Syncup

.github/linters/.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
-skip = None, .git,OFsolvers,tutorial_cases,experimental_cases,build,_build,__pycache__,data_conditional_mean,Figures,assets
+skip = None, .git,OFsolvers,*.pdf, tutorial_cases,experimental_cases,build,_build,__pycache__,data_conditional_mean,Figures,assets
 ignore-words = .github/linters/.codespell-ignore-words

.github/workflows/ci.yml

@@ -52,7 +52,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.13']
         os: ['ubuntu-latest', 'macos-latest']
     defaults:
       run:
@@ -67,15 +67,8 @@ jobs:
           pip install --upgrade pip
           pip install .
           pip install pytest
-      - name: Test preprocess
-        run: |
-          pytest tests/preprocess
-      - name: Test mesh
-        run: |
-          pytest tests/meshing
-      - name: Test postprocessing
-        run: |
-          pytest tests/postprocess
+      - name: Test
+        run: pytest .
 
   Test-pypi-Bird:
     name: Test-pypi-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -176,4 +169,9 @@ jobs:
           cd tutorial_cases/airlift_40m
           bash run.sh
           cd ../../
+      - name: Run flat panel reactor tutorial
+        run: |
+          cd tutorial_cases/FlatPanel_250L_ASU
+          bash run.sh
+          cd ../../
 

.gitignore

@@ -136,3 +136,4 @@ dmypy.json
 *.stl
 
 *.swp
+.vim

README.md

@@ -47,12 +47,15 @@ To cite BiRD, please use these articles on [CO2 interphase mass transfer](https:
 
