class Experiment:
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP, ATOM_ATT = 0, 1, 2, 3, 4, 5
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = 0, 1, 2
# Monomer Temp
moleculeTemp1 = {'atomList': map(Atom.fromTuple, [\
(ATOM_MONOMER,0,0), \
(ATOM_REP,0,1),(ATOM_REP,1,0),(ATOM_REP,-1,0), \
(ATOM_REP,1,1),(ATOM_REP,-1,1)]), 'dir': (0,1)}
# I Dimer
moleculeTemp2 = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)])
# L Dimer
moleculeTemp3 = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0 ),(ATOM_SITE, 0, 0)])
def __init__(\
self, dimX, dimY, energyScale, rate, \
monomerAppear, monomerVanish, dimerVanish, dimerBreak, \
monomerInitNum, dimer1InitNum, dimer2InitNum):
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.lat = Lattice(dimX, dimY)
self.energyScale = energyScale
self.rate = rate
self.monomerNum = monomerInitNum
self.dimer1Num = dimer1InitNum
self.dimer2Num = dimer2InitNum
self.monomerAppear = monomerAppear
self.monomerVanish = monomerVanish
self.dimerVanish = dimerVanish
self.dimerBreak = dimerBreak
self.__initVars()
self.lat.setAtomTypeNum(6)
self.lat.setEnergyMatrix(array([\
[ 5, 5, 5, -3, 0, 0],\
[ 5, 5, 5, 0, 3, -3],\
[ 5, 5, 5, 0, 3, -3],\
[-3, 0, 0, 0, 0, 0],\
[ 0, 3, 3, 0, 0, 0],\
[ 0, -3, -3, 0, 0, 0]]) * self.energyScale)
self.lat.bindingEnergy = -5.0 * self.energyScale;
mNum = monomerInitNum + dimer1InitNum + dimer2InitNum
self.moleculeNum = mNum
initX = randint(0, self.lat.dimX, mNum)
initY = randint(0, self.lat.dimY, mNum)
for n in range(self.monomerNum):
self.lat.addMolecule(Molecule(MOL_MONOMER, initX[n], initY[n], self.moleculeTemp1))
for n in range(self.dimer1Num):
self.lat.addMolecule(Molecule(MOL_DIMER1, initX[n], initY[n], self.moleculeTemp2))
for n in range(self.dimer2Num):
self.lat.addMolecule(Molecule(MOL_DIMER2, initX[n], initY[n], self.moleculeTemp3))
def __initVars(self):
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP, self.ATOM_ATT = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE, self.ATOM_REP, self.ATOM_ATT
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.newDimerTemp = range(8)
self.newDimerTemp[0] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, 1, -1)] )
self.newDimerTemp[1] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, -1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[2] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)] )
self.newDimerTemp[3] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, -1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, -1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[4] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, 1), (ATOM_SITE, -1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[5] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, 1), (ATOM_SITE, 1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[6] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, -1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[7] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.reactDirMap = [[1,0],[-1,0],[0,1],[0,-1],[1,1],[-1,1],[-1,-1],[1,-1]]
colorScale = ( [
[0.20, 0.20, 0.20],\
[0.30, 0.00, 0.00],\
[0.00, 0.30, 0.00],\
[0.00, 0.00, 0.00],\
[0.05, 0.05, 0.05],\
[0.05, 0.05, 0.05]] )
def colorMap(self, lattice):
return clip(tensordot(lattice.atomNumMap, self.colorScale, axes=([0,0])), 0, 1)
def run(self, simulationTime, outputPeriod, display, outputFileName):
simTime = simulationTime
#display = display
#outputFileName = outputFileName
lat = self.lat
reactDirMap = self.reactDirMap
moleculeNum = self.moleculeNum
moleculeTemp1 = self.moleculeTemp1
newDimerTemp = self.newDimerTemp
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE, self.ATOM_REP
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
if outputFileName == None:
fileFlag = False
else:
fileFlag = True
file = open(outputFileName, 'w')
if display:
fig = figure()
img = imshow(self.colorMap(lat), interpolation='none')
ioff()
newDimerNum = zeros((3,3), int)
tMoveMol = zeros(simTime, int)
tMoveDir = zeros(simTime, int)
tMoveDis = zeros(simTime, int)
tMoveProb = zeros(simTime)
rMoveMol = zeros(simTime, int)
