def dReal_process(filename):
problem_string = exampleParametricCRN()
print problem_string
with open("./" + filename, "w") as f:
f.write(problem_string)
sc = SolverCallerDReal(model_path="./" + filename)
result_file = sc.single_synthesis(precision=0.1)
param_values = sc.getCRNValues(result_file[0])
print param_values
quit()
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):
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):
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 = [{"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 process_solver_output(project_id):
"""Solve problem."""
current_project = Project.query.filter_by(id=project_id).first()
if current_project.user != current_user:
flash('Not your project!', 'danger')
return redirect('.')
# TODO: check status
if not current_project.status:
flash('Input files fo iSAT/dReach not yet generated!', 'danger')
return redirect(url_for('project.project', project_id=project_id))
# construct CRN object and input files for solvers
directory = os.path.join(current_app.config.get("UPLOAD_FOLDER"),
str(project_id))
isat_problem, dreal_problem, flow, crn = getProblem(
current_project.crn_sketch, current_project.spec)
solver = request.form.get("solver")
if solver == "iSAT":
sc = SolverCallerISAT("./iSAT.hys",
isat_path=current_app.config.get("ISAT_PATH"))
elif solver == "dReach":
sc = SolverCallerDReal("./dReach.drh",
dreal_path=current_app.config.get("DREAL_PATH"))
# pass as string isntead of file
file_name = os.path.join(directory, "results")
with open(file_name) as f:
f.write(request.form.get("result"))
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
with open(file_name + "-parameters.txt", "w") as f:
f.write("Initial Conditions: %s\n" % initial_conditions)
f.write("Flow: %\n" % parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions,
parametrised_flow,
plot_name=file_name +
"-simulation.png")
savetxt(file_name + "-simulation.csv",
sol,
delimiter=",",
header=",".join(variable_names))
return redirect(url_for('project.project', project_id=project_id))
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=",")
def solve_project(project_id):
"""Solve problem."""
current_project = Project.query.filter_by(id=project_id).first()
if current_project.user != current_user:
flash('Not your project!', 'danger')
return redirect('.')
# save form details
current_project.crn_semantics = request.form.get("semantics")
current_project.solver = request.form.get("solver")
current_project.save()
# Construct CRN object
print current_project.crn_sketch
# Make directory for project
directory = os.path.join(current_app.config.get("UPLOAD_FOLDER"),
str(project_id))
if not os.path.exists(directory):
os.makedirs(directory)
open(os.path.join(directory, 'results.txt'), 'a').close()
# construct CRN object and input files for solvers
isat_problem, dreal_problem, flow, crn = getProblem(
current_project.crn_sketch, current_project.crn_code,
current_project.spec)
with open(os.path.join(directory, 'iSAT.hys'), 'w') as fp:
fp.write(isat_problem)
with open(os.path.join(directory, 'dReach.drh'), 'w') as fp:
fp.write(dreal_problem)
if request.form.get("solver") == "None":
current_project.status = "Config file generated"
current_project.save()
return redirect(url_for('project.project', project_id=project_id))
if not current_app.config.get("SOLVERS_ENABLED"):
flash('SAT-ODE Solvers not enabled!', 'danger')
return redirect(url_for('project.project', project_id=project_id))
# Run solvers if requested
current_project.status = "Running"
current_project.save()
if request.form.get("solver") == "iSAT":
sc = SolverCallerISAT("./iSAT.hys",
isat_path=current_app.config.get("ISAT_PATH"))
elif request.form.get("solver") == "dReach":
sc = SolverCallerDReal("./dReach.drh",
dreal_path=current_app.config.get("DREAL_PATH"))
result_files = sc.single_synthesis(cost=0)
for file_name in result_files:
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
with open(file_name + "-parameters.txt", "w") as f:
f.write("Initial Conditions: %s\n" % initial_conditions)
f.write("Flow: %\n" % parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions,
parametrised_flow,
plot_name=file_name +
"-simulation.png")
savetxt(file_name + "-simulation.csv",
sol,
delimiter=",",
header=",".join(variable_names))
current_project.status = "Complete"
current_project.save()
return redirect(url_for('project.project', project_id=project_id))