def synthesize_with_dreal(crn):
derivatives = [{"variable": 'PThree', "order": 1, "is_variance": False, "name": "PThree_dot"}]
flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', 'PThree > 0.4 '), ('', '', 'PThree < 0.3')]
specification_dreal = [('','PThree_dot >= 0','and (PThree_dot < 0.01) (PThree > 0.4) '),('','PThree_dot <= 0','(PThree < 0.3)')]
#specification_dreal = [('', 'PThree_dot >= 0', '(and (PThree > 0.3) (PThree_dot = 0))'), ('', 'PThree_dot <= 0', '(and (PThree >= 0)(PThree < 0.1))')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow, other_constraints='(PThree < 0.4)',scale_factor=1)
with open('sixreactionnetwork.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./sixreactionnetwork.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./sixreactionnetwork_1_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png", t = linspace(0, 10, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
isLNA = False
derivatives = []
#specification_dreal = [('','','')]
specification_dreal = [('', '', '(and (inputTime > 70)(cIts > 10))')]
flow = crn.flow(False, derivatives)
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=100)
with open('toggleswitch.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./toggleswitch.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./toggleswitch_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 100, 200)) # mode_times=all_vals["time"])
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = []
flow = crn.flow(False, derivatives)
specification_dreal = [('', '', '(X < 0.1)')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow)
with open('simple.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./simple.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0)
for file_name in result_files:
print("\n\n")
# print(sc.getCRNValues(file_name))
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = [{"variable": 'PThreeStar', "order": 1, "is_variance": False, "name": "PThreeStar_dot"}]
flow = crn.flow(False, derivatives)
specification_dreal = [('', '', '(inputTime > 20)'),
('', '(PThreeStar_dot > 0)', '(and (PThreeStar > 0.5)(abs(PThreeStar_dot) < 0.01))'),
('', 'abs(PThreeStar_dot) < 0.01', 'inputTime > 100')]
#flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', '')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow, max_time=350, other_constraints='', scale_factor=1)
with open('switch.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./switch.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1, max_depth=len(specification_dreal))
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./switch_2_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 300, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = []
flow = crn.flow(True, derivatives)
specification_dreal = [('', 'varA >= A', 'A > 0.3')]
#specification_dreal = [('','','')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=20)
with open('superpoisson.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./superpoisson.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./superpoisson_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions,
parametrised_flow,
plot_name=file_name +
"-simulationdreal.png",
t=linspace(0, 20, 100),
lna=True)
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = [{
"variable": 'PThreeStar',
"order": 1,
"is_variance": False,
"name": "PThreeStar_dot"
}]
flow = crn.flow(False, derivatives)
# specification_dreal = [('', '', 'PThree > 0.4 '), ('', '', 'PThree < 0.3')]
# specification_dreal = [('','','(PThreeStar > 0.5) '),('','','(PThreeStar < 0.4)')]
# specification_dreal = [('', 'PThree_dot >= 0', '(and (PThree > 0.3) (PThree_dot = 0))'), ('', 'PThree_dot <= 0', '(and (PThree >= 0)(PThree < 0.1))')]
# specification_dreal = [('', '', '(and ((inputTime > 100)(PThreeStar < 0.75))'),
# ('', '', '(PThreeStar > 0.9)')]
specification_dreal = [('', '', 'inputTime > 20'),
('', 'PThreeStar_dot < 0', '(PThreeStar_dot=0)'),
('', 'PThreeStar_dot > 0', '(PThreeStar_dot=0)'),
('', 'PThreeStar_dot < 0', 'PThreeStar_dot = 0'),
('', 'PThreeStar_dot = 0', 'inputTime > 100')]
#flow = crn.flow(False, [])
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=350,
other_constraints='',
scale_factor=1)
with open('topology365.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./topology365.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./topology365_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 300, 1000),
hidden_variables="POne,POneStar,PTwo,PTwoStar,PThree")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn, name, specification_dreal, result_file):
derivatives = [{
"variable": 'PThreeStar',
"order": 1,
"is_variance": False,
"name": "PThreeStar_dot"
}]
flow = crn.flow(False, derivatives)
#flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', '')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=350 / SF,
other_constraints='',
scale_factor=SF)
with open(name, 'w') as file:
file.write(drh)
#sc = SolverCallerDReal(name, dreal_path="/code/dReal-3.16.06.02-linux/bin/dReach")
sc = SolverCallerDReal(
name, dreal_path="/code/dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in [result_file]: # TODO: remove ths aegument
print file_name
# './inverted-bell_3_0.smt2.proof'
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 350, 1000),
mode_times=all_vals["time"],
hidden_variables="POne,POneStar,PTwo,PTwoStar,PThree")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = [{
"variable": 'L3p',
"order": 1,
"is_variance": False,
"name": "L3p_dot"
}, {
"variable": 'L3p',
"order": 2,
"is_variance": False,
"name": "L3p_dot_dot"
}]
flow = crn.flow(False, derivatives)
specification_dreal = [('', '(and (L3p_dot >= 0)(L3p_dot_dot >= 0))',
'(and (L3p_dot_dot = 0)(B > 4/SF))'),
('', '(and (L3p_dot >= 0)(L3p_dot_dot <= 0))', '')]
#specification_dreal = [('','','')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=50 / SF,
scale_factor=SF)
with open('phosphorelay.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./phosphorelay.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./phosphorelay_1_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals, scale_factor=SF)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 50 / SF, 100),
mode_times=all_vals["time"],
hidden_variables="B")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")