m.set_all_repulsive()
s.set_model(m)
s.throw_in_particles(S, N / 2, box1)
s.throw_in_particles(P, N / 2, box1)
#l = Logger('dimer')
l = None
interrupter = None
if l is not None:
interrupter = FixedIntervalInterrupter(s, 1e-7, l.log)
import myrandom
myrandom.seed(0)
def profrun():
if l is not None:
l.start(s)
for _ in xrange(15000):
if interrupter is not None:
interrupter.step()
else:
s.step()
PROFMODE = True
if PROFMODE:
# gfrd
from model2 import *
from egfrd import *
from logger import *
import myrandom
# for calculating and sampling
import numpy as np
import matplotlib.pyplot as plt
try:
import mpmath as m
except ImportError:
import sympy.mpmath as m
myrandom.seed(0)
# settings and parameters for the sampling run
#
# files
# --------------ADAPT THIS!-----------
DATADIR = '/home/miedema/code/simulations/nils/runs/fp_sampling'
DATAFN = 'sample'
#
# outer loop count. each time there are 9 particles running in parallel.
# therefore, the total number of counts in the histogram is about 9*NUMEROFRUNS
NUMBEROFRUNS = int(1e2)
#
# upper cutoff time for sampling: if a particle stays alive longer than this time,
# it is discarded
CUTOFFTIME = .2
# the geometry and kinetic constants, collected here for easy reference
def run_single(T, V, N):
print 'T =', T, '; V= ', V, '; N=', N
# disable gc
import gc
gc.disable()
L = math.pow(V * 1e-3, 1.0 / 3.0)
matrix_size = max(3, int((3 * N)**(1.0 / 3.0)))
print 'matrix_size=', matrix_size
D = 1e-12
m = model.ParticleModel(L)
A = model.Species('A', D, 2.5e-9)
m.add_species_type(A)
m.set_all_repulsive()
w = gfrdbase.create_world(m, matrix_size)
nrw = _gfrd.NetworkRulesWrapper(m.network_rules)
#s = EGFRDSimulator(w, myrandom.rng, nrw)
myrandom.seed(3964642685656813207)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng)
#s.paranoiac = True
gfrdbase.throw_in_particles(w, A, N)
print 'stir'
stir_time = T * .1
while 1:
s.step()
next_time = s.t + s.dt
if next_time > stir_time:
s.step(stir_time)
break
stir_steps = s.num_steps
#print 'reset'
#s.reset()
print 'run'
run_time = T + stir_time
start = time.time()
while s.t < run_time:
s.step()
end = time.time()
timing = end - start
steps = s.num_steps - stir_steps
stepspersec = float(steps) / timing
print 'steps (total)= ', steps
print 'steps/sec= ', stepspersec, ', steps/N= ', float(steps) / N
print 'TIMING:\n', timing, '\n'
gc.collect()
gc.enable()
return end - start, steps, stepspersec
def run_single(T, V, N):
print 'T =', T, '; V= ', V, '; N=', N
# disable gc
import gc
gc.disable()
L = math.pow(V * 1e-3, 1.0 / 3.0)
matrix_size = max(3, int((3 * N) ** (1.0/3.0)))
print 'matrix_size=', matrix_size
D = 1e-12
m = model.ParticleModel(L)
A = model.Species('A', D, 2.5e-9)
m.add_species_type(A)
m.set_all_repulsive()
w = gfrdbase.create_world(m, matrix_size)
nrw = _gfrd.NetworkRulesWrapper(m.network_rules)
#s = EGFRDSimulator(w, myrandom.rng, nrw)
myrandom.seed(3964642685656813207)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng)
#s.paranoiac = True
gfrdbase.throw_in_particles(w, A, N)
print 'stir'
stir_time = T * .1
while 1:
s.step()
next_time = s.t + s.dt
if next_time > stir_time:
s.step(stir_time)
break
stir_steps = s.num_steps
#print 'reset'
#s.reset()
print 'run'
run_time = T + stir_time
start = time.time()
while s.t < run_time:
s.step()
end = time.time()
timing = end - start
steps = s.num_steps - stir_steps
stepspersec = float(steps) / timing
print 'steps (total)= ', steps
print 'steps/sec= ', stepspersec, ', steps/N= ', float(steps) / N
print 'TIMING:\n', timing, '\n'
gc.collect()
gc.enable()
return end - start, steps, stepspersec
'''Settings ''' # Make multis run 'BD_DT_FACTOR' times faster than normal. BD_DT_FACTOR = 1 RADIUS_FACTOR = 1 SINGLE_RATE_FACTOR = 1 PAIR_RATE_FACTOR = 1 N_PARTICLES_FACTOR = 1 WORLD_SIZE_FACTOR = 1 N_STEPS = 15000 MY_SEED = 0 myrandom.seed(MY_SEED) L = WORLD_SIZE_FACTOR * 1e-6 # Size of simulation box. D = 1e-12 # Diffusion constant. radius = RADIUS_FACTOR * 2.5e-9 # Radius of particles. '''Reaction rates ''' sigma = 2 * radius D_tot = D tau = sigma * sigma / D_tot # Bimolecular reaction type. kf_2 = PAIR_RATE_FACTOR * 100 * sigma * D_tot # Unimolecular reaction type.
