def __init__(self, h5obj, pfixed, length, temperature, pressure):
"""
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Parameters")
#
# Fixed plasma check
self.pfixed = mh5u.Attrib("pfixed", int(pfixed))
#
# Electrode gap in meters
self.length = mh5u.Attrib("length", length)
#
# Temperature in Kelvin
self.temperature = mh5u.Attrib("temperature", temperature)
#
# Pressure Pascal
self.pressure = mh5u.Attrib("pressure", pressure)
#
ng = (self.pressure() / (constants.Boltzmann * self.temperature()))
self.neutral_density = mh5u.Attrib("neutral_density", ng)
#
self.writable_list = [
self.pfixed, self.length, self.temperature, self.pressure,
self.neutral_density
]
def __init__(self, h5obj, nsections, maxpositive, maxnegative, grid_type):
""" Initial values
"""
self.h5obj = h5obj
# Create group
self.h5path = self.h5obj.create_group("Charge_sections")
#
self.nsections = mh5u.Attrib("NSections", nsections)
#
self.maxpositive = mh5u.Attrib("Max_positive", maxpositive)
#
self.maxnegative = mh5u.Attrib("Max_negative", maxnegative)
if not grid_type['special']:
# charges
charges = np.arange(-maxnegative, maxpositive + 1)
else:
# charges
#charges = np.concatenate((np.arange(-maxnegative, -maxnegative+30),
#np.arange(-14, 6)))
charges = np.concatenate(
(np.arange(-maxnegative, -maxnegative + 30),
np.arange(-maxnegative + 32, -14, 5), np.arange(-14, 6)))
if grid_type['small']:
charges = np.concatenate(
(np.array([-235, -225,
-215]), np.array([-130, -119,
-107]), np.arange(-20, 6)))
#self.maxpositive = 5
#self.maxnegative = -235
print('len charges', len(charges))
#nsecs = len(charges)
#self.nsections = mh5u.Attrib("NSections", nsecs)
if grid_type['medium']:
charges = np.concatenate((np.array([-235, -225,
-215]), np.arange(-130, -106),
np.array([-20, -10, -2, -1, 0, 1])))
#self.maxpositive = 1
#self.maxnegative = -235
#nsecs = len(charges)
#self.nsections = mh5u.Attrib("NSections", nsecs)
print('len charges', len(charges))
if grid_type['big']:
charges = np.concatenate(
(np.arange(-235, -214), np.array([-130, -119, -107]),
np.array([-20, -10, -2, -1, 0, 1])))
#self.maxpositive = 1
#self.maxnegative = -235
#nsecs = len(charges)
#self.nsections = mh5u.Attrib("NSections", nsecs)
print('len charges', len(charges))
self.charges = mh5u.DataSet("Charges", (nsections, ), "f", charges)
#
self.writable_list = [
self.nsections, self.maxpositive, self.maxnegative, self.charges
]
def __init__(self, h5obj, description_text=""):
""" Initial values
"""
self.h5obj = h5obj
# root path
self.h5path = h5obj
# date and time
datetime = str(dt.datetime.now())
#
self.description = mh5u.Attrib("Description", description_text)
#
self.timestamp = mh5u.Attrib("Timestamp", datetime)
#
self.timestamp = mh5u.Attrib("Timestamp", datetime)
#
sysinfo = os.uname()
sysinfostr = ["Sysname", "Nodename", "Release", "Version", "Machine"]
self.sysinfo = [None] * 5
for i, si in enumerate(sysinfostr):
self.sysinfo[i] = mh5u.Attrib(si, str(os.uname()[i]))
# list of lists
writlist = [[self.description, self.timestamp], self.sysinfo]
# flatten list
self.writable_list = [y for x in writlist for y in x]
def __init__(self, h5obj, nsections, rmin, base, power, grid_type):
""" Initial values
"""
self.h5obj = h5obj
#
self.nsections = mh5u.Attrib("NSections", nsections)
#
minvoliface, self.ifaces, self.vols, self.rads, self.diams = compute_sections(
nsections, rmin, base, power, grid_type)
self.miniface = mh5u.Attrib("Min_interface", minvoliface)
#
self.base = mh5u.Attrib("Base", base)
#
self.power = mh5u.Attrib("Power", power)
#
# Create sections
self.interfaces = mh5u.DataSet("Interfaces", (nsections + 1, ), "f",
self.ifaces)
#
self.volumes = mh5u.DataSet("Volumes", (nsections, ), "f", self.vols)
#
self.radii = mh5u.DataSet("Radii", (nsections, ), "f", self.rads)
#
self.diameters = mh5u.DataSet("Diameters", (nsections, ), "f",
self.diams)
# WARNING FIXME horrible hack
self.h5path = self.h5obj.create_group("Volume_sections")
self.writable_list = [
self.nsections, self.miniface, self.base, self.power,
self.interfaces, self.volumes, self.radii, self.diameters
]
def __init__(self, h5obj, emean, ne):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Electrons")
# Set emean electronic mean energy in eV
self.emean = mh5u.Attrib("emean", emean)
#
# Set electronic density 1/m3
self.ne = mh5u.Attrib("ne", ne)
#
self.writable_list = [self.emean, self.ne]
def __init__(self, h5obj, vdw=0, cutoff=0.0, bf=0):
""" Initial values
"""
self.h5obj = h5obj
# Create group
self.h5path = self.h5obj.create_group("vanderWaals_interaction")
#
self.vdw = mh5u.Attrib("On", vdw)
#
self.cutoff = mh5u.Attrib("Cutoff", cutoff)
#
self.bf = mh5u.Attrib("Brute_force", bf)
#
self.writable_list = [self.vdw, self.cutoff, self.bf]
def __init__(self, h5obj, wnu, nucleation_rate, wsg, sgrowth_rate, wco, wch, wsih4, sih4ratio, sih4nmol):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
#
# hdf5 path
self.h5path = self.h5obj.create_group("Rates")
#
# With nucleation
self.wnu = mh5u.Attrib("wnu", int(wnu))
#if not wnu:
#nucleation_rate = 0.0
#
# Nucleation rate
self.nucleation_rate = mh5u.Attrib("nucleation_rate", nucleation_rate)
#
# With surface growth
self.wsg = mh5u.Attrib("wsg", int(wsg))
#if not wsg:
#sgrowth_rate = 0.0
#
# Surface growth rate
self.sgrowth_rate = mh5u.Attrib("sgrowth_rate", sgrowth_rate)
#
# With coagulation
self.wco = mh5u.Attrib("wco", int(wco))
#
# With charging
self.wch = mh5u.Attrib("wch", int(wch))
# With SiH4
self.wsih4 = mh5u.Attrib("wsih4", int(wsih4))
# SiH4 : gas ratio
self.sih4ratio = mh5u.Attrib("sih4ratio", sih4ratio)
# Number of SiH4 per nucleated particle
self.sih4nmol = mh5u.Attrib("sih4nmol", sih4nmol)
# mass of SiH4
sih4mass = 1.67e-27*(28.+4.)
