def _MakeMDFProblem(self):
"""Create a CVXOPT problem for finding the Maximal Thermodynamic
Driving Force (MDF).
Does not set the objective function... leaves that to the caller.
Returns:
the linear problem object, and the three types of variables as arrays
"""
A, b, c, y, l = self._GetPrimalVariablesAndConstants()
B = Variable('mdf')
x = y + l + [B]
lp = Model(name="MDF_PRIMAL")
cnstr_names = ["driving_force_%02d" % j for j in range(self.Nr_active)] + \
["covariance_var_ub_%02d" % j for j in range(self.Nr)] + \
["covariance_var_lb_%02d" % j for j in range(self.Nr)] + \
["log_conc_ub_%02d" % j for j in range(self.Nc)] + \
["log_conc_lb_%02d" % j for j in range(self.Nc)]
constraints = []
for j in range(A.shape[0]):
row = [A[j, i] * x[i] for i in range(A.shape[1])]
constraints.append(
Constraint(sum(row), ub=b[j, 0], name=cnstr_names[j]))
lp.add(constraints)
row = [c[i, 0] * x[i] for i in range(c.shape[0])]
lp.objective = Objective(sum(row), direction='max')
return lp, y, l, B
def _MakeMDFProblemDual(self):
"""Create a CVXOPT problem for finding the Maximal Thermodynamic
Driving Force (MDF).
Does not set the objective function... leaves that to the caller.
Returns:
the linear problem object, and the four types of variables as arrays
"""
A, b, c, w, g, z, u = self._GetDualVariablesAndConstants()
x = w + g + z + u
lp = Model(name="MDF_DUAL")
cnstr_names = ["y_%02d" % j for j in range(self.Nr)] + \
["l_%02d" % j for j in range(self.Nc)] + \
["MDF"]
constraints = []
for i in range(A.shape[1]):
row = [A[j, i] * x[j] for j in range(A.shape[0])]
constraints.append(
Constraint(sum(row),
lb=c[i, 0],
ub=c[i, 0],
name=cnstr_names[i]))
lp.add(constraints)
row = [b[i, 0] * x[i] for i in range(A.shape[0])]
lp.objective = Objective(sum(row), direction='min')
return lp, w, g, z, u
def setUp(self):
x = Variable("x", lb=0)
y = Variable("y", lb=0)
z = Variable("z", lb=0)
c1 = Constraint(x, ub=10)
c2 = Constraint(y - 2 * z, lb=0, ub=0)
c3 = Constraint(x - z, lb=3, ub=15)
obj = Objective(x + y + z)
model = Model()
model.add([c1, c2, c3])
model.objective = obj
self.model = model
self.c1 = c1
def _GetTotalEnergyProblem(self, min_driving_force=0.0, direction='min'):
A, b, _c, y, l = self._GetPrimalVariablesAndConstants()
x = y + l + [min_driving_force]
lp = Model(name='MDF')
constraints = []
for j in range(A.shape[0]):
row = [A[j, i] * x[i] for i in range(A.shape[1])]
constraints.append(
Constraint(sum(row), ub=b[j, 0], name='row_%d' % j))
total_g0 = float(self.fluxes @ self.dG0_r_prime)
total_reaction = self.S @ self.fluxes.T
row = [total_reaction[i, 0] * x[i] for i in range(self.Nc)]
total_g = total_g0 + sum(row)
lp.add(constraints)
lp.objective = Objective(total_g, direction=direction)
return lp