rMoveDir = zeros(simTime, int)
rMoveProb = zeros(simTime)
reactMol = zeros(simTime, int)
reactDir = zeros(simTime, int)
reactAtom = zeros(simTime, int)
reactProb = rand(simTime)
degProb = rand(simTime)
newX = zeros(simTime, int)
newY = zeros(simTime, int)
newProb = rand(simTime)
bindProb = rand(simTime)
for t in range(simTime):
# Translate one molecule
tMoveMol[t] = randint(0, lat.moleculeNum)
tMoveDir[t] = randint(0, 2)
tMoveDis[t] = randint(0, 2) * 2 - 1
tMoveProb[t] = rand()
dx = tMoveDis[t] * tMoveDir[t]
dy = tMoveDis[t] * (1 - tMoveDir[t])
lat.translateMoleculeByIndex(tMoveMol[t], dx, dy, tMoveProb[t])
# Rotate one molecule
rMoveDir[t] = randint(0, 2)
rMoveMol[t] = randint(0, lat.moleculeNum)
rMoveProb[t] = rand()
if lat.moleculeList[rMoveMol[t]] != MOL_MONOMER:
if rMoveDir[t] == 0:
lat.rotateMoleculeCWByIndex(rMoveMol[t], rMoveProb[t])
else:
lat.rotateMoleculeCCWByIndex(rMoveMol[t], rMoveProb[t])
if reactProb[t] < self.rate:
# Pick one monomer atom and see if a dimer can be formed
molN = len(lat.atomList[ATOM_MONOMER]) + len(lat.atomList[ATOM_DIMER1])/2 + len(lat.atomList[ATOM_DIMER2])/2;
reactAtom[t] = randint(0, molN)
if reactAtom[t] < len(lat.atomList[ATOM_MONOMER]):
ra = lat.atomList[ATOM_MONOMER][reactAtom[t]]
rd = reactDir[t] = randint(0, 8)
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
#anl = lat.getAtomNumAt(x2, y2)
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER and ra.parent.dir == ra2.parent.dir:
# I-shaped dimer
if rd < 4:
lat.addMolecule(Molecule(MOL_DIMER1, ra.x, ra.y, newDimerTemp[rd]))
# L-shaped dimer
else:
lat.addMolecule(Molecule(MOL_DIMER2, ra2.x, ra.y, newDimerTemp[rd]))
newDimerNum[ra.parent.type, ra2.parent.type] = newDimerNum[ra.parent.type, ra2.parent.type] + 1
# Remove the involved monomers
for atom in [ra, ra2]:
rm = atom.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
lat.raiseMolecule(rm)
atom.type = ATOM_SITE
lat.layMolecule(rm)
break
reactMol[t] = randint(0, lat.moleculeNum)
rm = lat.moleculeList[reactMol[t]]
# Death of monomer
if rm.type == MOL_MONOMER:
if degProb[t] < self.monomerVanish:
lat.removeMolecule(rm)
elif (rm.type == MOL_DIMER1 or rm.type == MOL_DIMER2):
# Death of dimer
if degProb[t] < self.dimerVanish:
for atom in rm.atomList:
if atom.type == ATOM_MONOMER:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
moleculeNum -= 1
# Degradation of dimer into monomers
elif degProb[t] > (1-self.dimerBreak):
for atom in rm.atomList:
if atom.type != ATOM_SITE:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
else:
pass
#for atom in rm.atomList:
# # Attach monomer to adsorption site of dimer
# if atom.type == ATOM_SITE:
# aL1 = lat.getAtomListAt(atom.x, atom.y)
# for atom1 in filter(lambda x: x.parent.type == MOL_MONOMER, aL1):
# lat.raiseMolecule(rm)
# atom.type = ATOM_MONOMER
# lat.layMolecule(rm)
# lat.removeMolecule(atom1.parent)
# break
# # Detach monomer from adsorption site of dimer
# elif atom.type == ATOM_MONOMER:
# if bindProb[t] < min(1,exp(atom.copies*lat.bindingEnergy)):
# lat.raiseMolecule(rm)
# atom.type = ATOM_SITE
# lat.layMolecule(rm)
# lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
# Add monomers randomly to the system
if newProb[t] < self.monomerAppear/lat.moleculeNum:
newX[t] = randint(floor(lat.dimX*0.0), floor(lat.dimX*1.0))
newY[t] = randint(floor(lat.dimY*0.0), floor(lat.dimY*1.0))
lat.addMolecule(Molecule(MOL_MONOMER, newX[t], newY[t], moleculeTemp1))
# Update the animation per ## moves
if (t+1)%(outputPeriod) == 0:
if display:
img.set_array(self.colorMap(lat))
draw()
if fileFlag:
file.write('# New Dimer Num Per Interval\n')
for mt1 in newDimerNum:
file.write('# ')
for mt2 in mt1:
file.write('{} '.format(mt2))
file.write('\n')
file.write('# \n')
newDimerNum = newDimerNum * 0;
for atomType in lat.atomNumMap:
for row in atomType:
for col in row:
file.write('{} '.format(col))
file.write('\n')
file.write('\n')
file.write('\n')
if fileFlag:
file.close()
class Experiment:
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = 0, 1, 2, 3
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = 0, 1, 2
# Monomer Temp
moleculeTemp1 = map(Atom.fromTuple, [\
