def birthConstant(size):
# dx/dt =
# n is the size.
# p is the propensity factor.
# t is the time.
# n * 2^(p t) = 2^t
# n = 2^(t (1 - p))
# log_2 n = t (1 - p)
# (1/t) log_2 n = (1 - p)
# p = 1 - (1/t) log_2 n
#p = 1 - (1./15.) * math.log(size) / math.log(2)
# n 2^t = 2^15
# n = 2^(15 - t)
# log_2 n = 15 - t
# t = 15 - log_2 n
file = open('Birth' + str(size) + 'Constant.txt', 'w')
# Propensity factors sum to unity.
file.write('%s' % Birth.output(size, 1, lambda n: 1))
# number of frames
file.write('1\n')
# list of frame times
file.write('%f\n' % (15 - math.log(size) / math.log(2)))
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def deathConstant(size, initialAmount):
file = open('Death' + str(size) + 'Constant.txt', 'w')
file.write('%s' % Death.output(size, initialAmount, lambda n: 1))
# number of frames
file.write('1\n')
# list of frame times
file.write('1000\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def decayingDimerizingConstant(size):
file = open('DecayingDimerizing' + str(size) + '.txt', 'w')
file.write('%s' % DecayingDimerizing.output(size))
# number of frames
file.write('1\n')
# list of frame times
file.write('30\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def immigrationConstant(size):
file = open('Immigration' + str(size) + 'Constant.txt', 'w')
file.write('%s' % Immigration.output(size, 0,
lambda n: 1. / size))
# number of frames
file.write('1\n')
# list of frame times
file.write('1000000\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def deathGeometric(size, initialAmount, factor):
file = open('Death' + str(size) + 'Geometric' + str(factor) + '.txt', 'w')
file.write('%s' % Death.output(size, initialAmount,
lambda n: factor**(float(n)/max(size-1,1))))
# number of frames
file.write('1\n')
# list of frame times
file.write('1000\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def immigrationGeometric(size, factor):
file = open('Immigration' + str(size) + 'Geometric' + str(factor) +
'.txt', 'w')
sum = 0
for n in range(size):
sum += factor**(float(n)/max(size-1,1))
file.write('%s' % Immigration.output(size, 0,
lambda n: factor**(float(n)/max(size-1,1)) / sum))
# number of frames
file.write('1\n')
# list of frame times
file.write('1000000\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
def birthGeometric(size, factor):
file = open('Birth' + str(size) + 'Geometric' + str(factor) + '.txt', 'w')
# Propensity factors sum to unity.
sum = 0
for n in range(size):
sum += factor**(float(n)/max(size-1,1))
file.write('%s' % Birth.output(size, 1,
lambda n: factor**(float(n)/max(size-1,1)) / sum))
# number of frames
file.write('1\n')
# list of frame times
file.write('1000\n')
# maximum allowed steps
file.write('0\n')
# list of MT 19937 state
file.write('%s' % MT19937.output())
# number of trajectories
file.write('1\n')
numberOfBins = int(sys.argv[3])
# The recorded species.
recordedSpecies = [int(x) for x in sys.argv[4:-1]]
# The number of trajectories.
numberOfTrajectories = int(sys.argv[-1])
#
# Write the input file.
#
# Number of frames
print '1'
# List of frame times
print endTime
# Maximum allowed steps
print maximumAllowedSteps
# Number of species to record.
print len(recordedSpecies)
# List of species to record.
print ('%s ' * len(recordedSpecies)) % tuple(recordedSpecies)
# Number of bins.
print numberOfBins
# Number of parameters.
print '0'
# Empty line for the parameters.
print ''
# List of MT 19937 state
sys.stdout.write(MT19937.output())
# Number of trajectories
print numberOfTrajectories