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BUG: key error about montycarlo HOT 5 CLOSED

ruifilipecampos commented on August 30, 2024

BUG: key error

from montycarlo.

Comments (5)

RuiFilipeCampos commented on August 30, 2024

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

from montycarlo.

RuiFilipeCampos commented on August 30, 2024

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")

from montycarlo.

RuiFilipeCampos commented on August 30, 2024

MontyCarlo/MontyCarlo/materials/electron/main.pyx

Line 614 in b855154

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

from montycarlo.

RuiFilipeCampos commented on August 30, 2024

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()

from montycarlo.

RuiFilipeCampos commented on August 30, 2024

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

from montycarlo.

BUG: key error about montycarlo HOT 5 CLOSED

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	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")

	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] + Eself.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] += [ap1[i], bp1[i], Wk, 0, 0., 0.]
	arr[i] += [ap2[i], bp2[i], Wk, 0, 0., 0.]
	arr[i] += [ap3[i], bp3[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] += [ap1[i], bp1[i], Wk, Uk, <double> atom_index, <double> shell.INDEX[j]]
	arr[i] += [ap2[i], bp2[i], Wk, Uk, <double> atom_index, <double> shell.INDEX[j]]
	arr[i] += [ap3[i], bp3[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()

	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