def check_cadet(self):
"""Wrapper around a basic CADET example for testing functionality"""
if platform.system() == 'Windows':
lwe_path = self.install_path / "bin" / "createLWE.exe"
else:
lwe_path = self.install_path / "bin" / "createLWE"
ret = subprocess.run(
[lwe_path.as_posix()],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.temp_dir
)
if ret.returncode != 0:
if ret.stdout:
print('Output', ret.stdout.decode('utf-8'))
if ret.stderr:
print('Errors', ret.stderr.decode('utf-8'))
raise CADETProcessError(
"Failure: Creation of test simulation ran into problems"
)
lwe_hdf5_path = Path(self.temp_dir) / 'LWE.h5'
sim = CadetAPI()
sim.filename = lwe_hdf5_path.as_posix()
data = sim.run()
os.remove(sim.filename)
if data.returncode == 0:
print("Test simulation completed successfully")
else:
print(data)
raise CADETProcessError(
"Simulation failed"
)
def main():
simulation = Cadet(common.common.root)
simulation.filename = "f:/temp/LWE.h5"
createSimulation(simulation)
simulation.save()
simulation.run()
simulation.load()
#read sensitivity data
#sensitivity of protein 1 to nu 1
#s1 = simulation.root.output.sensitivity.param_000.unit_001.sens_column_outlet_comp_001
#sensitivity of protein 2 to nu 1
#s2 = simulation.root.output.sensitivity.param_000.unit_001.sens_column_outlet_comp_002
#sensitivity of protein 1 to nu 2
#s3 = simulation.root.output.sensitivity.param_001.unit_001.sens_column_outlet_comp_001
#sensitivity of protein 1 to sigma 1
#s4 = simulation.root.output.sensitivity.param_002.unit_001.sens_column_outlet_comp_001
#sensitivity of protein 1 to lambda
#s5 = simulation.root.output.sensitivity.param_003.unit_001.sens_column_outlet_comp_001
#Sensitvity of first species to loads of all species (except salt)
#s6 = simulation.root.output.sensitivity.param_004.unit_001.sens_column_outlet_comp_001
#Sensitvity of first species to velocity
#s7 = simulation.root.output.sensitivity.param_005.unit_001.sens_column_outlet_comp_001
plotSimulation(simulation)
def main():
simulation = Cadet(common.common.root)
simulation.filename = "MSSMA.h5"
createSimulation(simulation)
simulation.save()
simulation.run()
simulation.load()
plotSimulation(simulation)
def main():
simulation = Cadet(common.common.root)
simulation.filename = "MSSMA_2comp.h5"
createSimulation(simulation)
simulation.save()
data = simulation.run()
print(data)
simulation.load()
plotSimulation(simulation)
def main():
smb = Cadet()
smb.filename = 'F:/temp/SMB.h5'
createSimulation(smb)
print("Simulated Created")
smb.save()
smb.run()
smb.load()
print("Simulation Run")
plotSimulation(smb)
def main():
#sim = Cadet(common.root, column_setup.root, io.root, connectivity.root)
#sim.filename = "F:/temp/test_file.h5"
#createSimulation(sim)
#sim.save()
#sim.run()
#sim.load()
#plotSimulation(sim)
sim = Cadet(common.root, cstr.root, io.root, connectivity.root)
sim.root.input['return'].unit_001.write_solution_volume = 1
sim.root.input.model.connections.switch_000.connections = [
0, 1, -1, -1, 1.5, 1, 2, -1, -1, 1.0
]
sim.filename = "F:/temp/test_file_cstr.h5"
sim.save()
sim.run()
sim.load()
plotSimulation(sim)
plotVolume(sim)
writer = pandas.ExcelWriter('F:/temp/test_file_cstr.xlsx')
inputs = pandas.DataFrame.from_items([
('Time', sim.root.output.solution.solution_times),
('Concentration',
sim.root.output.solution.unit_002.solution_inlet_comp_000)
])
outputs = pandas.DataFrame.from_items([
('Time', sim.root.output.solution.solution_times),
('Concentration',
sim.root.output.solution.unit_002.solution_outlet_comp_000)
])
volumes = pandas.DataFrame.from_items([
('Time', sim.root.output.solution.solution_times),
('Volume',
numpy.squeeze(sim.root.output.solution.unit_001.solution_volume))
])
inputs.to_excel(writer, 'Input', index=False)
outputs.to_excel(writer, 'Output', index=False)
volumes.to_excel(writer, 'Volume', index=False)
writer.save()
def main():
sim = Cadet(common.root, dpfr.root, io.root, cstr.root, connectivity.root)
sim.filename = r"F:\jurgen\Pilot_test.h5"
#createSimulation(sim)
sim.save()
sim.run()
sim.load()
plotSimulation(sim)