(ATOM_MONOMER,0,0)])
# I Dimer
moleculeTemp2 = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)])
# L Dimer
moleculeTemp3 = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
def __init__(\
self, dimX, dimY, energyScale, rate1, rate2, cat, \
monomerAppear, monomerVanish, dimerVanish, dimerBreak, \
monomerInitNum, dimer1InitNum, dimer2InitNum):
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.lat = Lattice(dimX, dimY)
self.energyScale = energyScale
self.rate1 = rate1
self.rate2 = rate2
self.cat = cat
self.monomerNum = monomerInitNum
self.dimer1Num = dimer1InitNum
self.dimer2Num = dimer2InitNum
self.monomerAppear = monomerAppear
self.monomerVanish = monomerVanish
self.dimerVanish = dimerVanish
self.dimerBreak = dimerBreak
self.__initVars()
self.lat.setAtomTypeNum(4)
self.lat.setEnergyMatrix(array([\
[ 2, 2, 2, 0],\
[ 2, 2, 2, 0],\
[ 2, 2, 2, 0],\
[ 0, 0, 0, 0]]) * self.energyScale)
self.lat.bindingEnergy = -1.0 * self.energyScale;
mNum = monomerInitNum + dimer1InitNum + dimer2InitNum
self.moleculeNum = mNum
initX = randint(0, self.lat.dimX, mNum)
initY = randint(0, self.lat.dimY, mNum)
for n in range(self.monomerNum):
self.lat.addMolecule(Molecule(MOL_MONOMER, initX[n], initY[n], self.moleculeTemp1))
for n in range(self.dimer1Num):
self.lat.addMolecule(Molecule(MOL_DIMER1, initX[n], initY[n], self.moleculeTemp2))
for n in range(self.dimer2Num):
self.lat.addMolecule(Molecule(MOL_DIMER2, initX[n], initY[n], self.moleculeTemp3))
def __initVars(self):
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.newDimerTemp = range(8)
self.newDimerTemp[0] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, 1, -1)] )
self.newDimerTemp[1] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, -1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[2] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)] )
self.newDimerTemp[3] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, -1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, -1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[4] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, 1), (ATOM_SITE, -1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[5] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, 1), (ATOM_SITE, 1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[6] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, -1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[7] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.reactDirMap = [[1,0],[-1,0],[0,1],[0,-1],[1,1],[-1,1],[-1,-1],[1,-1]]
colorScale = ( [
[0.20, 0.20, 0.20],\
[0.30, 0.00, 0.00],\
[0.00, 0.30, 0.00],\
[0.05, 0.05, 0.05]] )
def colorMap(self, lattice):
return clip(tensordot(lattice.atomNumMap, self.colorScale, axes=([0,0])), 0, 1)
def run(self, simulationTime, outputPeriod, display, outputFileName):
simTime = simulationTime
#display = display
#outputFileName = outputFileName
lat = self.lat
colorMap = self.colorMap
reactDirMap = self.reactDirMap
moleculeNum = self.moleculeNum
moleculeTemp1 = self.moleculeTemp1
newDimerTemp = self.newDimerTemp
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
if outputFileName == None:
fileFlag = False
else:
fileFlag = True
file = open(outputFileName, 'w')
if display:
fig = figure()
img = imshow(self.colorMap(lat), interpolation='none')
ioff()
lat.newDimerNum = zeros((3,3), int)
tMoveMol = zeros(simTime, int)
tMoveDir = zeros(simTime, int)
tMoveDis = zeros(simTime, int)
tMoveProb = zeros(simTime)
rMoveMol = zeros(simTime, int)
rMoveDir = zeros(simTime, int)
rMoveProb = zeros(simTime)
reactMol = zeros(simTime, int)
reactDir = zeros(simTime, int)
reactAtom = zeros(simTime, int)
reactProb = rand(simTime)
degProb = rand(simTime)
newX = zeros(simTime, int)
newY = zeros(simTime, int)
newProb = rand(simTime)
bindProb = rand(simTime)
def expRandTime(rate=1.):
if rate > 0.:
return -log(rand())/rate
else:
return float('inf')
class Movement:
def reset(self):
newSpeed = float(self.speedFunc())
if newSpeed > 0.:
self.wait = self.timeFunc()/newSpeed
self.currentSpeed = newSpeed
else:
self.wait = float('inf')
self.currentSpeed = 0.
