def experiment_ab(num_particles):
L = 0.5
#L = 50e-9
D = 1
#D = 1e-10
timesteps = 100000
#timesteps = 10000
max_t = 4.0/(2.0*num_particles**0.5);
mol_dt = max_t/timesteps
#mol_dt = 0.025*1e-8
#max_t = mol_dt * timesteps
k2 = num_particles
#k2 = 6.67e6
k1 = 1.0
#k1 = (k2*L**3)/num_particles
binding = 0.00303416
#binding = 3.76432e-10
unbinding = 0.15*0.00303416
#unbinding = 0.01*3.76432e-10
A = tyche.new_species(D)
B = tyche.new_species(D)
C = tyche.new_species(D)
bd = tyche.new_diffusion()
bd.add_species(A)
bd.add_species(B)
bd.add_species(C)
xlow = tyche.new_xplane(0,1)
xhigh = tyche.new_xplane(L,-1)
ylow = tyche.new_yplane(0,1)
yhigh = tyche.new_yplane(L,-1)
zlow = tyche.new_zplane(0,1)
zhigh = tyche.new_zplane(L,-1)
xminboundary = tyche.new_jump_boundary(xlow,[L,0,0])
xmaxboundary = tyche.new_jump_boundary(xhigh,[-L,0,0])
yminboundary = tyche.new_jump_boundary(ylow,[0,L,0])
ymaxboundary = tyche.new_jump_boundary(yhigh,[0,-L,0])
zminboundary = tyche.new_jump_boundary(zlow,[0,0,L])
zmaxboundary = tyche.new_jump_boundary(zhigh,[0,0,-L])
boundaries = tyche.group([xminboundary, xmaxboundary, yminboundary, ymaxboundary, zminboundary, zmaxboundary])
boundaries.add_species(A)
boundaries.add_species(B)
boundaries.add_species(C)
dr2 = tyche.new_bi_reaction(k1, A, B, [C], binding,unbinding, mol_dt,
[0,0,0], [L,L,L], [True, True, True],True)
dr3 = tyche.new_bi_reaction(k1, A, B, [C], mol_dt,
[0,0,0], [L,L,L], [True, True, True],True)
dr = tyche.new_uni_reaction(k2,C,[A,B],unbinding)
algorithm = tyche.group([bd,boundaries,dr2,dr,boundaries])
A.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
B.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
C.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
output_dt = max_t/100.0
time = 0;
print algorithm
for i in range(100):
print A,B,C
print 'time = ',time,' ',i,' percent done'
time = algorithm.integrate_for_time(output_dt,mol_dt)
# grid = tvtk.to_tvtk(A.get_vtk())
# g = init_vis(grid)
print algorithm
def experiment(num_particles):
L = 1
#L = 50e-9
D = 1
#D = 1e-10
timesteps = 100000
#timesteps = 10000
max_t = 4.0/(2.0*num_particles**0.5);
mol_dt = max_t/timesteps
#mol_dt = 0.025*1e-8
#max_t = mol_dt * timesteps
A = tyche.new_species(D)
B = tyche.new_species(D)
C = tyche.new_species(D)
bd = tyche.new_diffusion()
bd.add_species(A)
bd.add_species(B)
bd.add_species(C)
xlow = tyche.new_xplane(0,1)
xhigh = tyche.new_xplane(L,-1)
ylow = tyche.new_yplane(0,1)
yhigh = tyche.new_yplane(L,-1)
zlow = tyche.new_zplane(0,1)
zhigh = tyche.new_zplane(L,-1)
xminboundary = tyche.new_jump_boundary(xlow,[L,0,0])
xmaxboundary = tyche.new_jump_boundary(xhigh,[-L,0,0])
yminboundary = tyche.new_jump_boundary(ylow,[0,L,0])
ymaxboundary = tyche.new_jump_boundary(yhigh,[0,-L,0])
zminboundary = tyche.new_jump_boundary(zlow,[0,0,L])
zmaxboundary = tyche.new_jump_boundary(zhigh,[0,0,-L])
boundaries = tyche.group([xminboundary, xmaxboundary, yminboundary, ymaxboundary, zminboundary, zmaxboundary])
boundaries.add_species(A)
boundaries.add_species(B)
boundaries.add_species(C)
algorithm = tyche.group([bd,boundaries])
A.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
B.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
C.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3))
output_dt = max_t/100.0
time = 0;
print algorithm
for i in range(100):
print A,B,C
print 'time = ',time,' ',i,' percent done'
time = algorithm.integrate_for_time(output_dt,mol_dt)