self.sih4mass = mh5u.Attrib("sih4mass", sih4mass)
#
self.writable_list = [self.wnu,
self.nucleation_rate,
self.wsg,
self.sgrowth_rate,
self.wco,
self.wch,
self.wsih4,
self.sih4ratio,
self.sih4nmol,
self.sih4mass]
def __init__(self, h5obj, itemp, ni, imass):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Ions")
# Set ion temperature in Kelvin
self.itemp = mh5u.Attrib("itemp", itemp)
# Set ion density 1/m3s
self.ni = mh5u.Attrib("ni", ni)
# Set ion mass in Kg
self.imass = mh5u.Attrib("imass", imass)
#
self.writable_list = [self.itemp, self.ni, self.imass]
def __init__(self, h5obj, qpivot, temperature, nmdensity):
"""
"""
# WARNING FIXME TODO input validation
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Grid_system")
# pivot in charges
self.qpivot = mh5u.Attrib("Charge_pivot", int(qpivot))
# nanoparticle temperature
self.temperature = mh5u.Attrib("Temperature", temperature)
# nanoparticle mass density
self.nmdensity = mh5u.Attrib("Mass_density", nmdensity)
#
self.writable_list = [self.qpivot, self.temperature, self.nmdensity]
def __init__(self, h5obj, ndeltat, qdeltat, tstop):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Time")
# Set nanoparticle delta t
self.ndeltat = mh5u.Attrib("ndeltat", ndeltat)
#
# Set charging delta t
self.qdeltat = mh5u.Attrib("qdeltat", qdeltat)
#
# Set time stop
self.tstop = mh5u.Attrib("tstop", tstop)
#
self.writable_list = [self.ndeltat,
self.qdeltat,
self.tstop]
def __init__(self, h5obj, nm):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Metastables")
# Set metastable density 1/m3s
self.nm = mh5u.Attrib("nm", nm)
#
self.writable_list = [self.nm]
def __init__(self, h5obj, multiplier, dconstant, method, terms=25):
""" Initial values
"""
self.h5obj = h5obj
# Create group
self.h5path = self.h5obj.create_group("Electrostatic_interaction")
#
self.multiplier = mh5u.Attrib("Multiplier", multiplier)
#
self.dconstant = mh5u.Attrib("Dielectric_constant", dconstant)
#
self.method = mh5u.Attrib("Method", method)
#
if method == 2: # method == 2 is Coulomb
terms = 0
self.terms = mh5u.Attrib("Terms", terms)
#
self.writable_list = [
self.multiplier, self.dconstant, self.method, self.terms
]
def __init__(self, h5obj, tunnel, eaffinity, accfactor):
"""
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Nanoparticles")
#
# Fixed tunnel current check
self.tunnel = mh5u.Attrib("tunnel", int(tunnel))
#
# Electron affinity
self.eaffinity = mh5u.Attrib("eaffinity", eaffinity)
#
# Accomodation factor
self.accfactor = mh5u.Attrib("accfactor", accfactor)
#
self.writable_list = [self.tunnel,
self.eaffinity,
self.accfactor]
def __init__(self, h5obj, indens, qtol, distribution, peakpos, width,
withchargewidth, chargewidth):
""" Initial values
"""
# hdf5 file object
self.h5obj = h5obj
# hdf5 path
self.h5path = self.h5obj.create_group("Density")
# Set nanoparticle initial density
self.indens = mh5u.Attrib("indens", indens)
#
# Set qtol
self.qtol = mh5u.Attrib("qtol", qtol)
#
# Set distribution
self.distribution = mh5u.Attrib("distribution", distribution)
#
# Set peakpos
self.peakpos = mh5u.Attrib("peakpos", peakpos)
#
# Set width (in terms of section number)
self.width = mh5u.Attrib("width", width)
#
# Set chargewidth
self.chargewidth = mh5u.Attrib("chargewidth", int(withchargewidth))
self.chargenegwidth = mh5u.Attrib("chargenegwidth", chargewidth["negative"])
self.chargeposwidth = mh5u.Attrib("chargeposwidth", chargewidth["positive"])
self.writable_list = [self.indens,
self.qtol,
self.distribution,
self.peakpos,
self.width,
self.chargewidth,
self.chargenegwidth,
self.chargeposwidth]