def openConfig(self):
"""
Open and read the configuration of the interface system and simulation
tabs. This file must end with extension .ini.
"""
self.cfgFile = QFileDialog.getOpenFileName(self, 'Open File', '',\
"(*.ini)")[0]
if self.cfgFile == '':
return
with open(self.cfgFile, 'r') as f:
try:
config.read(self.cfgFile)
grid = config.get('System', 'Grid')
materials = config.get('System', 'Materials')
defects = config.get('System', 'Defects')
gen, param = config.get('System', 'Generation rate'),\
config.get('System', 'Generation parameter')
self.setSystem(ev(grid), ev(materials), ev(defects), gen, param)
voltageLoop = config.getboolean('Simulation', 'Voltage loop')
loopValues = config.get('Simulation', 'Loop values')
workDir = config.get('Simulation', 'Working directory')
fileName = config.get('Simulation', 'Simulation name')
ext = config.get('Simulation', 'Extension')
BCs = config.getboolean('Simulation', 'Transverse boundary conditions')
ScnL = config.get('Simulation', 'Electron recombination velocity in 0')
ScpL = config.get('Simulation', 'Hole recombination velocity in 0')
ScnR = config.get('Simulation', 'Electron recombination velocity in L')
ScpR = config.get('Simulation', 'Hole recombination velocity in L')
L_contact = config.get('Simulation', 'Contact boundary condition in 0')
R_contact = config.get('Simulation', 'Contact boundary condition in L')
L_WF = config.get('Simulation', 'Contact work function in 0')
R_WF = config.get('Simulation', 'Contact work function in L')
precision = config.get('Simulation', 'Newton precision')
maxSteps = config.get('Simulation', 'Maximum steps')
useMumps = config.getboolean('Simulation', 'Use Mumps')
iterative = config.getboolean('Simulation', 'Iterative solver')
ramp = config.get('Simulation', 'Generation ramp')
iterPrec = config.get('Simulation', 'Iterative solver precision')
htpy = config.get('Simulation', 'Newton homotopy')
self.setSimulation(voltageLoop, loopValues, workDir, fileName, \
ext, BCs, L_contact, R_contact, L_WF, R_WF,\
ScnL, ScpL, ScnR, ScpR, precision,\
maxSteps, useMumps, iterative, ramp,\
iterPrec, htpy)
f.close()
except Exception:
msg = QMessageBox()
msg.setWindowTitle("Processing error")
msg.setIcon(QMessageBox.Critical)
msg.setText("The file could not be read.")
msg.setEscapeButton(QMessageBox.Ok)
msg.exec_()
return
def parseSettings(settings):
# 1. create grid
grid = settings['grid']
dimension = len(grid)
xgrid = ev(grid[0].lstrip())
xpts = parseGrid(xgrid)
ypts = None
zpts = None
if dimension == 2 or dimension == 3:
ygrid = ev(grid[1].lstrip())
ypts = parseGrid(ygrid)
if dimension == 3:
zgrid = ev(grid[2].lstrip())
zpts = parseGrid(zgrid)
# build a sesame system
system = Builder(xpts, ypts, zpts)
# 2. set materials
materials = settings['materials']
for mat in materials:
location = mat['location']
# define a function that returns true/false dpending on location
f = parseLocation(location, dimension)
system.add_material(mat, f)
# set the doping
N_D = float(mat['N_D'])
if N_D != 0:
system.add_donor(N_D, f)
N_A = float(mat['N_A'])
if N_A != 0:
system.add_acceptor(N_A, f)
# 4. set the defects if present
defects = settings['defects']
defects = defects
for defect in defects:
loc = ev(defect['location'])
N = float(defect['Density'])
E = float(defect['Energy'])
sh = float(defect['sigma_h'])
se = float(defect['sigma_e'])
transition = defect['Transition'].replace("/", ",")
transition = (ev(transition))
if isinstance(loc, float):
system.add_point_defects(loc, N, se, sigma_h=sh, E=E, \
transition=transition)
elif len(loc) == 2:
system.add_line_defects(loc, N, se, sigma_h=sh, E=E,\
transition=transition)
elif len(loc) == 4:
system.add_plane_defects(loc, N, se, sigma_h=sh, E=E,\
transition=transition)
return system
def test_to_dict(self):
t = """
# Serializing / PrettyPrint
Configurative state can be pretty printed and dict-dumped:
"""
md(t)
res = bash_run([
'calc_tree_nav.py av=1 i.D.dv=42 du # du matched to dump',
'calc_tree_nav.py app_var=2 inner.Deep.deep_var=42 dump asdict=true', # long form
])
assert res[0]['res'].strip().startswith('App(app_var=1,')
assert ev(res[1]['res'].strip()) == {
'app_var': 2,
'inner': {
'Deep': {
'deep_var': 42
},
'inner_var': 1
},
}
md("""
The dict format can be piped as is into a config file for subsequent runs.