grid = tvtk.to_tvtk(A.get_vtk())
g = init_vis(grid)
print algorithm
def experiment(num_particles):
L = 0.25
D = 1
timesteps = 100000;
max_t = 4.0/(2.0*num_particles**0.5);
mol_dt = max_t/timesteps;
k2 = num_particles
k1 = 0.01
print 'hcrit = ',k1/(2.0*D)
binding = 0.01
unbinding = 0.01
A = tyche.new_species(D)
bd = tyche.new_diffusion()
bd.add_species(A)
xlow = tyche.new_xplane(0,1)
xhigh = tyche.new_xplane(L,-1)
ylow = tyche.new_yplane(0,1)
yhigh = tyche.new_yplane(L,-1)
zlow = tyche.new_zplane(0,1)
zhigh = tyche.new_zplane(L,-1)
xminboundary = tyche.new_jump_boundary(xlow,[L,0,0])
xmaxboundary = tyche.new_jump_boundary(xhigh,[-L,0,0])
yminboundary = tyche.new_jump_boundary(ylow,[0,L,0])
ymaxboundary = tyche.new_jump_boundary(yhigh,[0,-L,0])
zminboundary = tyche.new_jump_boundary(zlow,[0,0,L])
zmaxboundary = tyche.new_jump_boundary(zhigh,[0,0,-L])
boundaries = tyche.group([xminboundary, xmaxboundary, yminboundary, ymaxboundary, zminboundary, zmaxboundary])
boundaries.add_species(A)
dr2 = tyche.new_bi_reaction(k1, A, A, [A], binding,unbinding, mol_dt,
[0,0,0], [L,L,L], [True, True, True],True)
dr3 = tyche.new_bi_reaction(k1, A, A, [A], mol_dt,
[0,0,0], [L,L,L], [True, True, True],True)
dr = tyche.new_uni_reaction(k2,A,[A,A],unbinding)
algorithm = tyche.group([bd,boundaries,dr2,dr,boundaries])
A.fill_uniform([0,0,0],[L,L,L],int(num_particles*L**3/k1))
output_dt = max_t/100.0
time = 0;
print algorithm
for i in range(100):
print A
print 'time = ',time,' ',i,' percent done'
time = algorithm.integrate_for_time(output_dt,mol_dt)
# grid = tvtk.to_tvtk(A.get_vtk())
# g = init_vis(grid)
print algorithm
def experiment(num_particles,timesteps):
L = 1
D = 1
k2 = 1000.0
k1 = k2/num_particles**3
max_t = 1.0
DAB = D+D;
DABC = D + D*D/DAB;
Rsq = ( k1 / (4*3.14**3*(DAB*DABC)**(3.0/2.0) ) )**0.5;
mol_dt = Rsq/10000;
A = tyche.new_species(D)
B = tyche.new_species(D)
C = tyche.new_species(D)
bd = tyche.new_diffusion()
bd.add_species(A)
bd.add_species(B)
bd.add_species(C)
xlow = tyche.new_xplane(0,1)
xhigh = tyche.new_xplane(L,-1)
ylow = tyche.new_yplane(0,1)
yhigh = tyche.new_yplane(L,-1)
zlow = tyche.new_zplane(0,1)
zhigh = tyche.new_zplane(L,-1)
xminboundary = tyche.new_jump_boundary(xlow,[L,0,0])
xmaxboundary = tyche.new_jump_boundary(xhigh,[-L,0,0])
yminboundary = tyche.new_jump_boundary(ylow,[0,L,0])
ymaxboundary = tyche.new_jump_boundary(yhigh,[0,-L,0])
zminboundary = tyche.new_jump_boundary(zlow,[0,0,L])
zmaxboundary = tyche.new_jump_boundary(zhigh,[0,0,-L])
boundaries = tyche.group([xminboundary, xmaxboundary, yminboundary, ymaxboundary, zminboundary, zmaxboundary])
boundaries.add_species(A)
boundaries.add_species(B)
boundaries.add_species(C)
dr3 = tyche.new_tri_reaction(k1, A, B, C, [B,C], mol_dt,
[0,0,0], [L,L,L], [True, True, True])
dr = tyche.new_zero_reaction(k2,[0,0,0],[L,L,L])
dr.add_species(A)
algorithm = tyche.group([bd,boundaries,dr,dr3])
A.fill_uniform([0,0,0],[L,L,L],int(num_particles))
B.fill_uniform([0,0,0],[L,L,L],int(num_particles))
C.fill_uniform([0,0,0],[L,L,L],int(num_particles))
N = 1000
output_dt = max_t/N
time = 0;
print algorithm
grid = tvtk.to_tvtk(A.get_vtk())
numA = np.zeros(N)
for i in range(N):
print A,B,C
numA[i] = A.get_concentration([0,0,0],[L,L,L],[1,1,1])[0]
print 'time = ',time,' ',i*100.0/N,' percent done'
time = algorithm.integrate_for_time(output_dt,mol_dt)
# grid = tvtk.to_tvtk(A.get_vtk())
# g = init_vis(grid)
print algorithm
return numA