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Updated parmest Estimator class to use experiments #2

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fabf7a9
Added parmest_redesign.py and updated example
kaklise Dec 4, 2023
8f84909
updated todos
kaklise Dec 4, 2023
eb1bbf9
Isolated deprecated API, examples, and tests
kaklise Dec 6, 2023
910ebca
replaced parmest.py with the new API and moved example
kaklise Dec 6, 2023
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0 ...st/examples/reaction_kinetics/__init__.py → .../parmest/examples/_deprecated/__init__.py
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0 ...rmest/examples/rooney_biegler/__init__.py → ..._deprecated/reaction_kinetics/__init__.py
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2 changes: 1 addition & 1 deletion ...netics/simple_reaction_parmest_example.py → ...netics/simple_reaction_parmest_example.py
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exp,
value,
)
import pyomo.contrib.parmest.parmest as parmest
import pyomo.contrib.parmest.parmest_deprecated as parmest


def simple_reaction_model(data):
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0 ...ib/parmest/examples/semibatch/__init__.py → ...es/_deprecated/reactor_design/__init__.py
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4 changes: 2 additions & 2 deletions ...mples/reactor_design/bootstrap_example.py → ...cated/reactor_design/bootstrap_example.py
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import pandas as pd
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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4 changes: 2 additions & 2 deletions ...xamples/reactor_design/datarec_example.py → ...recated/reactor_design/datarec_example.py
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import numpy as np
import pandas as pd
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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4 changes: 2 additions & 2 deletions ...mples/reactor_design/leaveNout_example.py → ...cated/reactor_design/leaveNout_example.py
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import numpy as np
import pandas as pd
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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4 changes: 2 additions & 2 deletions ...eactor_design/likelihood_ratio_example.py → ...eactor_design/likelihood_ratio_example.py
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import pandas as pd
from itertools import product
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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4 changes: 2 additions & 2 deletions ...eactor_design/multisensor_data_example.py → ...eactor_design/multisensor_data_example.py
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import pandas as pd
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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4 changes: 2 additions & 2 deletions ...or_design/parameter_estimation_example.py → ...or_design/parameter_estimation_example.py
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import pandas as pd
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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20 changes: 20 additions & 0 deletions pyomo/contrib/parmest/examples/_deprecated/reactor_design/reactor_data.csv
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sv,caf,ca,cb,cc,cd
1.06,10010,3407.4,945.4,1717.1,1931.9
1.11,10010,3631.6,1247.2,1694.1,1960.6
1.16,10010,3645.3,971.4,1552.3,1898.8
1.21,10002,3536.2,1225.9,1351.1,1757.0
1.26,10002,3755.6,1263.8,1562.3,1952.2
1.30,10007,3598.3,1153.4,1413.4,1903.3
1.35,10007,3939.0,971.4,1416.9,1794.9
1.41,10009,4227.9,986.3,1188.7,1821.5
1.45,10001,4163.1,972.5,1085.6,1908.7
1.50,10002,3896.3,977.3,1132.9,2080.5
1.56,10004,3801.6,1040.6,1157.7,1780.0
1.60,10008,4128.4,1198.6,1150.0,1581.9
1.66,10002,4385.4,1158.7,970.0,1629.8
1.70,10007,3960.8,1194.9,1091.2,1835.5
1.76,10007,4180.8,1244.2,1034.8,1739.5
1.80,10001,4212.3,1240.7,1010.3,1739.6
1.85,10004,4200.2,1164.0,931.5,1783.7
1.90,10009,4748.6,1037.9,1065.9,1685.6
1.96,10009,4941.3,1038.5,996.0,1855.7
0 ...actor_design/reactor_data_multisensor.csv → ...actor_design/reactor_data_multisensor.csv
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0 ...eactor_design/reactor_data_timeseries.csv → ...eactor_design/reactor_data_timeseries.csv
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104 changes: 104 additions & 0 deletions pyomo/contrib/parmest/examples/_deprecated/reactor_design/reactor_design.py
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# ___________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2022
# National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and
# Engineering Solutions of Sandia, LLC, the U.S. Government retains certain
# rights in this software.
# This software is distributed under the 3-clause BSD License.
# ___________________________________________________________________________
"""
Continuously stirred tank reactor model, based on
pyomo/examples/doc/pyomobook/nonlinear-ch/react_design/ReactorDesign.py
"""
import pandas as pd
from pyomo.environ import (
ConcreteModel,
Param,
Var,
PositiveReals,
Objective,
Constraint,
maximize,
SolverFactory,
)


def reactor_design_model(data):
# Create the concrete model
model = ConcreteModel()

# Rate constants
model.k1 = Param(initialize=5.0 / 6.0, within=PositiveReals, mutable=True) # min^-1
model.k2 = Param(initialize=5.0 / 3.0, within=PositiveReals, mutable=True) # min^-1
model.k3 = Param(
initialize=1.0 / 6000.0, within=PositiveReals, mutable=True
) # m^3/(gmol min)

# Inlet concentration of A, gmol/m^3
if isinstance(data, dict) or isinstance(data, pd.Series):
model.caf = Param(initialize=float(data["caf"]), within=PositiveReals)
elif isinstance(data, pd.DataFrame):
model.caf = Param(initialize=float(data.iloc[0]["caf"]), within=PositiveReals)
else:
raise ValueError("Unrecognized data type.")

