def getNextPosition(self):
# Diffusion is one-way down.
positions = Position.getSameHeightNeighborPositions(self.position)
unoccupied_positions = []
for position in positions:
if not Context.getField().isSiteOccupied(position):
unoccupied_positions.append(position)
if len(unoccupied_positions) == 0:
return self.position
rn = random.randint(0, len(unoccupied_positions)-1)
position = unoccupied_positions[rn]
return Context.getField().getLowestUnoccupiedPosition(position.x, position.y)
def run(self):
logger = logging.getLogger()
logger.info("Clock %d Atom %s adsorb at (%d,%d,%d). " % (Context.getEnv().now, self.id, self.position.x, self.position.y, self.position.z))
while True:
try:
yield self.request
break
except simpy.Interrupt as i:
(reason, info) = i.cause
if reason == 'Stop':
self.status = 'Stop'
elif reason == 'Freeze':
self.status = 'Freeze'
self.info = info
else:
raise ValueError('Unknown interruption! ')
while True:
while True:
if self.status == 'Active':
try:
yield Context.getEnv().timeout(1)
logger.debug("Atom %s at Site (%d,%d,%d) check. " % (self.id, self.position.x, self.position.y, self.position.z))
break
except simpy.Interrupt as i:
(reason, info) = i.cause
if reason == 'Stop':
self.status = 'Stop'
elif reason == 'Freeze':
self.status = 'Freeze'
self.info = info
else:
raise ValueError('Impossible interruption reason! ')
except Exception, e:
logger.error("Atom %s at Site (%d,%d,%d) impossible interruption type. " % (self.id, self.position.x, self.position.y, self.position.k), exc_info=True)
raise(e)
elif self.status == 'Freeze':
wait_for = self.info
try:
yield wait_for.reactivate
self.status = 'Active'
logger.debug('Atom %s at Site (%d,%d,%d) reactivated. % (self.id, self.position.x, self.position.y, self.position.k)')
except simpy.Interrupt as i:
(reason, info) = i.cause
if reason == 'Stop':
self.status = 'Stop'
else:
raise ValueError('Impossible interruption reason! ')
except Exception, e:
logger.error("Atom %s at Site (%d,%d,%d) impossible interruption type. " % (self.id, self.position.x, self.position.y, self.position.k), exc_info=True)
raise(e)
def getNumNeighbors(self):
num_neighbors = 0
positions = Position.getNeighborPositions(self.position)
for position in positions:
if Context.getField().isSiteOccupied(position):
num_neighbors += 1
return num_neighbors
def createOne(cls):
# create one at lowest position
position = Position()
position = Context.getField().getLowestUnoccupiedPosition(position.x, position.y)
if position is None:
return
cls.num += 1
cls(cls.id, position)
cls.id += 1
def createInit(cls, num):
cls.id = 0
while cls.id < num:
while True:
position = Position()
if not Context.getField().isSiteOccupied(position):
cls.num += 1
cls(cls.id, position)
cls.id += 1
break
def __init__(self, id, position):
super(Atom, self).__init__(id, position)
self.process = Context.getEnv().process(self.run())
Context.addAtom(self)
self.request = Context.getField().requestSite(position)
Context.getField().setSiteAtom(position, self)
# deactivate the atom underneath
self.deactivate()
def isDiffuse(self):
# only surface atom diffuse.
if not Context.getField().isSurface(self.position):
return False
rate = 0
num_neighbor = self.getNumNeighbors()
if num_neighbor == 0: # free adatom
rate = Config.diffusion_rate_by_num_neighbor[0]
if num_neighbor == 1:
rate = Config.diffusion_rate_by_num_neighbor[1]
if num_neighbor == 2: # kink atom.
rate = Config.diffusion_rate_by_num_neighbor[2]
if num_neighbor == 3:
rate = Config.diffusion_rate_by_num_neighbor[3]
if num_neighbor == 4:
rate = Config.diffusion_rate_by_num_neighbor[4]
if num_neighbor == 5:
rate = Config.diffusion_rate_by_num_neighbor[5]
if random.random() < rate:
return True
else:
return False
def isDesorb(self):
# only surface atom evaporate
if not Context.getField().isSurface(self.position):
return False
# evaporation rate depends on direct neighbors
rate = 0
num_neighbor = self.getNumNeighbors()
if num_neighbor == 0: # free adatom
rate = Config.desorption_rate_by_num_neighbor[0]
if num_neighbor == 1:
rate = Config.desorption_rate_by_num_neighbor[1]
if num_neighbor == 2: # kink atom.
rate = Config.desorption_rate_by_num_neighbor[2]
if num_neighbor == 3:
rate = Config.desorption_rate_by_num_neighbor[3]
if num_neighbor == 4:
rate = Config.desorption_rate_by_num_neighbor[4]
if num_neighbor == 5:
rate = Config.desorption_rate_by_num_neighbor[5]
if random.random() < rate:
return True
else:
return False
def __init__(self, id, position):
self.id = id
self.position = position
self.status = 'Active'
self.reactivate = Context.getEnv().event()
def requestSite(self, position):
Context.getField().setSiteAtom(position, self)
self.position = position
def releaseSite(self):
Context.getField().releaseSite(self.position, self.request)
Context.getField().setSiteAtom(self.position, None)
def deactivate(self):
if self.position.z == 0:
return
# only deactivate atom underneath
atom = Context.getField().getSiteAtom(Position.getDownPosition(self.position))
atom.process.interrupt(('Freeze', self))
logger.error("Atom %s at Site (%d,%d,%d) impossible interruption type. " % (self.id, self.position.x, self.position.y, self.position.k), exc_info=True)
raise(e)
elif self.status == 'Stop':
Context.removeAtom(self)
self.reactivate.succeed() # reactivate atom underneath
logger.debug('Atom %s process terminated' % self.id)
return
else:
raise ValueError('Unknown statues! ')
if self.isDesorb():
# evaporation affected only by neighbors
self.releaseSite()
self.num -= 1
logger.info("Clock %d Atom %s desorb from (%d,%d,%d). " % (Context.getEnv().now, self.id, self.position.x, self.position.y, self.position.z))
self.status = 'Stop'
elif self.isDiffuse():
next_position = self.getNextPosition()
self.releaseSite()
self.request = Context.getField().requestSite(next_position)
logger.debug('Atom %s requests to Site (%d,%d,%d). Migration' % (self.id, next_position.x, next_position.y, next_position.z))
logger.info('Clock %d Atom %s diffuse from (%d,%d,%d) to (%d,%d,%d).' % (Context.getEnv().now, self.id, self.position.x, self.position.y, self.position.z, next_position.x, next_position.y, next_position.z))
self.requestSite(next_position)
self.reactivate.succeed()
self.reactivate = Context.getEnv().event()
while True:
try:
yield self.request
break
