def readSpectra(self):
self.j = []
self.epsilon = []
self.states = defaultdict(list)
filename = util.getSpectralDataDir() + self.species + '.dat'
with open(filename) as dataFile:
next(dataFile)
for row in dataFile:
if not row.strip():
continue
elif row[0:5] == 'Limit':
self.ionizationEnergy = float(row.rstrip('\n').split(', ')[1])
break
values = row.rstrip('\n').split(', ')
self.j.append(float(values[2]))
self.epsilon.append(float(values[3])*constants.Cm_1ToJoules)
# create new energy state for imported values
state = EnergyState(values[0], values[1], values[2], values[3])
# append to dict organised by core configuration
self.states[state.config].append(state)
def readProperties(self):
jsonFilePath = util.getSpectralDataDir() + '/atomData.json'
with open(jsonFilePath, 'r') as jsonFile:
jsonData = json.load(jsonFile)
speciesProperties = jsonData[self.name]
self.atomicNumber = speciesProperties['atomicNumber']
self.charge = speciesProperties['charge']
self.noElectrons = speciesProperties['noElectrons']
self.Io = speciesProperties['Io'] * self.constants.eVToCm_1
self.cores = []
for key, core in speciesProperties['cores'].items():
self.cores.append(core)
def importFromFile(species):
NistFilename = util.getSpectralDataDir() + species + ' NIST.dat'
badSymbols = [' ', '|', '[', ']', '-', 'i', 't', '+', 'x', '?', '*']
badSymbolsTerm = [' ', '|', '-', 'i', 't', '+', 'x', '?', '*']
with open(NistFilename) as NistFile:
with open(util.getSpectralDataDir() + species + '.dat',
'w') as writeFile:
writeFile.write('config, term, J, epsion\n')
next(NistFile)
row = NistFile.readline()
levelIdx = row.index('L')
termIdx = row.index('T')
jIdx = row.index('J')
next(NistFile)
next(NistFile)
oldTerm = ''
oldConfig = ''
for row in NistFile:
config = row[0:termIdx - 5]
term = row[termIdx - 2:termIdx + 5]
j = row[jIdx - 4:jIdx + 5]
level = row[levelIdx - 5:levelIdx + 15]
for symbol in badSymbols:
j = j.replace(symbol, '')
level = level.replace(symbol, '')
for symbol in badSymbolsTerm:
config = config.replace(symbol, '')
term = term.replace(symbol, '')
if term == '':
term = oldTerm
if config == '':
config = oldConfig
if '/' in j:
j = float(j.split('/')[0]) / float(j.split('/')[1])
j = str(j)
if not row[0].isalpha():
if j.strip() and level != '':
writeFile.write(config + ', ')
writeFile.write(term + ', ')
writeFile.write(j + ', ')
writeFile.write(level + '\n')
else:
writeFile.write('\n')
else:
writeFile.write('Limit, ' + level)
break
oldConfig = config
oldTerm = term
def importFromFile(species):
NistFilename = util.getSpectralDataDir() + species + ' NIST.dat'
badSymbols = [' ', '|', '[', ']', '-', '+', 'x', '?', '*', 'w', 'x']
badSymbolsTerm = [' ', '|', '-', '+', 'x', '?', '*']
with open(NistFilename) as NistFile:
with open(util.getSpectralDataDir() + species + '.dat',
'w') as writeFile:
writeFile.write('config, term, J, epsion\n')
next(NistFile)
row = NistFile.readline()
levelIdx = row.index('L')
termIdx = row.index('T')
jIdx = row.index('J')
next(NistFile)
next(NistFile)
oldTerm = ''
oldConfig = ''
for row in NistFile:
config = row[0:termIdx - 3]
term = row[termIdx - 2:termIdx + 5]
j = row[jIdx - 4:jIdx + 5]
level = row[levelIdx - 5:levelIdx + 15]
for symbol in badSymbols:
j = j.replace(symbol, '')
level = level.replace(symbol, '')
for symbol in badSymbolsTerm:
config = config.replace(symbol, '')
term = term.replace(symbol, '')
if term == '':
term = oldTerm
if config == '':
config = oldConfig
if '<' in config:
openParIdx = config.index('<')
closeParIdx = config.index('>')
coreJ = config[openParIdx:closeParIdx + 1]
config = config[:openParIdx] + str(
coreJ) + config[closeParIdx + 1:]
if '/' in j:
j = float(j.split('/')[0]) / float(j.split('/')[1])
j = str(j)
#### Removes consideration for LK coupling #######
if '[' not in term:
if not row[0].isalpha():
if j.strip():
if level == '':
level = 'None'
writeFile.write(config + ', ')
writeFile.write(term + ', ')
writeFile.write(j + ', ')
writeFile.write(level + '\n')
else:
writeFile.write('\n')
oldConfig = config
oldTerm = term
def readNISTSpectra(species):
NIST = []
filename = util.getSpectralDataDir() + species.name + '.dat'
def isNumber(string):
try:
int(string)
return True
except ValueError:
return False
def formatConfig(string):
nStr = ''
LStr = ''
noElectronsStr = ''
LIdx = len(string) + 1
for i, char in enumerate(string):
if isNumber(char) and i < LIdx:
nStr += char
elif not isNumber(char):
LStr += char
LIdx = i
if isNumber(char) and i >= LIdx:
noElectronsStr += char
n = int(nStr)
L = util.subShellMap.index(LStr)
if noElectronsStr != '':
noElectrons = int(noElectronsStr)
else:
noElectrons = 1
return n, L, noElectrons
def readConfiguration(inputStr):
configs = inputStr.split('.')