#sim = Cadet(common.root, cstr.root, io.root, connectivity.root)
#sim.root.input['return'].unit_001.write_solution_volume = 1
#sim.root.input.model.connections.switch_000.connections = [0, 1, -1, -1, 1.5,
# 1, 2, -1, -1, 1.0]
#sim.filename = r"C:\Users\Kohl\Desktop\Cadet\test_file_cstr.h5"
#sim.save()
#sim.run()
#sim.load()
#plotSimulation(sim)
#plotVolume(sim)
writer = pandas.ExcelWriter(r'F:\jurgen\test_file_cstr.xlsx')
inputs = pandas.DataFrame.from_items([
('Time', sim.root.output.solution.solution_times),
('Concentration',
sim.root.output.solution.unit_000.solution_inlet_comp_000)
])
outputs = pandas.DataFrame.from_items([
('Time', sim.root.output.solution.solution_times),
('Concentration',
sim.root.output.solution.unit_002.solution_outlet_comp_000)
])
#volumes = pandas.DataFrame.from_items([('Time', sim.root.output.solution.solution_times), ('Volume', numpy.squeeze(sim.root.output.solution.unit_001.solution_volume))])
inputs.to_excel(writer, 'Input', index=False)
outputs.to_excel(writer, 'Output', index=False)
#volumes.to_excel(writer, 'Volume', index=False)
writer.save()
def load_from_h5(self, file_path):
cadet = CadetAPI()
cadet.filename = file_path
cadet.load()
return cadet
def save_to_h5(self, process, file_path):
cadet = CadetAPI()
cadet.root = self.get_process_config(process)
cadet.filename = file_path
cadet.save()
def run(self, process, file_path=None):
"""Interface to the solver run function
The configuration is extracted from the process object and then saved
as a temporary .h5 file. After termination, the same file is processed
and the results are returned.
Cadet Return information:
- 0: pass (everything allright)
- 1: Standard Error
- 2: IO Error
- 3: Solver Error
Parameters
----------
process : Process
process to be simulated
Returns
-------
results : SimulationResults
Simulation results including process and solver configuration.
Raises
------
TypeError
If process is not instance of Process
See also
--------
get_process_config
get_simulation_results
"""
if not isinstance(process, Process):
raise TypeError('Expected Process')
cadet = CadetAPI()
cadet.root = self.get_process_config(process)
if file_path is None:
cadet.filename = self.get_tempfile_name()
else:
cadet.filename = file_path
cadet.save()
try:
start = time.time()
return_information = cadet.run(timeout=self.timeout)
elapsed = time.time() - start
except TimeoutExpired:
raise CADETProcessError('Simulator timed out')
if return_information.returncode != 0:
self.logger.error(
'Simulation of {} with parameters {} failed.'.format(
process.name, process.config
)
)
raise CADETProcessError(
'CADET Error: {}'.format(return_information.stderr)
)
try:
cadet.load()
results = self.get_simulation_results(
process, cadet, elapsed, return_information
)
except TypeError:
raise CADETProcessError('Unexpected error reading SimulationResults.')
# Remove files
if file_path is None:
os.remove(cadet.filename)
return results
from cadet import Cadet fix = Cadet() fix.filename = r"F:\output\dextran\dextran_pulse.h5" fix.load() fix.root.input.model.unit_001.adsorption_model = "LINEAR" fix.root.input.model.unit_001.adsorption.is_kinetic = 1 fix.root.input.model.unit_001.adsorption.lin_ka = [0.0] fix.root.input.model.unit_001.adsorption.lin_kd = [1e3] fix.save()
# Return data
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].unit_000.write_solution_bulk = 1
model.root.input['return'].unit_000.write_solution_inlet = 1
model.root.input['return'].unit_000.write_solution_outlet = 1
# Copy settings to the other unit operations
model.root.input['return'].unit_001 = model.root.input['return'].unit_000
model.root.input['return'].unit_002 = model.root.input['return'].unit_000
# Solution times
model.root.input.solver.user_solution_times = np.linspace(0, 1200, 1001)
# Save and run simulation
model.filename = 'model.h5'
model.save()
data = model.run()
if data.returncode == 0:
print("Simulation completed successfully")
model.load()
else:
print(data)
raise Exception("Simulation failed")
# Plot restuls
plt.figure()
time = model.root.output.solution.solution_times