def __init__(self, src="", id="", loglevel=0, debug=0):
self.ckin = 0
self._owner = 0
self.verbose = 1
fname = os.path.basename(src)
ff = os.path.splitext(fname)
if src:
root = XML.XML_Node(name="doc", src=src, preprocess=1, debug=debug)
if id:
s = root.child(id=id)
else:
s = root.child(name="phase")
self._name = s["id"]
# initialize the equation of state
ThermoPhase.__init__(self, xml_phase=s)
# initialize the kinetics model
ph = [self]
Kinetics.__init__(self, xml_phase=s, phases=ph)
# initialize the transport model
Transport.__init__(self, xml_phase=s, phase=self, model="", loglevel=loglevel)
def __init__(self, src="", id="", loglevel=0, debug=0):
self.ckin = 0
self._owner = 0
self.verbose = 1
fname = os.path.basename(src)
ff = os.path.splitext(fname)
if src:
root = XML.XML_Node(name='doc', src=src, preprocess=1, debug=debug)
if id:
s = root.child(id=id)
else:
s = root.child(name="phase")
self._name = s['id']
# initialize the equation of state
ThermoPhase.__init__(self, xml_phase=s)
# initialize the kinetics model
ph = [self]
Kinetics.__init__(self, xml_phase=s, phases=ph)
# initialize the transport model
Transport.__init__(self,
xml_phase=s,
phase=self,
model='',
loglevel=loglevel)
def __init__(self, src="", root=None, surfaces=[]):
"""
src - CTML or CTI input file name. If more than one phase is
defined in the file, src should be specified as 'filename\#id'
If the file is not CTML, it will be run through the CTI -> CTML
preprocessor first.
root - If a CTML tree has already been read in that contains
the definition of this interface, the root of this tree can be
specified instead of specifying 'src'.
phases - A list of all objects representing the neighboring
surface phases which participate in the reaction mechanism.
"""
self.ckin = 0
self._owner = 0
self.verbose = 1
# src has the form '<filename>#<id>'
fn = src.split("#")
id = ""
if len(fn) > 1:
id = fn[1]
fn = fn[0]
# read in the root element of the tree if not building from
# an already-built XML tree. Enable preprocessing if the film
# is a .cti file instead of XML.
if src and not root:
root = XML.XML_Node(name="doc", src=fn, preprocess=1)
# If an 'id' tag was specified, find the node in the tree with
# that tag
if id:
s = root.child(id=id)
# otherwise, find the first element with tag name 'phase'
# (1D, 2D and 3D phases use the CTML tag name 'phase'
else:
s = root.child(name="phase")
# build the surface phase
EdgePhase.__init__(self, xml_phase=s)
# build the reaction mechanism. This object (representing the
# surface phase) is added to the end of the list of phases
Kinetics.__init__(self, xml_phase=s, phases=surfaces + [self])
def __init__(self, src="", root=None, surfaces=[]):
"""
src - CTML or CTI input file name. If more than one phase is
defined in the file, src should be specified as 'filename\#id'
If the file is not CTML, it will be run through the CTI -> CTML
preprocessor first.
root - If a CTML tree has already been read in that contains
the definition of this interface, the root of this tree can be
specified instead of specifying 'src'.
phases - A list of all objects representing the neighboring
surface phases which participate in the reaction mechanism.
"""
self.ckin = 0
self._owner = 0
self.verbose = 1
# src has the form '<filename>#<id>'
fn = src.split('#')
id = ""
if len(fn) > 1:
id = fn[1]
fn = fn[0]
# read in the root element of the tree if not building from
# an already-built XML tree. Enable preprocessing if the film
# is a .cti file instead of XML.
if src and not root:
root = XML.XML_Node(name='doc', src=fn, preprocess=1)
# If an 'id' tag was specified, find the node in the tree with
# that tag
if id:
s = root.child(id=id)
# otherwise, find the first element with tag name 'phase'
# (1D, 2D and 3D phases use the CTML tag name 'phase'
else:
s = root.child(name="phase")
# build the surface phase
EdgePhase.__init__(self, xml_phase=s)
# build the reaction mechanism. This object (representing the
# surface phase) is added to the end of the list of phases
Kinetics.__init__(self, xml_phase=s, phases=surfaces + [self])
def __init__(self, src="", root=None):
self.ckin = 0
self._owner = 0
self.verbose = 1
# get the 'phase' element
s = XML.find_XML(src=src, root=root, name="phase")
# get the equation of state model
ThermoPhase.__init__(self, xml_phase=s)
# get the kinetics model
Kinetics.__init__(self, xml_phase=s, phases=[self])
SolidTransport.__init__(self, phase=self)
def __init__(self, src="", root=None):
self.ckin = 0
self._owner = 0
self.verbose = 1
# get the 'phase' element
s = XML.find_XML(src=src, root=root, name="phase")
# get the equation of state model
ThermoPhase.__init__(self, xml_phase=s)
# get the kinetics model
Kinetics.__init__(self, xml_phase=s, phases=[self])
SolidTransport.__init__(self, phase=self)
def __del__(self):
Transport.__del__(self)
Kinetics.__del__(self)
ThermoPhase.__del__(self)
def __del__(self):
"""Delete the Edge instance."""
Kinetics.__del__(self)
EdgePhase.__del__(self)
def __del__(self):
"""Delete the Edge instance."""
Kinetics.__del__(self)
EdgePhase.__del__(self)
def __del__(self):
"""Delete the Interface instance."""
Kinetics.__del__(self)
SurfacePhase.__del__(self)
def __del__(self):
"""Delete the Interface instance."""
Kinetics.__del__(self)
SurfacePhase.__del__(self)
def __del__(self):
SolidTransport.__del__(self)
Kinetics.__del__(self)
ThermoPhase.__del__(self)
import sys sys.path.append(r"D:\Desktop\VASP practical\Pymatgen") from Kinetics import Kinetics my_Kinetics = Kinetics(r'D:\Desktop\Date\calculate\AIMDforwaterincalcumsulful\fig1') my_Kinetics.Firstorderreaction(dirr='D'):
#Standard setup stuff
import ROOT as R
RF = R.RooFit
import sys
import os
sys.path.append(os.environ["NEUTRONS"]+'/RooFit')
from pyUtils import *
outputDir = "../figures/"
#fPDF = pdf(outputDir+"kinetics_wall_electron_neutron_comparison.pdf")
from Kinetics import Kinetics
k = Kinetics("k")
k.SetTitle("Muon Kinetics Signals")
k.frame.GetXaxis().SetTitle("time [ns]")
k.frame.GetYaxis().SetTitle("signal")
can = R.TCanvas("can")
k.DrawComponent(k.electron, [RF.LineColor(R.kBlue), RF.Name("el_d")])
k.DrawComponent(k.capture, [RF.LineColor(R.kRed), RF.Name("neu_d")])
k.L_d = 0.01
k.L_q = 0.01
k.DrawComponent(k.electron, [RF.LineColor(R.kBlue), RF.LineStyle(2), RF.Name("el_w")])
k.DrawComponent(k.capture, [RF.LineColor(R.kRed), RF.LineStyle(2), RF.Name("neu_w")])
can.SetLogy()
k.frame.GetXaxis().SetRangeUser(0,4000)
k.frame.GetYaxis().SetRangeUser(1e-7,1e-2)
leg = R.TLegend(0.5,0.7,0.9,0.9)
leg.AddEntry(k.frame.findObject("el_d"), "Decay Electrons (Deuterium)", "l")