coreShells = [SubShell(1, 0, 2)]
coreJ = None
_, _, finalSubShellNoElectrons = formatConfig(configs[-1])
if finalSubShellNoElectrons == 1:
coreTerm = None
for config in configs[:-1]:
if config[0] == '(':
if '<' in config:
openIdx = config.index('<')
closeIdx = config.index('>')
if '/' in config:
slashIdx = config.index('/')
num = float(config[openIdx + 1:slashIdx])
denom = float(config[slashIdx + 1:closeIdx])
coreJ = num / denom
else:
coreJ = float(config[openIdx + 1:closeIdx])
coreS = (float(config[1]) - 1.) / 2.
coreL = util.termMap.index(config[2])
coreTerm = Term(coreL, coreS, coreShells[-1].n)
else:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
core = Core(coreShells, coreTerm)
n, L, noElectrons = formatConfig(configs[-1])
excitedShell = SubShell(n, L, noElectrons)
excitedState = ExcitedState(excitedShell)
else:
for config in configs:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
core = Core(coreShells, None)
excitedState = None
return core, excitedState, coreJ
def readTerm(inputStr):
LStr = ''
SStr = ''
LIdx = len(inputStr) + 1
for i, char in enumerate(inputStr):
if isNumber(char) and i < LIdx:
SStr += char
elif not isNumber(char):
LStr += char
LIdx = i
L = util.termMap.index(LStr)
S = (float(SStr) - 1.) / 2.
return L, S
with open(filename) as dataFile:
next(dataFile)
IDs = []
for row in dataFile:
if not row.strip():
continue
values = row.rstrip('\n').split(', ')
core, excitedState, coreJ = readConfiguration(values[0])
L, S = readTerm(values[1])
if excitedState:
n = excitedState.subShell.n
else:
n = core.maxN
term = Term(L, S, n)
configuration = Configuration(core, excitedState, term)
if configuration.ID not in IDs:
IDs.append(configuration.ID)
NIST.append(configuration)
else:
configuration = NIST[IDs.index(configuration.ID)]
for level in configuration.term.levels:
if configuration.term.L == L and configuration.term.S == S and level.J == float(
values[2]):
if values[3] != 'None':
level.setEnergy(float(values[3]))
return NIST
def readNISTSpectra(species):
NIST = []
filename = util.getSpectralDataDir() + species.name + '.dat'
def isNumber(string):
try:
int(string)
return True
except ValueError:
return False
def formatConfig(string):
nStr = ''
LStr = ''
noElectronsStr = ''
LIdx = len(string) + 1
for i, char in enumerate(string):
if isNumber(char) and i < LIdx:
nStr += char
elif not isNumber(char):
LStr += char
LIdx = i
if isNumber(char) and i >= LIdx:
noElectronsStr += char
n = int(nStr)
L = util.subShellMap.index(LStr)
if noElectronsStr != '':
noElectrons = int(noElectronsStr)
else:
noElectrons = 1
return n, L, noElectrons
def readConfiguration(inputStr):
configs = inputStr.split('.')
coreShells = [SubShell(1, 0, 2)]
#coreTerms = []
#cores = []
_, _, finalSubShellNoElectrons = formatConfig(configs[-1])
if finalSubShellNoElectrons == 1:
for config in configs[:-1]:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
'''
maxElectrons = 2.*(L * 2. + 1.)
if noElectrons < maxElectrons:
coreSLs = getTerms(L, noElectrons)
for coreSL in coreSLs:
termObj = Term(coreSL[0], coreSL[1], n)
cores.append(Core(coreShells, termObj))
'''
core = Core(coreShells, None)
n, L, noElectrons = formatConfig(configs[-1])
excitedShell = SubShell(n, L, noElectrons)
excitedState = ExcitedState(excitedShell)
else:
for config in configs:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
core = Core(coreShells, None)
excitedState = None
return core, excitedState
def readTerm(inputStr):
LStr = ''
SStr = ''
LIdx = len(inputStr) + 1
for i, char in enumerate(inputStr):
if isNumber(char) and i < LIdx:
SStr += char
elif not isNumber(char):
LStr += char
LIdx = i
L = util.termMap.index(LStr)
S = (float(SStr) - 1.) / 2.
