nd','Ce','Dy','Ho','Tm','Pr','Er','Tb','Yb']:
onesite = asuc
break
## Check for multiply defined atoms
differentPositionsA = []
differentPositionsB = []
for ii, at in enumerate(cif.unitcell):
if at[4] < 0: print('negative atom!',ii, at)
if at[0][-1] in ["'", "B", "b"]:
differentPositionsA.append(at[0])
differentPositionsB.append(at[0].replace("'","").replace("B","A").replace("b","a"))
if len(differentPositionsA) > 0:
cif_a = deepcopy(cif)
cif_b = deepcopy(cif)
unitcellA = []
unitcellB = []
for ii, at in enumerate(cif.unitcell):
if at[0] in differentPositionsA:
unitcellA.append(at)
elif at[0] in differentPositionsB:
unitcellB.append(at)
else:
unitcellA.append(at)
unitcellB.append(at)
cif_a.unitcell = unitcellA
cif_b.unitcell = unitcellB
cifs = [cif, cif_a, cif_b]
else:
cifs = [cif]
unitcellshifts = np.array([[0,0,0], [1,0,0], [0,1,0], [0,0,1],
[-1,0,0],[0,-1,0],[0,0,-1],
[1,1,0], [0,1,1], [1,0,1],
[-1,1,0],[0,-1,1],[1,0,-1],
[1,-1,0],[0,1,-1],[-1,0,1],
[-1,-1,0],[0,-1,-1],[-1,0,-1],
[1,1,1], [1,1,-1], [1,-1,1], [-1,1,1],
[-1,-1,-1], [-1,-1,1], [-1,1,-1],[1,-1,-1]])
#neighborlist = []
distlist = []
for ii, at in enumerate(cifs[0].unitcell):
if at[4] < 0: print('negative atom!',ii, at)
#if ion not in at[0]:
for ucs in unitcellshifts:
distVec0 = cifs[0].latt.cartesian(np.array(onesite[2:5]) - (np.array(at[2:5]) + ucs))
#neighborlist.append([at[1], np.linalg.norm(distVec0), distVec0])
distlist.append(np.linalg.norm(distVec0))
return np.sort(distlist)
import numpy as np
import matplotlib.pyplot as plt
import PyCrystalField as cef
########### Import CIF file
YTOLig, Yb = cef.importCIF('yto.cif','Yb1')
Yb.diagonalize()
########### print eigenvectors
Yb.printEigenvectors()
########### plot neutron spectrum
hw = np.linspace(0,100,200)
intens = Yb.neutronSpectrum(hw, Temp=20, Ei=120, ResFunc= lambda x: 4, gamma = 1)
plt.figure()
plt.plot(hw, intens)
plt.show()
import sys
from pythonlib.functions import SimDat
ions = [
'Sm3+', 'Pm3+', 'Nd3+', 'Ce3+', 'Dy3+', 'Ho3+', 'Tm3+', 'Pr3+', 'Er3+',
'Tb3+', 'Yb3+'
]
for ion in ions:
print('*' * 40, ion)
filename = ion[:2] + 'TO'
Data = SimDat('SimulatedData/{}_simdat.txt'.format(filename))
YTOLig, Yb = cef.importCIF('SimulatedDataCode/{}.cif'.format(filename),
ion[:2] + '1')
Yb.diagonalize()
maxE = np.max(Yb.eigenvalues) * 1.1 + 5
RF = lambda x: 0.03 * (maxE - x / 1.3)
#############
npts = len(Data.hw) * len(Data.Temps)
def err_global(CFLevelsObject, coeff, gammas, pref):
"""Global error to all functions passed to it, used for fitting"""
# define new Hamiltonian
newH = np.sum([a * b for a, b in zip(CFLevelsObject.O, coeff)], axis=0)
CFLevelsObject.diagonalize(newH)
erro = 0
import numpy as np
import matplotlib.pyplot as plt
import PyCrystalField as cef
########### Import CIF file
# We can specify the Z axis of the point charge model if we choose.
# PyCrystalField will then find a y axis orthogonal to it with a
# mirror plane (if one exists)
# You can also specify the y axis if you want with "Yaxis = [ , , ]"
YTOLig, Yb = cef.importCIF('yto.cif', 'Yb1', Zaxis=[1, 1, 0])
########### print eigenvectors
Yb.printEigenvectors()
########### plot neutron spectrum
hw = np.linspace(0, 100, 200)
intens = Yb.neutronSpectrum(hw, Temp=20, Ei=120, ResFunc=lambda x: 4, gamma=1)
plt.figure()
plt.plot(hw, intens)
plt.show()
cifname = cf.split('/')[1]
#YTOLig, Yb = cef.importCIF(cf, NumIonNeighbors=3)
sample_ID = cifIDs[i]
name = str(sample_ID)
try:
coordnum = int(SD.data['coordination_number'][sample_ID])
if 'Carbon' in SD.data['coordination_elements'][sample_ID]:
raise ValueError
elif 'carbon' in SD.data['coordination_elements'][sample_ID]:
raise ValueError
except ValueError:
coordnum = None
print('CoordinationNumber:', coordnum)
PCFoutput = cef.importCIF(cf,
NumIonNeighbors=1,
CoordinationNumber=coordnum)
### See how many neighbors. If there's less than seven, redo.
if coordnum == None:
nin = 1
while True:
try:
YTOLig, Yb = PCFoutput
except ValueError:
YTOLig = PCFoutput[0][0]
if len(YTOLig.bonds) < 7:
nin += 1
PCFoutput = cef.importCIF(cf,
NumIonNeighbors=nin,
CoordinationNumber=coordnum)
elif len(YTOLig.bonds) >= 20:
import numpy as np
import PyCrystalField as cef
########### Import CIF file
NCNFLig, Ni = cef.importCIF('NaCaNi2F7.cif', 'Ni1', ionS=1, ionL=3)
########### print eigenvectors
Ni.printEigenvectors()
'Sm3+', 'Pm3+', 'Nd3+', 'Ce3+', 'Dy3+', 'Ho3+', 'Tm3+', 'Pr3+', 'Er3+',
'Tb3+', 'Yb3+'
]
for ion in ions:
filename = ion[:2] + 'TO'
####### Create copies of cif files
with open('kes.cif') as f1:
with open(filename + '.cif', 'w') as f2:
for line in f1.readlines():
f2.write(
line.replace('Er3+', ion).replace('Er1', ion[:2] + '1'))
########### Import CIF file
YTOLig, Yb = cef.importCIF(filename + '.cif', ion[:2] + '1')
########### print eigenvectors
Yb.printEigenvectors()
maxE = np.max(Yb.eigenvalues) * 1.1 + 5
########### plot neutron spectrum
RF = lambda x: 0.03 * (maxE - x / 1.3)
hw = np.linspace(5, maxE, 200)
Temps = [10, 200]
intens1 = Yb.normalizedNeutronSpectrum(hw,
Temp=10,
ResFunc=RF,
gamma=0.5 * maxE / 100)