def __init__(self):
sf.Application.__init__(self)
# Set up the physics world
self.world = ode.dWorld()
self.world.setGravity(0, -9.81, 0)
ssid = ode.dSimpleSpace()
self.space = ode.dSimpleSpace(1) # dQuadTreeSpace, dHashSpace
self.contactgroup = ode.JointGroup()
self.bodyList = []
def sensitivity(self, scenario, value, ranges):
self.data.max_P = []
self.data.max_T = []
self.data.max_conversion = []
self.data.max_vent = []
for i in tqdm(ranges):
if value == "Rupture Disc Diameter":
scenario.D_RD = i
elif value == "Rupture Disc Burst Pressure":
scenario.P_RD = i
elif value == "Backpressure Regulator Set-Point":
scenario.P_BPR = i
elif value == "Hydrogen Peroxide Concentration":
scenario.XH2O2 = i / 100
elif value == "Reactor Charge":
scenario.mR = i
elif value == "Contamination Factor":
scenario.kf = i
elif value == "Reaction Temperature":
scenario.rxn_temp = i
ode = ODE.ODE(scenario)
ode.initialize_heatup()
ode.integrate()
tc = ode.termination_code()
# if self.data.RD is True and tc == "Process Finished Successfully (Rupture disc burst)":
ode.initialize_vent(integrator='vode')
ode.integrate()
self.data.max_P.append(ode.max_P())
self.data.max_T.append(ode.max_T())
self.data.max_conversion.append(ode.max_conversion())
self.data.max_vent.append(ode.max_vent())
def _nearcb(self, args, geom1, geom2):
"""
Create contact joints between colliding geoms.
"""
body1, body2 = geom1.getBody(), geom2.getBody()
if (body1 is None):
body1 = ode.environment
if (body2 is None):
body2 = ode.environment
if (ode.areConnected(body1, body2)):
return
contacts = ode.collide(geom1, geom2)
for c in contacts:
c.setBounce(0.2)
c.setMu(10000)
j = ode.ContactJoint(self.world, self._cjoints, c)
j.attach(body1, body2)
def main_functions():
inputData = input()
m1 = inputData.get('m1')
m2 = inputData.get('m2')
L1 = inputData.get('L1')
L2 = inputData.get('L2')
theta1 = inputData.get('theta1')
theta2 = inputData.get('theta2')
g = inputData.get('g')
t = inputData.get('t')
temp = ODE(theta1, theta2, m1, m2, L1, L2, g, t)
output(temp[0], temp[1], temp[2])
plot(temp[0], temp[1], temp[2])
def run_scenario_menu(self):
if None in [self.data.VR, self.data.RD, self.data.kf]:
print(' ')
print(
'Scenario not fully specified. Update scenario configuration and try again'
)
print(' ')
input("Press [Enter] to continue...")
else:
answers = self.setup_plot_rt_q()
plot_rt = answers.get("plot_rt")
scen = Scenario(self.data.VR, self.data.rxn_temp,
self.data.rxn_time, self.data.XH2O2, self.data.mR,
self.data.D_RD, self.data.P_RD, self.data.P_BPR,
self.data.D_BPR, self.data.BPR_max_Cv,
self.data.P0, self.data.kf, self.data.T0,
self.data.Ux, self.data.AR, self.data.MAWP,
self.data.max_rate, self.data.Kp, self.data.Ki,
self.data.Kd, self.data.flow_regime, self.data.BPR,
self.data.RD, self.data.cool_time, self.data.TF)
ode1 = ODE.ODE(scen)
ode1.initialize_heatup()
print('Integrating Heatup...')
print(' ')
ode1.integrate(plot_rt)
tc = ode1.termination_code()
print(' ')
print(tc)
print(' ')
if self.data.RD is True and ode1.tc == 1:
print('Integrating ERS...')
print(' ')
ode1.initialize_vent(integrator='vode')
ode1.integrate(plot_rt)
tc = ode1.termination_code()
print(' ')
print(tc)
print(' ')
self.data.ode = ode1
self.summary_stats_menu()
def near_callback(self, args, geom1, geom2):
# Check if the objects do collide
contacts = ode.collide(geom1, geom2)
# Create contact joints
self.world,self.contactgroup = args
for c in contacts:
c.setMode(ode.ContactBounce)
c.setBounce(0.2)
c.setBounceVel(0.15)
c.setMu(250.0)
j = ode.ContactJoint(self.world, self.contactgroup, c)
j.attach(geom1.getBody(), geom2.getBody())
def nearCallback (data, o1, o2):
## exit without doing anything if the two bodies are connected by a joint
b1 = ode.dGeomGetBody(o1)
b2 = ode.dGeomGetBody(o2)
if b1 and b2 and ode.dAreConnected (b1,b2):
return
## @@@ it's still more convenient to use the C interface here.
contact = ode.dContact()
contact.surface.mode = 0
contact.surface.mu = ode.dInfinity
if ode.dCollide ( o1,o2,0,contact.geom,sizeof(ode.dContactGeom) ):
c = dJointCreateContact (world.id(),contactgroup.id(),&contact)
ode.dJointAttach (c,b1,b2)
# Created by: # Felipe Uribe @ MIT, TUM, DTU # ============================================================================= # Version 2020-04 # ============================================================================= import numpy as np import matplotlib import matplotlib.pyplot as plt # import ODE from SuS import SuS #============================================================================ # numerical model: defined in ODE.py dim = 50+1 # RF plus flux: <= 203+1, otherwise increase dim_max in ODE.py u_ODE = lambda theta: ODE.analytical(theta) # LSF u_thres = 2.7 # maximum allowed pressure head g_LSF_single = lambda theta: u_thres - max(u_ODE(theta)) #============================================================================ # SuS method NSIM = int(30) # number of independent simulations N = int(1e3) # total number of samples per level p0 = 0.1 # prescribed level probability # LSF for all samples g_LSF = lambda theta: np.array([ g_LSF_single(theta[:,i]) for i in range(N) ]) #============================================================================
0.70541941, # HypoWCCn
0.03008159, # HyperWCCn
0.08212058, # aWCC
0., # laWCC
0., # vvdm
0., # VVDc
0., # VVDn
0.