return L, S
with open(filename) as dataFile:
next(dataFile)
IDs = []
for row in dataFile:
if not row.strip():
continue
values = row.rstrip('\n').split(', ')
core, excitedState = readConfiguration(values[0])
L, S = readTerm(values[1])
if excitedState:
n = excitedState.subShell.n
coreS = [S - 0.5, S + 0.5]
coreL = clebschGordon(L, excitedState.L)
print(core.atomicNotation,
excitedState.subShell.getSubShellString(), coreS, coreL)
subShellTerms = []
for subShell in core.subShells:
if subShell.noElectrons != (4. * subShell.L + 2.):
subShellTerms.append(
getTerms(subShell.L, subShell.noElectrons))
print(subShellTerms)
coreShellTerms = subShellTerms[
0] #Will need to change this to combine multiple shells
for L in coreL:
for S in coreS:
print([L, S])
if [L, S] in coreShellTerms:
print('matched ', [L, S])
matchedL = L
matchedS = S
break
'''
combinedTerms = [[0], [0]]
for subShell in subShellTerms:
LArr = [x[0] for x in subShell]
SArr = [x[1] for x in subShell]
maxL = max([x + y for x in LArr for y in combinedTerms[0]])
minL = min([abs(x - y) for x in LArr for y in combinedTerms[0]])
maxS = max([x + y for x in SArr for y in combinedTerms[1]])
minS = min([abs(x - y) for x in SArr for y in combinedTerms[1]])
def fRange(x, y):
while x <= y:
yield x
x += 1.
if minL != maxL:
combinedTerms[0] = list(fRange(minL, maxL))
else:
combinedTerms[0] = list(minS)
if minS != maxS:
combinedTerms[1] = list(fRange(minS, maxS))
else:
combinedTerms[0] = list(minS)
print(combinedTerms)
for L in coreL:
for S in coreS:
print([L, S])
if L in combinedTerms[0] and S in combinedTerms[1]:
print('matched', [L, S])
break
'''
coreN = core.maxN
core.term = Term(matchedL, matchedS, coreN)
else:
n = core.maxN
core.term = Term(L, S, n)
term = Term(L, S, n)
if excitedState:
print(excitedState.subShell.getSubShellString(),
term.getTermString(), 'core - ', core.atomicNotation,
core.term.getTermString())
configuration = Configuration(core, excitedState, term)
if configuration.ID not in IDs:
IDs.append(configuration.ID)
NIST.append(configuration)
else:
configuration = NIST[IDs.index(configuration.ID)]
for level in configuration.term.levels:
if configuration.term.L == L and configuration.term.S == S and level.J == float(
values[2]):
level.setEnergy(float(values[3]))
return NIST
def readNISTSpectra(species):
NIST = []
filename = util.getSpectralDataDir() + species.name + '.dat'
def isNumber(string):
try:
int(string)
return True
except ValueError:
return False
def formatConfig(string):
nStr = ''
LStr = ''
noElectronsStr = ''
LIdx = len(string) + 1
for i, char in enumerate(string):
if isNumber(char) and i < LIdx:
nStr += char
elif not isNumber(char):
LStr += char
LIdx = i
if isNumber(char) and i >= LIdx:
noElectronsStr += char
n = int(nStr)
L = util.subShellMap.index(LStr)
if noElectronsStr != '':
noElectrons = int(noElectronsStr)
else:
noElectrons = 1
return n, L, noElectrons
def readConfiguration(inputStr):
configs = inputStr.split('.')
coreShells = []
for config in configs[:-1]:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
core = Core(coreShells, 0)
n, L, noElectrons = formatConfig(configs[-1])
excitedShell = SubShell(n, L, noElectrons)
excitedState = ExcitedState(excitedShell)
#print(core.atomicNotation, excitedState.subShell.getSubShellString())
return core, excitedState
def readTerm(inputStr):
LStr = ''
SStr = ''
LIdx = len(inputStr) + 1
for i, char in enumerate(inputStr):
if isNumber(char) and i < LIdx:
SStr += char
elif not isNumber(char):
LStr += char
LIdx = i
L = util.termMap.index(LStr)
S = (float(SStr) - 1.)/2.