> Currently we do not serialize function parameter changes.
""")
def up_tri_copy_from_file(filename):
'''Return the upper triagular part of the array in filename. The file
must be a binary .npy file.'''
f = open(filename, 'rb')
# The first 6 bytes are a magic string: exactly "\x93NUMPY".
numpy_string = f.read(6)
# The next 1 byte is an unsigned byte: the major version number
# of the file format, e.g. \x01.
major_ver = ord(f.read(1))
# The next 1 byte is an unsigned byte: the minor version number
# of the file format, e.g. \x00.
minor_ver = ord(f.read(1))
# Check that the version of the file used is what this code can handle.
if ((numpy_string != "\x93NUMPY") or (major_ver != 1) or (minor_ver != 0)):
msg = "Array can only be read from a '\93NUMPY' version 1.0 .npy file "
msg += "not %s %d.%d" % (numpy_string, major_ver, minor_ver)
raise ce.DataError(msg)
# The next 2 bytes form a little-endian unsigned short int: the
# length of the header data HEADER_LEN.
byte2,byte1 = f.read(2)
# Get the value from a short int (2 bytes) to decimal.
header_len = (16**2)*ord(byte1) + ord(byte2)
# The next HEADER_LEN bytes form the header data describing the
# array's format. It is an ASCII string which contains a Python
# literal expression of a dictionary. It is terminated by a newline
# ('\n') and padded with spaces ('\x20') to make the total length of
# the magic string + 4 + HEADER_LEN be evenly divisible by 16 for
# alignment purposes.
raw_dict = f.read(header_len)
# Take off trailing uselessness.
raw_dict = raw_dict.rstrip('\n')
raw_dict = raw_dict.rstrip()
header_dict = ev(raw_dict)
# Check that it is possible to read array.
# "fortran_order" : bool
# Whether the array data is Fortran-contiguous or not.
if (header_dict['fortran_order']):
msg = "Array must be in C order, not fortran order."
raise ce.DataError(msg)
# "shape" : tuple of int
# The shape of the array.
arr_shape = header_dict['shape']
# "descr" : dtype.descr
# An object that can be passed as an argument to the
# numpy.dtype() constructor to create the array's dtype.
dt = np.dtype(header_dict['descr'])
# Where to save all the data. Note this does not make a new array in memory.
num_nums = np.product(arr_shape)
# Assume array is square
row_len = int(np.sqrt(num_nums))
num_rows = row_len
loaded_arr = np.empty((row_len,row_len))
print "Rows copied:"
# Load the array reading n numbers at a time. Reading one number at
# a time is best for memory but requires too many disk seeks for a
# memory map. Loading too many numbers at once requires too much memory,
# so choose a happy medium.
# Assume array is square. Reads n rows of numbers at a time.
rows_to_read = 1000
n = rows_to_read*row_len
row_pos = 0
while (row_pos < num_rows):