return self.wait
def updateParam(self):
newSpeed = float(self.speedFunc())
if newSpeed == self.currentSpeed:
pass
elif self.currentSpeed > 0.:
if newSpeed > 0.:
self.wait = self.wait * (self.currentSpeed/newSpeed)
self.currentSpeed = newSpeed
else:
self.wait = float('inf')
self.currentSpeed = 0.
else:
return self.reset()
def __call__(self):
return self.moveFunc(self)
def __init__(self,moveFunc,timeFunc,speedFunc):
self.moveFunc = moveFunc
self.timeFunc = timeFunc
self.speedFunc = speedFunc
self.currentSpeed = 0.
self.wait = 0.
def doTranslation(self):
# Translate one molecule
tMoveMol = randint(0, lat.moleculeNum)
tMoveDir = randint(0, 2)
tMoveDis = randint(0, 2) * 2 - 1
tMoveProb = rand()
dx = tMoveDis * tMoveDir
dy = tMoveDis * (1 - tMoveDir)
lat.translateMoleculeByIndex(tMoveMol, dx, dy, tMoveProb)
return False
def doRotation(self):
# Rotate one molecule
rMoveDir = randint(0, 2)
rMoveMol = randint(0, lat.moleculeNum)
rMoveProb = rand()
if lat.moleculeList[rMoveMol] != MOL_MONOMER:
if rMoveDir == 0:
lat.rotateMoleculeCWByIndex(rMoveMol, rMoveProb)
else:
lat.rotateMoleculeCCWByIndex(rMoveMol, rMoveProb)
return False
def subVacateMonomer(ra):
rm = ra.parent
rm.boundMonomer -= ra.copies
lat.raiseMolecule(rm)
ra.type = ATOM_SITE
lat.layMolecule(rm)
def subGetMonomer(ra):
rm = ra.parent
rm.boundMonomer += ra.copies
lat.raiseMolecule(rm)
ra.type = ATOM_MONOMER
lat.layMolecule(rm)
def doAttachDetach(self):
lm = lat.atomList[ATOM_MONOMER]
ra = lm[randint(0,len(lm))]
if ra.parent.type == MOL_MONOMER:
ls = filter(lambda a:a.type == ATOM_SITE,lat.getAtomListAt(ra.x, ra.y))
if len(ls) == 0:
return False
ra2 = ls[0]
subGetMonomer(ls[0])
lat.removeMolecule(ra.parent)
return True
else:
p = rand()
if p < exp(ra.copies*lat.bindingEnergy):
subVacateMonomer(ra)
lat.addMolecule(Molecule(MOL_MONOMER, ra.x, ra.y, moleculeTemp1))
return True
return False
def doMonomerBirth(self):
newX = randint(floor(lat.dimX*0.0), floor(lat.dimX*1.0))
newY = randint(floor(lat.dimY*0.0), floor(lat.dimY*1.0))
lat.addMolecule(Molecule(MOL_MONOMER, newX, newY, moleculeTemp1))
return True
def doMonomerBirth2(self):
newX = randint(floor(lat.dimX*0.4), floor(lat.dimX*0.6))
newY = randint(floor(lat.dimY*0.4), floor(lat.dimY*0.6))
lat.addMolecule(Molecule(MOL_MONOMER, newX, newY, moleculeTemp1))
return True
def doMonomerDeath(self):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
rm = ra.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
return True
else:
p = rand()
if p < exp(ra.copies*lat.bindingEnergy):
subVacateMonomer(ra)
return True
return False
def subRemoveDimer(rm):
for atom in rm.atomList:
if atom.type == ATOM_MONOMER:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
def doDimerDeath(self):
a1,a2 = lat.atomList[ATOM_DIMER1],lat.atomList[ATOM_DIMER2]
n1,n2 = len(a1),len(a2)
m = randint(0,n1+n2)
if m < n1:
ra = a1[m]
else:
ra = a2[m-n1]
subRemoveDimer(ra.parent)
return True
def subMakeDimer(type,rd,ra,ra2):
# I-shaped dimer
if type == 0:
lat.addMolecule(Molecule(MOL_DIMER1, ra.x, ra.y, newDimerTemp[rd]))
# L-shaped dimer
else:
lat.addMolecule(Molecule(MOL_DIMER2, ra2.x, ra.y, newDimerTemp[rd]))
