BUG: key error

[RuiFilipeCampos]

seeding with: 0, 0, 0, 123
seeding with: 0, 0, 0, 89715
Traceback (most recent call last):
D:\a\MontyCarlo\MontyCarlo\tests\_cmd.py
  File "D:\a\MontyCarlo\MontyCarlo\MontyCarlo\materials\database.py", line 553, in __getitem__
['import_test.py', '--built_inplace']
The path 'D:\a\MontyCarlo\MontyCarlo' has been appended to `sys.path`. If the path looks weird, you probably ran the script as a python file. Please run it as a module:
`python -m unit_test --built_inplace`
Importing MontyCarlo
Importing .settings
_________________________________________________________________
INSTALL PATH:  D:\a\MontyCarlo\MontyCarlo\MontyCarlo
----
DEBUG: False
---------------
PHOTON CUT OFF: 5110.0 MeV
----
ELECTRON CUT OFF: 100000.0 MeV
---------------------------------------------


BRANCH: pre-alpha/0.0.41

____INIT_____
Importing `.plotter`
Importing .tools.interpol1
Importing .tools.CubicInverseTransform ...
Importing `.materials.pyRelax`
Importing .materials.database
Importing .tools.vectors
Importing .tools.RITA
>>>> IMPORTING material.photon.CrossSection.pyx
>>>> IMPORTING material.photon.pyx
Importing `.materials.materials`
Importing `.materials.logger`
>>>> IMPORTING main.pyx
Importing .materials.electron.main
Importing `.types`
Importing .particles.particle
Importing .geometry.main
Importing .geometry.CSG
Importing .particles.positrons
Importing particles.photons
Importing .particles.electrons
Size of mater 128
Importing .sources
SEED: 725832839
Creating a material
Compiling data for material 'Untitled'
0
NUMBER OF PROFILES 1
1 1
0
1
2
NUMBER OF PROFILES 3
8 4
        DATA PROCESSING IN PYTHON
        > a = 2.9395944556963114
                err =  0.0 %
    2x<Atom Z=1, Aw = 1.00797 amu, I = 19.2 eV> 
    <Shell #1, fk = 1.0, Uk = 13.6 eV, Wk = 40.360955827712104 eV> 
 
    1x<Atom Z=8, Aw = 15.9994 amu, I = 95.0 eV> 
    <Shell #1, fk = 2.0, Uk = 538.0 eV, Wk = 1581.521246377744 eV> 
    <Shell #3, fk = 3.33, Uk = 21.049999999999997 eV, Wk = 62.8342736655728 eV> 
 

        GENERATING GOS MODEL IN CYTHON
        > creating shells
        > making density corrections
        > note: KE = logspace(1, 9, 5_000)
        GENERATING FULL SP
    return self.__cache__[Z+1]
KeyError: 8.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\a\MontyCarlo\MontyCarlo\tests\import_test.py", line 14, in <module>
    myco.Mat({1:2, 8:1}, 1)
  File "MontyCarlo\materials\materials.pyx", line 894, in MontyCarlo.materials.materials.Mat
  File "MontyCarlo\materials\materials.pyx", line 990, in MontyCarlo.materials.materials.Material.__init__
  File "MontyCarlo\materials\electron\main.pyx", line 295, in MontyCarlo.materials.electron.main.Electron.__init__
  File "MontyCarlo\materials\electron\main.pyx", line 614, in MontyCarlo.materials.electron.main.Inelastic.__init__
  File "MontyCarlo\materials\electron\GOSfinal.pyx", line 127, in MontyCarlo.materials.electron.GOSfinal.gosMolecule.__init__
  File "MontyCarlo\materials\electron\GOSfinal.pyx", line 368, in MontyCarlo.materials.electron.GOSfinal.gosAtom.__init__
  File "MontyCarlo\materials\electron\GOSfinal.pyx", line 1088, in MontyCarlo.materials.electron.GOSfinal.gosInnerShell.__init__
  File "D:\a\MontyCarlo\MontyCarlo\MontyCarlo\materials\database.py", line 555, in __getitem__
    self.__cache__[Z+1] = getEEDL(Z+1)
  File "D:\a\MontyCarlo\MontyCarlo\MontyCarlo\materials\database.py", line 294, in getEEDL
    EEDL_dict = get_bookmarked_text(EEDL_path)
NameError: name 'EEDL_path' is not defined
Error: Process completed with exit code 1.