# n may not divide evenly into the total number of numbers.
# This statement can only be True at the end of the array.
if ((num_rows-row_pos) < rows_to_read):
rows_to_read = num_rows-row_pos
n = rows_to_read*row_len
read_n_numbers(f,loaded_arr,dt,n,row_len,row_pos)
# Changing row_pos in the function called does not change it here.
row_pos += rows_to_read
sys.stderr.write(str(row_pos)+' ')
print
f.close()
return loaded_arr
def init():
global factor, polygons, colours, direcs, midpoints, rotIns, permu,moveKeys
polygons, colours, direcs, midpoints, rotIns = [], [], [], [], []
moveKeys, permu = {}, []
lines = fullFile.split("\n\n\n")
for i in range(len(lines)):
lines[i] = ev("".join(lines[i].split()))
indivFactor = lines[0]
factor = (y/4*(y<=x) + x/4*(x<y)) / indivFactor
faceLengths = []
for face in lines[1]:
if type(face) == list:
faceDefn = len(polygons)
for piece in face:
if type(piece) == list:
pieceDefn = len(polygons)
points = []
for point in piece:
if type(point) == list:
pointDefn = len(points)
points += [point]
elif type(point) == tuple:
points += [tr(points[pointDefn], point)]
polygons += [offset(array(points), off*indivFactor)]
elif type(piece) == tuple:
polygons += [tr( copy(polygons[pieceDefn]), piece )]
piecesPerFace = len(polygons) - faceDefn
elif type(face) == tuple:
for i in range(piecesPerFace):
polygons += [tr( copy(polygons[faceDefn + i]) , face )]
faceLengths += [int(len(polygons) - sum(faceLengths))]
fls = faceLengths
for face in lines[2]:
if type(face) == tuple:
colours += [face] * fls[0]
elif type(face) == list:
colours += face
fls = fls[1:]
for face in lines[3]:
direcs += [face] * faceLengths[0]
faceLengths = faceLengths[1:]
for polygon in polygons:
midpoints += [centroid(polygon)]
for face in lines[4]:
rotIns += [array(piece) for piece in face]
for i in range(len(lines[5])):
moveKeys[ord(lines[5][i])] = (i+1, arbiRot(lines[6][i]), lines[7][i])
for i in range(len(lines[8])):
permu += [[lines[8][i], list(array(order(lines[8][i]))+1)]]
mostPoints = max(map(len,polygons))
for i in range(len(polygons)):
diff = mostPoints - len(polygons[i])
polygons[i] = array(list(polygons[i]) + ([polygons[i][-1]] * diff))
polygons, colours, direcs = array(polygons), array(colours), array(direcs)
midpoints, rotIns, permu = array(midpoints), array(rotIns), array(permu)
direcs = direcs.astype('float64')
def parseSettings(settings):
# 1. create grid
grid = settings['grid']
dimension = len(grid)
xgrid = ev(grid[0].lstrip())
xpts = parseGrid(xgrid)
ypts = np.array([0])
if dimension == 2:
ygrid = ev(grid[1].lstrip())
ypts = parseGrid(ygrid)
# build a sesame system
if 'periodicBCs' in settings:
system = Builder(xpts, ypts, periodic=settings['periodicBCs'])
else:
system = Builder(xpts, ypts)
# 2. set materials
materials = settings['materials']
for mat in materials:
location = mat['location']
# define a function that returns true/false dpending on location
f = parseLocation(location, dimension)
system.add_material(mat, f)
# set the doping
N_D = float(mat['N_D'])
if N_D != 0:
system.add_donor(N_D, f)
N_A = float(mat['N_A'])
if N_A != 0:
system.add_acceptor(N_A, f)
# 4. set the defects if present
defects = settings['defects']
defects = defects
for defect in defects:
loc = ev(defect['location'])
N = float(defect['Density'])
E = float(defect['Energy'])
sh = float(defect['sigma_h'])
se = float(defect['sigma_e'])
transition = defect['Transition'].replace("/", ",")
transition = (ev(transition))
if isinstance(loc, float):
system.add_defects(loc, N, se, sigma_h=sh, E=E, \
transition=transition)
elif len(loc) == 2:
system.add_defects(loc, N, se, sigma_h=sh, E=E,\
transition=transition)
## ok i would go ahead and construct g for non-manual case here!
lambda_power = np.array([])
power = np.array([])
lambda_alpha = np.array([])
alpha = np.array([])
if settings['use_manual_g'] is False:
########################################
# illumination properties
########################################
# use one sun power spectrum
if settings['ill_onesun'] is True:
lambda_power = onesundata[:, 0]
power = onesundata[:, 1] * 1e-4 # converting to W/cm^2
# read lambda and power
if settings['ill_monochromatic'] is True:
laserlambda = float(settings['ill_wavelength'])
powertot = float(np.asarray(settings['ill_power']))
# generate a distribution, Gaussian with fixed spread of 10 nm
width = 100.