]) # WVC
frq_ind = 2
period = 21.62451
##### Below is example solving and plotting frq mRNA for Tseng's model #####
ModTseng = ODE('Tseng\'s Model',
frq_ind,
Y,
p,
p_add,
dY,
Y0,
period,
findQ=False)
tot_time = 100
t_test = np.linspace(0, tot_time, 100 * tot_time)
sol_test = ModTseng.solve(ModTseng.lim_cyc_vals, t_test)
frq_sol = sol_test[:, frq_ind]
plt.plot(t_test, frq_sol)
import matplotlib.pyplot as plt
import astropy.units as u
import astropy.constants as c
import ODE
def f2Prime(x,y1,y2):
#print(f"{x} {y1} {y2}")
return [3*x**2+8*y1-3*y2]*2
def fPrime(x,y):
return [5*y+1]
solvePoints = [0,1,2,3]
#Euler
print(ODE.euler(f2Prime,0,[-1,0],solvePoints))
print(ODE.euler(fPrime,0,[-1],solvePoints))
#Heun
print(ODE.heun(f2Prime,0,[-1,0],solvePoints))
print(ODE.heun(fPrime,0,[-1],solvePoints))
#RK4
print(ODE.rk4(f2Prime,0,[-1,0],solvePoints))
print(ODE.rk4(fPrime,0,[-1],solvePoints))
#Scipy odeint test
def pend(y, t, b, c):
theta, omega = y
dydt = [omega, -b*omega - c*np.sin(theta)]
return dydt
qD = sympy.Symbol('qD')
# Parameters as additive pulses
p_add = [qA, qB, qC, qD]
# Symbolic ODE RHS
dA = k3*D**m/(K**m+D**m) - k4*A # frq mRNA
dB = k5*A - k6*B + k7*C - k8*B*D # FRQ Protein
dC = k8*B*D - k7*C - k9*C # WC-1:FRQ complex
dD = k1 - k2*D + k7*C - k8*B*D # WC-1 protein
dY = sympy.Matrix([dA, dB, dC, dD]) # Vector ODE RHS
# Initial values on the limit cycle at frq mRNA max.
Y0 = np.array([0.958658, # A0
0.7892854, # B0
0.3232268, # C0
0.5296776]) # D0
frq_ind = 0
period = 22.
##### Below is example solving and plotting frq mRNA for the simple model #####
ModSimple = ODE('The Simple Model',frq_ind,Y,p,p_add,dY,Y0,period,findQ=False)
tot_time=100
t_test = np.linspace(0,tot_time, 100*tot_time)
sol_test = ModSimple.solve(ModSimple.lim_cyc_vals, t_test)
frq_sol = sol_test[:,frq_ind]
plt.plot(t_test, frq_sol)
for index in range(len(collocation_points)):
params_eq = {
"gravity": 9.81,
"density": collocation_points["density"][index],
"radius": collocation_points["radius"][index],
"mass": collocation_points["mass"][index],
"drag_coefficient": collocation_points["drag_coefficient"][index]
}
param_initial_conditions = {
"h": collocation_points["h"][index],
"alpha": collocation_points["alpha"][index],
"v0": collocation_points["v0"][index],
}
time, x, y = Solver.solve_object_ODE(delta_t, param_initial_conditions,
params_eq)
time_vec.append(time)
x_vec.append(x)
y_vec.append(y)
len_max = 0
index_len = 0
for i in range(len(x_vec)):
if len(x_vec[i]) > len_max:
len_max = len(x_vec[i])
index_len = index
print(len_max)
print(index_len)
x_vec_new = list()
import ODE as ode
NUM= 10 ## number of boxes
SIDE = 0.2 ## side length of a box
MASS= 1.0 ## mass of a box
RADIUS =0.1732 ## sphere radius
## dynamics and collision objects
body=[]
box=[]
joint = []
for i in range(NUM):
body.append(ode.dBody() )
box.append(ode.dBox() )
joint.append (ode.dBallJoint() )
contactgroup= ode.dJointGroup()
space = ode.dSimpleSpace(None)
world = ode.dWorld()
## this is called by space.collide when two objects in space are
## potentially colliding.
def nearCallback (data, o1, o2):
## exit without doing anything if the two bodies are connected by a joint
b1 = ode.dGeomGetBody(o1)
b2 = ode.dGeomGetBody(o2)
if b1 and b2 and ode.dAreConnected (b1,b2):
return
0.0110685024, # Fn0
3.70361114, # Mw0
0.00666226484, # Wc0
0.924361228, # Wn0
0.0820481701, # FWn0
0.05214823, # Mc0
1.93780501
]) # C0
frq_ind = 0
period = 22.3934820284
##### Below is example solving and plotting frq mRNA for Dovzhenok's model #####
ModDovzhenok = ODE('The Dovzhenok Model',
frq_ind,
Y,
p,
p_add,
dY,
Y0,
period,
findQ=False)
tot_time = 100
t_test = np.linspace(0, tot_time, 100 * tot_time)
sol_test = ModDovzhenok.solve(ModDovzhenok.lim_cyc_vals, t_test)
frq_sol = sol_test[:, frq_ind]
plt.plot(t_test, frq_sol)