[RuiFilipeCampos]

https://github.com/RuiFilipeCampos/MontyCarlo/tree/fix/%2321

[RuiFilipeCampos]

MontyCarlo/MontyCarlo/materials/electron/main.pyx

Lines 608 to 628 in b855154

	print(" GENERATING FULL SP")
	# these values are not supposed to change after renormalization
	# I'll be collecting data here, and use that to renormalize
	FULL = [np.array(self.get(E, True)) for E in eax]
	FULL = np.array(FULL)
	self.gosMOLECULE = GOSfinal.gosMolecule(self.GOSmodel, formula)
	# interp = np.array(self.gosMOLECULE.totalCS)
	# interp = interp*formula.N
	# self.imfpA = interp[0]
	# self.imfpB = interp[1]
	print(" CUTTING SHELLS FROM MODEL")

[RuiFilipeCampos]

MontyCarlo/MontyCarlo/materials/electron/main.pyx

Line 614 in b855154

self.gosMOLECULE = GOSfinal.gosMolecule(self.GOSmodel, formula)

[RuiFilipeCampos]

MontyCarlo/MontyCarlo/materials/electron/GOSfinal.pyx

Lines 86 to 292 in b855154

	cdef class gosMolecule:
	def __reduce__(self):
	this = MAP()
	this.Nat = self.Nat
	import numpy as np
	this.totalCS = np.array(self.totalCS)
	this.number_density = self.number_density
	this.gosATOMS = np.array(self.gosATOMS)
	return rebuildgosMolecule, (this, )
	def __init__(gosMolecule self, CMolecule cmolecule, formula):
	self.Nat = cmolecule.N + 1 #to include CB shell
	self.totalCS = makeLinLin(eax, cmolecule.SIGMA0)
	gosATOMS = []
	cdef CAtom catom
	self.number_density = formula.N
	#cb shell first, most likely one
	#catom = cmolecule.cb #cb inherits from CAtom
	gosATOMS.append(gosCBShell(cmolecule.cb, cmolecule.SIGMA0cb))
	for catom in cmolecule.ATOMS:
	gosATOMS.append(gosAtom(catom, formula))
	self.gosATOMS = np.array(gosATOMS)
	@cython.boundscheck(False)
	@cython.wraparound(False)
	@cython.initializedcheck(False)
	@cython.cdivision(True)
	cdef void sample(gosMolecule self, mixmax_engine* genPTR, int index, double E, PARTICLES *particles):
	cdef double r = genPTR.get_next_float()*(self.totalCS[0, index] + E*self.totalCS[1, index])
	cdef gosAtom atom
	cdef int i = 0
	cdef double cumul = 0
	for i in range(self.Nat):
	atom = self.gosATOMS[i]
	cumul += atom.totalCS[0, index] + E*atom.totalCS[1, index]
	if r < cumul:
	atom.sample(genPTR, index, E, particles)
	break
	def cut(self, double Wcc, shells_for_softIMFP):
	"""
	"""
	newATOMS = []
	currentATOMS = np.array(self.gosATOMS)
	cdef gosAtom atom
	atom = self.gosATOMS[0]
	if (<gosCBShell> atom).Wk > Wcc:
	return False
	shells_for_softIMFP.append([(<gosCBShell> atom).fk, (<gosCBShell> atom).Wk])
	cdef int i = 0
	for atom in currentATOMS[1:]:
	empty = atom.cut(Wcc, shells_for_softIMFP)
	if not empty:
	i += 1
	newATOMS.append(atom)
	if i == 0:
	self.totalCS = np.array(self.totalCS)*0
	return True
	self.Nat = len(newATOMS)
	self.gosATOMS = np.array(newATOMS)
	new_totalCS = np.array(self.totalCS)*0
	for atom in self.gosATOMS:
	new_totalCS += np.array(atom.totalCS)
