Update post process doc

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - '*.rst'
       - 'README*'
       - 'LICENSE'
-      - 'assets/*'
+      - 'docs/**'
 
    pull_request:
      branches: [main]
@@ -17,7 +17,7 @@ on:
       - '*.rst'
       - 'README*'
       - 'LICENSE'
-      - 'assets/*'
+      - 'docs/**'
 
 jobs:
   Lint:

README.md

@@ -43,17 +43,17 @@ See the [nrel.github.io/BioReactorDesign](https://nrel.github.io/BioReactorDesig
 
 Software record [SWR 24-35](https://www.osti.gov/biblio/2319227)
 
-To cite BioReactorDesign use these articles on [CO2 interphase mass transfer (open access)](https://arxiv.org/pdf/2404.19636) on [aerobic bioreactors](https://www.sciencedirect.com/science/article/pii/S0263876218304337) 
-and on [butanediol synthesis](https://www.sciencedirect.com/science/article/pii/S0263876223004689)
-```
-@article{hassanaly2024inverse,
-  title={Bayesian calibration of bubble size dynamics applied to \ce{CO2} gas fermenters},
-  author={Hassanaly, Malik and Parra-Alvarez, John M. and Rahimi, Mohammad J. and Sitaraman, Hariswaran},
-  journal={Under Review},
-  year={2024},
-}
+To cite BiRD, please use these articles on [CO2 interphase mass transfer](https://doi.org/10.1016/j.cherd.2025.01.034) (open access [link](https://arxiv.org/pdf/2404.19636) ) on [aerobic bioreactors](https://doi.org/10.1016/j.cherd.2018.08.033) and on [butanediol synthesis](https://doi.org/10.1016/j.cherd.2023.07.031)
 
 
+```
+@article{hassanaly2025inverse,
+    title={Bayesian calibration of bubble size dynamics applied to \ce{CO2} gas fermenters},
+    author={Hassanaly, Malik and Parra-Alvarez, John M. and Rahimi, Mohammad J., Municchi, Federico and Sitaraman, Hariswaran},
+    journal={Chemical Engineering Research and Design},
+    year={2025},
+  }
+
 @article{rahimi2018computational,
   title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution},
   author={Rahimi, Mohammad J and Sitaraman, Hariswaran and Humbird, David and Stickel, Jonathan J},

applications/compute_kla_uq.py

@@ -0,0 +1,65 @@
+import argparse
+import os
+
+from bird import BIRD_KLA_DATA_DIR
+from bird.postprocess.kla_utils import compute_kla, print_res_dict
+
+parser = argparse.ArgumentParser(description="KLA calculation with UQ")
+parser.add_argument(
+    "-i",
+    "--data_file",
+    type=str,
+    metavar="",
+    required=False,
+    help="data_file",
+    default=os.path.join(BIRD_KLA_DATA_DIR, "volume_avg.dat"),
+)
+parser.add_argument(
+    "-ti",
+    "--time_index",
+    type=int,
+    metavar="",
+    required=False,
+    help="column index for time",
+    default=0,
+)
+parser.add_argument(
+    "-ci",
+    "--conc_index",
+    type=int,
+    metavar="",
+    required=False,
+    help="column index for concentration",
+    default=1,
+)
+parser.add_argument(
+    "-no_db",
+    "--no_data_bootstrap",
+    action="store_true",
+    help="Do not do data bootstrapping",
+)
+parser.add_argument(
+    "-mc",
+    "--max_chop",
+    type=int,
+    metavar="",
+    required=False,
+    help="maximum number of early data to remove",
+    default=None,
+)
+
+args, unknown = parser.parse_known_args()
+
+if args.no_data_bootstrap:
+    bootstrap = False
+else:
+    bootstrap = True
+
+res_dict = compute_kla(
+    filename=args.data_file,
+    time_ind=args.time_index,
+    conc_ind=args.conc_index,
+    bootstrap=bootstrap,
+    max_chop=args.max_chop,
+)
+print_res_dict(res_dict)

docs/source/postprocess.rst

@@ -51,5 +51,45 @@ Generates (among others)
 
 
 
+Compute kLa with uncertainty estimates
+------------
+
+Based on the time-history of the concentration of a species, one can calculate kLa by fitting the function
+
+.. math::
+
+   (C^* - C_0) (1-\exp(-kLa (t-t_0)) + C_0 
+
+where :math:`C^*` is the equilibrium concentration (to be fitted), :math:`C_0` is the initial concentration, :math:`t` is time, :math:`t_0` is the initial time after which concentration is recorded 
+
+Accurate estimates can be obtained if sufficient data is acquired. Otherwise, it may be useful to derive uncertainty estimates about :math:`C^*` and :math:`kLa` (the parameters fitted)
+
+This can be achieved with a Bayesian calibration procedure. The calibration is conducted by removing transient data, and by doing a data bootstrapping. The number of data to remove in the transient phase is automatically determined by examining how accurate is the fit.
+
+
+.. code-block:: console
+
+   python applications/compute_kla_uq.py -i bird/postprocess/data_kla/volume_avg.dat -ti 0 -ci 1 -mc 10 
+
+Generates
+
+.. code-block:: console
+
+   Chopping index = 0
+   Chopping index = 1
+   Chopping index = 2
+   Chopping index = 3
+   Chopping index = 4
+   Doing data bootstrapping
+   	 scenario 0
+   	 scenario 1
+   	 scenario 2
+   	 scenario 3
+   For bird/postprocess/data_kla/volume_avg.dat with time index: 0, concentration index: 1
+   	kla = 0.09005 +/- 0.0006387
+   	cstar = 0.3107 +/- 0.0006122
+   Without data bootstrap
+   	kla = 0.09014 +/- 0.0005957
+   	cstar = 0.3105 +/- 0.0005472
 
 

docs/source/references.rst

@@ -3,16 +3,16 @@ References
 
 Software record `SWR 24-35 <https://www.osti.gov/biblio/2319227>`_
 
-To cite BiRD, please use these articles on `CO2 interphase mass transfer (open access) <https://arxiv.org/pdf/2404.19636>`_ on `aerobic bioreactors <https://www.sciencedirect.com/science/article/pii/S0263876218304337>`_ and on `butanediol synthesis <https://www.sciencedirect.com/science/article/pii/S0263876223004689>`_
+To cite BiRD, please use these articles on `CO2 interphase mass transfer <https://doi.org/10.1016/j.cherd.2025.01.034>`_ (open access `link <https://arxiv.org/pdf/2404.19636>`_ ) on `aerobic bioreactors <https://doi.org/10.1016/j.cherd.2018.08.033>`_ and on `butanediol synthesis <https://doi.org/10.1016/j.cherd.2023.07.031>`_
 
 
 .. code-block:: console 
 
-   @article{hassanaly2024inverse,
+   @article{hassanaly2025inverse,
      title={Bayesian calibration of bubble size dynamics applied to \ce{CO2} gas fermenters},
-     author={Hassanaly, Malik and Parra-Alvarez, John M. and Rahimi, Mohammad J. and Sitaraman, Hariswaran},
-     journal={Under Review},
-     year={2024},
+     author={Hassanaly, Malik and Parra-Alvarez, John M. and Rahimi, Mohammad J., Municchi, Federico and Sitaraman, Hariswaran},
+     journal={Chemical Engineering Research and Design},
+     year={2025},
    }