return L, S
with open(filename) as dataFile:
next(dataFile)
IDs = []
for row in dataFile:
if not row.strip():
continue
elif row[0:5] == 'Limit':
ionizationEnergy = float(row.rstrip('\n').split(', ')[1])
break
values = row.rstrip('\n').split(', ')
core, excitedState = readConfiguration(values[0])
configuration = Configuration(core, excitedState)
if configuration.ID not in IDs:
IDs.append(configuration.ID)
NIST.append(configuration)
else:
configuration = NIST[IDs.index(configuration.ID)]
for term in configuration.terms:
for level in term.levels:
#print(term.getTermString())
#print(values[2])#, values[2], values[3])
L, S = readTerm(values[1])
#print(L, S, '\n')
#term.J = values[2]
'''
if term.n < 3:
print('')
print(configuration.ID)
print(term.getTermString(), values[1])
print(term.L, L)
print(term.S, S)
print(level.J, values[2])
'''
if term.L == L and term.S == S and level.J == float(values[2]):
#print('matched')
#print(term.getTermString(), values)
level.setEnergy(float(values[3]))
#if term.n < 3:
#print('match')
#print(level.energy)
#print(term.energy)
#print('')
#level = Level(int(values[2]), float(values[3]))
#term = Term()
#self.j.append(float(values[2]))
#self.epsilon.append(float(values[3])*constants.Cm_1ToJoules)
# create new energy state for imported values
#state = EnergyState(values[0], values[1], values[2], values[3])
# append to dict organised by core configuration
#self.states[state.config].append(state)
return NIST
def readNISTSpectra(species):
NIST = []
filename = util.getSpectralDataDir() + species.name + '.dat'
def isNumber(string):
try:
int(string)
return True
except ValueError:
return False
def formatConfig(string):
nStr = ''
LStr = ''
noElectronsStr = ''
LIdx = len(string) + 1
for i, char in enumerate(string):
if isNumber(char) and i < LIdx:
nStr += char
elif not isNumber(char):
LStr += char
LIdx = i
if isNumber(char) and i >= LIdx:
noElectronsStr += char
n = int(nStr)
L = util.subShellMap.index(LStr)
if noElectronsStr != '':
noElectrons = int(noElectronsStr)
else:
noElectrons = 1
return n, L, noElectrons
def readConfiguration(inputStr):
configs = inputStr.split('.')
coreShells = [SubShell(1, 0, 2)]
for config in configs[:-1]:
n, L, noElectrons = formatConfig(config)
coreShells.append(SubShell(n, L, noElectrons))
core = Core(coreShells, 0)
#print(core.SMax)
n, L, noElectrons = formatConfig(configs[-1])
excitedShell = SubShell(n, L, noElectrons)
excitedState = ExcitedState(excitedShell)
#print(core.atomicNotation, excitedState.subShell.getSubShellString())
return core, excitedState
def readTerm(inputStr):
LStr = ''
SStr = ''
LIdx = len(inputStr) + 1
for i, char in enumerate(inputStr):
if isNumber(char) and i < LIdx:
SStr += char
elif not isNumber(char):
LStr += char
LIdx = i
L = util.termMap.index(LStr)
S = (float(SStr) - 1.)/2.
return L, S
with open(filename) as dataFile:
next(dataFile)
IDs = []
for row in dataFile:
if not row.strip():
continue
'''
elif row[0:5] == 'Limit':
ionizationEnergy = float(row.rstrip('\n').split(', ')[1])
break
'''
values = row.rstrip('\n').split(', ')
#print(values)
core, excitedState = readConfiguration(values[0])
#SArr = clebschGordon(core.maxS, excitedState.S)
#LArr = range(0, max(clebschGordon(core.maxL, excitedState.L))+1)
n = excitedState.subShell.n
'''
for L in LArr:
#print(L)
for S in SArr:
#print(L, S)
termL, termS = readTerm(values[1])
term = Term(termL, termS, n)
#print(term.getTermString())
configuration = Configuration(core, excitedState, term)
if configuration.ID not in IDs:
IDs.append(configuration.ID)
NIST.append(configuration)
else:
configuration = NIST[IDs.index(configuration.ID)]
L, S = readTerm(values[1])
for level in configuration.term.levels:
if configuration.term.L == L and configuration.term.S == S and level.J == float(values[2]):
level.setEnergy(float(values[3]))
'''
L, S = readTerm(values[1])
term = Term(L, S, n)
configuration = Configuration(core, excitedState, term)
if configuration.ID not in IDs:
IDs.append(configuration.ID)
NIST.append(configuration)
else:
configuration = NIST[IDs.index(configuration.ID)]
#print(configuration.term.levels)
for level in configuration.term.levels:
#print(level)
if configuration.term.L == L and configuration.term.S == S and level.J == float(values[2]):
#print(configuration.ID, level.J)
level.setEnergy(float(values[3]))
#print(level.energy)
return NIST