# Space velocity (flowrate/volume)
if isinstance(data, dict) or isinstance(data, pd.Series):
model.sv = Param(initialize=float(data["sv"]), within=PositiveReals)
elif isinstance(data, pd.DataFrame):
model.sv = Param(initialize=float(data.iloc[0]["sv"]), within=PositiveReals)
else:
raise ValueError("Unrecognized data type.")

# Outlet concentration of each component
model.ca = Var(initialize=5000.0, within=PositiveReals)
model.cb = Var(initialize=2000.0, within=PositiveReals)
model.cc = Var(initialize=2000.0, within=PositiveReals)
model.cd = Var(initialize=1000.0, within=PositiveReals)

# Objective
model.obj = Objective(expr=model.cb, sense=maximize)

# Constraints
model.ca_bal = Constraint(
expr=(
0
== model.sv * model.caf
- model.sv * model.ca
- model.k1 * model.ca
- 2.0 * model.k3 * model.ca**2.0
)
)

model.cb_bal = Constraint(
expr=(0 == -model.sv * model.cb + model.k1 * model.ca - model.k2 * model.cb)
)

model.cc_bal = Constraint(expr=(0 == -model.sv * model.cc + model.k2 * model.cb))

model.cd_bal = Constraint(
expr=(0 == -model.sv * model.cd + model.k3 * model.ca**2.0)
)

return model


def main():
# For a range of sv values, return ca, cb, cc, and cd
results = []
sv_values = [1.0 + v * 0.05 for v in range(1, 20)]
caf = 10000
for sv in sv_values:
model = reactor_design_model(pd.DataFrame(data={"caf": [caf], "sv": [sv]}))
solver = SolverFactory("ipopt")
solver.solve(model)
results.append([sv, caf, model.ca(), model.cb(), model.cc(), model.cd()])

results = pd.DataFrame(results, columns=["sv", "caf", "ca", "cb", "cc", "cd"])
print(results)


if __name__ == "__main__":
main()
4 changes: 2 additions & 2 deletions ...reactor_design/timeseries_data_example.py → ...reactor_design/timeseries_data_example.py
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import pandas as pd
from os.path import join, abspath, dirname

import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.reactor_design.reactor_design import (
reactor_design_model,
)

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10 changes: 10 additions & 0 deletions pyomo/contrib/parmest/examples/_deprecated/rooney_biegler/__init__.py
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# ___________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2022
# National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and
# Engineering Solutions of Sandia, LLC, the U.S. Government retains certain
# rights in this software.
# This software is distributed under the 3-clause BSD License.
# ___________________________________________________________________________
4 changes: 2 additions & 2 deletions ...mples/rooney_biegler/bootstrap_example.py → ...cated/rooney_biegler/bootstrap_example.py
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# ___________________________________________________________________________

import pandas as pd
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.rooney_biegler.rooney_biegler import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.rooney_biegler.rooney_biegler import (
rooney_biegler_model,
)

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4 changes: 2 additions & 2 deletions ...ooney_biegler/likelihood_ratio_example.py → ...ooney_biegler/likelihood_ratio_example.py
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import numpy as np
import pandas as pd
from itertools import product
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.rooney_biegler.rooney_biegler import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.rooney_biegler.rooney_biegler import (
rooney_biegler_model,
)

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4 changes: 2 additions & 2 deletions ...y_biegler/parameter_estimation_example.py → ...y_biegler/parameter_estimation_example.py
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# ___________________________________________________________________________

import pandas as pd
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.rooney_biegler.rooney_biegler import (
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.rooney_biegler.rooney_biegler import (
rooney_biegler_model,
)

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0 ...examples/rooney_biegler/rooney_biegler.py → ...precated/rooney_biegler/rooney_biegler.py
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10 changes: 10 additions & 0 deletions pyomo/contrib/parmest/examples/_deprecated/semibatch/__init__.py
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# ___________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2022
# National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and
# Engineering Solutions of Sandia, LLC, the U.S. Government retains certain
# rights in this software.
# This software is distributed under the 3-clause BSD License.
# ___________________________________________________________________________
0 ...ntrib/parmest/examples/semibatch/exp1.out → ...t/examples/_deprecated/semibatch/exp1.out
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4 changes: 2 additions & 2 deletions ...st/examples/semibatch/parallel_example.py → ..._deprecated/semibatch/parallel_example.py
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import pandas as pd
from itertools import product
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.semibatch.semibatch import generate_model
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.semibatch.semibatch import generate_model


def main():
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4 changes: 2 additions & 2 deletions ...semibatch/parameter_estimation_example.py → ...semibatch/parameter_estimation_example.py
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import json
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.semibatch.semibatch import generate_model
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.semibatch.semibatch import generate_model


def main():
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4 changes: 2 additions & 2 deletions ...st/examples/semibatch/scenario_example.py → ..._deprecated/semibatch/scenario_example.py
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import json
from os.path import join, abspath, dirname
import pyomo.contrib.parmest.parmest as parmest
from pyomo.contrib.parmest.examples.semibatch.semibatch import generate_model
import pyomo.contrib.parmest.parmest_deprecated as parmest
from pyomo.contrib.parmest.examples._deprecated.semibatch.semibatch import generate_model
import pyomo.contrib.parmest.scenariocreator as sc


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