lambda_power = np.linspace(280, 4000, 745)
power = powertot / (2 * np.pi * width**2)**.5 * np.exp(
-(lambda_power - laserlambda)**2 / (2 * width**2))
if not power.any():
power = np.zeros(10)
lambda_power = np.linspace(280, 4000, 745)
########################################
# absorption properties
########################################
if settings['abs_usefile'] is True:
abs_file = settings['abs_file']
lambda_alpha, alpha = parseAlphaFile(abs_file)
if settings['abs_useralpha'] is True:
alpha = np.asarray(settings['abs_alpha'])
lambda_alpha = []
if alpha.size == 0:
alpha = np.zeros(745)
lambda_alpha = np.linspace(280, 4000, 745)
g = getgeneration(lambda_power, power, lambda_alpha, alpha, xpts)
g = np.tile(g, system.ny)
system.generation(g)
return system
def up_tri_copy_from_file(filename):
'''Return the upper triagular part of the array in filename. The file
must be a binary .npy file.'''
f = open(filename, 'rb')
# The first 6 bytes are a magic string: exactly "\x93NUMPY".
numpy_string = f.read(6)
# The next 1 byte is an unsigned byte: the major version number
# of the file format, e.g. \x01.
major_ver = ord(f.read(1))
# The next 1 byte is an unsigned byte: the minor version number
# of the file format, e.g. \x00.
minor_ver = ord(f.read(1))
# Check that the version of the file used is what this code can handle.
if ((numpy_string != "\x93NUMPY") or (major_ver != 1) or (minor_ver != 0)):
msg = "Array can only be read from a '\93NUMPY' version 1.0 .npy file "
msg += "not %s %d.%d" % (numpy_string, major_ver, minor_ver)
raise ce.DataError(msg)
# The next 2 bytes form a little-endian unsigned short int: the
# length of the header data HEADER_LEN.
byte2, byte1 = f.read(2)
# Get the value from a short int (2 bytes) to decimal.
header_len = (16**2) * ord(byte1) + ord(byte2)
# The next HEADER_LEN bytes form the header data describing the
# array's format. It is an ASCII string which contains a Python
# literal expression of a dictionary. It is terminated by a newline
# ('\n') and padded with spaces ('\x20') to make the total length of
# the magic string + 4 + HEADER_LEN be evenly divisible by 16 for
# alignment purposes.
raw_dict = f.read(header_len)
# Take off trailing uselessness.
raw_dict = raw_dict.rstrip('\n')
raw_dict = raw_dict.rstrip()
header_dict = ev(raw_dict)
# Check that it is possible to read array.
# "fortran_order" : bool
# Whether the array data is Fortran-contiguous or not.
if (header_dict['fortran_order']):
msg = "Array must be in C order, not fortran order."
raise ce.DataError(msg)
# "shape" : tuple of int
# The shape of the array.
arr_shape = header_dict['shape']
# "descr" : dtype.descr
# An object that can be passed as an argument to the
# numpy.dtype() constructor to create the array's dtype.
dt = np.dtype(header_dict['descr'])
# Where to save all the data. Note this does not make a new array in memory.
num_nums = np.product(arr_shape)
# Assume array is square
row_len = int(np.sqrt(num_nums))
num_rows = row_len
loaded_arr = np.empty((row_len, row_len))
print "Rows copied:"
# Load the array reading n numbers at a time. Reading one number at
# a time is best for memory but requires too many disk seeks for a
# memory map. Loading too many numbers at once requires too much memory,
# so choose a happy medium.
# Assume array is square. Reads n rows of numbers at a time.
rows_to_read = 1000
n = rows_to_read * row_len
row_pos = 0
while (row_pos < num_rows):
# n may not divide evenly into the total number of numbers.
# This statement can only be True at the end of the array.
if ((num_rows - row_pos) < rows_to_read):
rows_to_read = num_rows - row_pos
n = rows_to_read * row_len
read_n_numbers(f, loaded_arr, dt, n, row_len, row_pos)
# Changing row_pos in the function called does not change it here.
row_pos += rows_to_read
sys.stderr.write(str(row_pos) + ' ')
print
f.close()
return loaded_arr