	self.totalCS = np.array(new_totalCS) #- np.array(atom.totalCS)
	return False
	def makearray(self):
	#cdef double [:, ::1]
	cdef double a, b, Uk, Wk
	arr = [list() for _ in range((len(eax)-1))]
	arr_atoms = list()
	cdef gosAtom atom
	cdef gosShell shell
	# ionizationCS[identify which shell, A OR B, ENERGY_index]
	cdef int lenposs = 0
	cdef int atom_index, shell_index
	for atom_index in range(self.Nat):
	print("molec.Nat", self.Nat)
	atom = self.gosATOMS[atom_index]
	arr_atoms.append(atom.ATOMptr)
	for shell_index in range(atom.Nsh):
	print("atom.Nsh", atom.Nsh)
	shell = atom.gosSHELLS[shell_index]
	Wk = shell.Wk
	if shell.Nsh == 0:
	for i in range(len(eax) - 1):
	CS = np.array(shell.totalCS)
	CS_E = CS[:, i]
	a = CS_E[0]*self.number_density
	b = CS_E[1]*self.number_density
	p1, p2, p3 = shell.p1, shell.p2, shell.p3
	arr[i] += [a*p1[i], b*p1[i], Wk, 0, 0., 0.]
	arr[i] += [a*p2[i], b*p2[i], Wk, 0, 0., 0.]
	arr[i] += [a*p3[i], b*p3[i], Wk, 0, 0., 0.]
	continue
	for j in range(shell.Nsh):
	print("shell.Nsh", shell.Nsh)
	CS = np.array(shell.ionizationCS[j])
	Uk = shell.BE[j]
	lenposs += 6*3
	p1, p2, p3 = shell.p1, shell.p2, shell.p3
	print(Uk)
	for i in range(len(eax) - 1):
	CS_E = CS[:, i]
	a = CS_E[0]*self.number_density
	b = CS_E[1]*self.number_density
	arr[i] += [a*p1[i], b*p1[i], Wk, Uk, <double> atom_index, <double> shell.INDEX[j]]
	arr[i] += [a*p2[i], b*p2[i], Wk, Uk, <double> atom_index, <double> shell.INDEX[j]]
	arr[i] += [a*p3[i], b*p3[i], Wk, Uk, <double> atom_index, <double> shell.INDEX[j]]
	# for j in range(shell.Nsh):
	# a = shell.ionizationCS[j, 0, i]
	# b = shell.ionizationCS[j, 1, i]
	# Uk = shell.BE[j]
	# arr[i] += [a, b, Wk, Uk]
	arr = np.array(arr, order = "C")
	arr_atoms = np.array(arr_atoms, order = "C")
	return arr, len(arr), arr_atoms
	def __getitem__(self, Z):
	cdef gosAtom atom
	for atom in self.gosATOMS:
	if atom.Z == Z:
	return atom
	def plot( self, units = "cm2"):
	import matplotlib.pyplot as plt
	import numpy as np
	fig = plt.figure()
	totalCS = np.array(self.totalCS)
	if units == "cm2":
	plt.plot(eax[:-1], totalCS[0] + totalCS[1]*eax[:-1])
	plt.ylabel("MOLECULE (cm^2) ")
	elif units == "barn":
	plt.plot(eax[:-1], (totalCS[0] + totalCS[1]*eax[:-1])*1e24)
	plt.ylabel("MOLECULE (barn) ")
	plt.xlabel("Energy of Incident Electron (eV)")
	plt.xscale("log"); plt.yscale("log");
	plt.grid(which = "both")
	plt.show()

[RuiFilipeCampos]

MontyCarlo/MontyCarlo/materials/database.py

Lines 280 to 300 in d6feeb5

	def getEEDL(Z):
	"""
	DATABASE DOCS:
	https://drive.google.com/file/d/1ef8Ww_0PPWuLEuwpfv9KOF4wyd75_eOp/
	"""
	Z = int(Z)
	file = str(Z) + ".txt"
	EPDL_path = str(__materials__/'EEDL'/file)
	del file
	#EEDL_path = directory + r"\\EEDL\\" + str(Z) + ".txt"
	EEDL_dict = get_bookmarked_text(EEDL_path)
	for Id in EEDL_dict:
	EEDL_dict[Id] = EEDLtable(EEDL_dict[Id], Id, Z)
	return EEDL_dict