lat.newDimerNum[ra.parent.type, ra2.parent.type] += 1
# Remove the involved monomers
for atom in [ra, ra2]:
rm = atom.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
subVacateMonomer(atom)
def doDimerization(self,type=0):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
rd = randint(0, 4) + type*4
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER:
subMakeDimer(type,rd,ra,ra2)
return True
return False
doDimerizationI = lambda s: doDimerization(s,0)
doDimerizationL = lambda s: doDimerization(s,1)
def doCatDimerization(self,type=0):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
if ra.parent.type != MOL_MONOMER:
rd = randint(0, 4) + type*4
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER and ra2.parent == ra.parent:
subMakeDimer(type,rd,ra,ra2)
return True
return False
doCatDimerizationI = lambda s: doCatDimerization(s,0)
doCatDimerizationL = lambda s: doCatDimerization(s,1)
def doAbsorbingBC(self):
i = randint(0, lat.moleculeNum)
rm = lat.moleculeList[i]
x = rm.x%lat.dimX
y = rm.y%lat.dimY
if 0 == x*y:
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
subRemoveDimer(rm)
return True
return False
def doDraw(self):
img.set_array(colorMap(lat))
draw()
return False
def doRecord(self):
newDimerNum = lat.newDimerNum
file.write('# New Dimer Num Per Interval\n')
for mt1 in newDimerNum:
file.write('# ')
for mt2 in mt1:
file.write('{} '.format(mt2))
file.write('\n')
file.write('# \n')
newDimerNum *= 0
for atomType in lat.atomNumMap:
for row in atomType:
for col in row:
file.write('{} '.format(col))
file.write('\n')
file.write('\n')
file.write('\n')
return False
mvList = [ \
Movement(doTranslation,expRandTime,lambda:lat.moleculeNum), \
Movement(doRotation,expRandTime,lambda:lat.moleculeNum), \
Movement(doAbsorbingBC,expRandTime,lambda:5. * lat.moleculeNum), \
Movement(doAttachDetach,expRandTime,lambda:5. * len(lat.atomList[ATOM_MONOMER])), \
#Movement(doDimerizationI,expRandTime,lambda:self.rate1 * len(lat.atomList[ATOM_MONOMER])), \
#Movement(doDimerizationL,expRandTime,lambda:self.rate2 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doCatDimerizationI,expRandTime,lambda:self.cat * self.rate1 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doCatDimerizationL,expRandTime,lambda:self.cat * self.rate2 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doDimerDeath,expRandTime,lambda:self.dimerVanish * (len(lat.atomList[ATOM_DIMER1])+len(lat.atomList[ATOM_DIMER2]))/2), \
Movement(doMonomerBirth2,expRandTime,lambda:self.monomerAppear), \
Movement(doMonomerDeath,expRandTime,lambda:self.monomerVanish * len(lat.atomList[ATOM_MONOMER])) ]
if display:
mvList.append(Movement(doDraw,lambda:1,lambda:1./outputPeriod))
if fileFlag:
mv = Movement(doRecord,lambda:1,lambda:1./outputPeriod)
#mv.newDimerNum = newDimerNum
mvList.append(mv)
t = 0
for m in mvList:
m.reset()
mvList.sort(key=attrgetter('wait'))
wait = mvList[0].wait
t += wait
while t < simTime:
for m in mvList:
m.wait -= wait
isToUpdate = mvList[0]()
if isToUpdate:
for m in mvList:
m.updateParam()
mvList[0].reset()
mvList.sort(key=attrgetter('wait'))
wait = mvList[0].wait
t += wait
if fileFlag:
file.close()
return