 
 ```
-@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{hassanaly2025bayesian,
+  title={Bayesian calibration of bubble size dynamics applied to CO2 gas fermenters},
+  author={Hassanaly, Malik and Parra-Alvarez, John M and Rahimi, Mohammad J and Municchi, Federico and Sitaraman, Hariswaran},
+  journal={Chemical Engineering Research and Design},
+  volume={215},
+  pages={312--328},
+  year={2025},
+  publisher={Elsevier}
+}
 
 @article{rahimi2018computational,
   title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution},

applications/sparger_placement_opt.py

@@ -0,0 +1,17 @@
+import os
+import pickle
+import shutil
+
+import numpy as np
+
+from bird.preprocess.json_gen.design_io import *
+from bird.preprocess.json_gen.generate_designs import *
+
+if __name__ == "__main__":
+
+    generate_single_scaledup_reactor_sparger_cases(
+        sparger_locs=[0.3, 0.5, 1.4],
+        sim_id=0,
+        vvm=0.4,
+        study_folder=".",
+    )

bird/__init__.py

@@ -5,6 +5,7 @@
 from bird.version import __version__
 
 BIRD_DIR = os.path.dirname(os.path.realpath(__file__))
+BIRD_CASE_DIR = os.path.join(BIRD_DIR, "../tutorial_cases")
 BIRD_MESH_DIR = os.path.join(BIRD_DIR, "meshing")
 BIRD_POST_DIR = os.path.join(BIRD_DIR, "postprocess")
 BIRD_PRE_DIR = os.path.join(BIRD_DIR, "preprocess")
@@ -34,4 +35,9 @@
 )
 BIRD_EARLY_PRED_DATA_DIR = os.path.join(BIRD_POST_DIR, "data_early")
 BIRD_KLA_DATA_DIR = os.path.join(BIRD_POST_DIR, "data_kla")
+BIRD_CASE_GEN_DATA_DIR = os.path.join(BIRD_PRE_DIR, "data_case_gen")
 BIRD_INV_DIR = os.path.join(BIRD_DIR, "inverse_modeling")
+
+from bird.logging_config import setup_logging
+
+setup_logging(level="INFO")

bird/calibration/param_nn.py

@@ -1,4 +1,5 @@
 import argparse
+import logging
 import os
 import sys
 import time
@@ -13,6 +14,8 @@
 from sklearn.preprocessing import MinMaxScaler, StandardScaler
 from tensorflow.keras import initializers, layers, optimizers, regularizers
 
+logger = logging.getLogger(__name__)
+
 
 def flexible_activation(x, activation):
     if activation is None:
@@ -36,7 +39,7 @@ def flexible_activation(x, activation):
     elif activation.lower() == "leakyrelu":
         out = layers.LeakyReLU()(x)
     else:
-        sys.exit(f"ERROR: unknown activation {activation}")
+        raise NotImplementedError(f"unknown activation {activation}")
     return out
 
 
@@ -185,7 +188,7 @@ def train(
         gradient_threshold=None,
     ):
         if gradient_threshold is not None:
-            print(f"INFO: clipping gradients at {gradient_threshold:.2g}")
+            logger.info("clipping gradients at {gradient_threshold:.2g}")
         # Make sure the control file for learning rate is consistent with main.py, at least at first
         self.prepareLog()
         bestLoss = None

bird/logging_config.py

@@ -0,0 +1,34 @@
+import logging
+from pathlib import Path
+
+
+class ConditionalFormatter(logging.Formatter):
+    def format(self, record):
+        """Change how to log if it is an INFO or a WARNING/ERROR"""
+        if record.levelno >= logging.WARNING:
+            self._style._fmt = (
+                "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
+            )
+        else:
+            self._style._fmt = "%(asctime)s [%(levelname)s] bird: %(message)s"
+        return super().format(record)
+
+
+def setup_logging(logfile: str | None = None, level=logging.INFO):
+    """Setup logging"""
+
+    logger = logging.getLogger()
+    logger.setLevel(level)
+
+    formatter = ConditionalFormatter()
+
+    # Console handler
+    ch = logging.StreamHandler()
+    ch.setFormatter(formatter)
+    logger.addHandler(ch)
+
+    # Optional file handler
+    if logfile:
+        fh = logging.FileHandler(Path(logfile))
+        fh.setFormatter(formatter)
+        logger.addHandler(fh)

bird/meshing/_mesh_tools.py

@@ -1,18 +1,46 @@
 import json
+import logging
+import os
 import sys
 from pathlib import Path
 
 import numpy as np
 from ruamel.yaml import YAML
 
+logger = logging.getLogger(__name__)
+
 
 def parseJsonFile(input_filename):
     with open(input_filename) as f:
         inpt = json.load(f)
     return inpt
 
 
+def check_for_tabs_in_yaml(file_path: str) -> None:
+    """
+    Checks if a YAML file contains any tab characters.
+    Raises a ValueError if tabs found.
+
+    Parameters
+    ----------
+    file_path: str
+        path to yaml filename
+    """
+
+    with open(file_path, "r", encoding="utf-8") as f:
+        lines = f.readlines()
+    for iline, line in enumerate(lines):
+        if "\t" in line:
+            raise ValueError(
+                f"Tab character found on line {iline} of '{file_path}'. "
+                "YAML files must use spaces for indentation."
+            )
+
+
 def parseYAMLFile(input_filename):
+    if not os.path.exists(input_filename):
+        raise FileNotFoundError(input_filename)
+    check_for_tabs_in_yaml(input_filename)
     yaml = YAML(typ="safe")
     inpt = yaml.load(Path(input_filename))
     return inpt
@@ -85,10 +113,8 @@ def bissection(val, stretch_fun, N1):
     resultmin = stretch_fun(Gmin, N1) - val
     resultmax = stretch_fun(Gmax, N1) - val
     if resultmin * resultmax > 0:
-        print(
-            "Error,the initial bounds of grading do not encompass the solution"
-        )
-        # stop
+        logger.error("Initial bounds of grading do not encompass the solution")
+        sys.exit()
 
     for i in range(1000):
         Gmid = 0.5 * (Gmax + Gmin)
@@ -202,8 +228,8 @@ def verticalCoarsening(
                         length / deltaE, stretch_fun, NVert[ind]
                     )
                 if iterate:
-                    print(
-                        f"WARNING: reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
+                    logger.warning(
+                        f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
                     )
                 block_cell_minus_length[ind] = deltaE
                 block_cell_plus_length[ind] = deltaE * gradVert[ind]
@@ -225,8 +251,8 @@ def verticalCoarsening(
                         length / deltaE, stretch_fun, NVert[ind]
                     )
                 if iterate:
-                    print(
-                        f"WARNING: reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
+                    logger.warning(
+                        f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
                     )
                 block_cell_minus_length[ind] = deltaE / gradVert[ind]
                 block_cell_plus_length[ind] = deltaE
@@ -316,8 +342,8 @@ def radialCoarsening(
                         length / deltaE, stretch_fun, NR[ind]
                     )
                 if iterate:
-                    print(
-                        f"WARNING: reduced NR[{ind}] from {origNR} to {NR[ind]}"
+                    logger.warning(
+                        f"reduced NR[{ind}] from {origNR} to {NR[ind]}"
                     )
                 block_cell_minus_length[ind] = deltaE
                 block_cell_plus_length[ind] = deltaE * gradR[ind]
@@ -334,8 +360,8 @@ def radialCoarsening(
                         length / deltaE, stretch_fun, NR[ind]
                     )
                 if iterate:
-                    print(
-                        f"WARNING: reduced NR[{ind}] from {origNR} to {NR[ind]}"
+                    logger.warning(
+                        f"reduced NR[{ind}] from {origNR} to {NR[ind]}"
                     )
                 block_cell_minus_length[ind] = deltaE / gradR[ind]
                 block_cell_plus_length[ind] = deltaE
@@ -359,9 +385,9 @@ def radialCoarsening(
     #    if (gradR[last_R] > 2 or gradR[last_R] < 0.5) and abs(
     #        ratio - 1
     #    ) <= 1e-12:
-    #        print(
-    #            "WARNING: radial smoothing had to be used because your mesh is very coarse"
+    #        logger.warning(
+    #            "radial smoothing had to be used because your mesh is very coarse"
     #        )
-    #        print("\tIncrease NS in input file to avoid this warning")
+    #        logger.warning("\tIncrease NS in input file to avoid this warning")
 
     return NR, gradR, minCell, maxCell

bird/meshing/_stirred_tank_reactor.py

@@ -2,7 +2,8 @@
 from pathlib import Path
 
 import numpy as np
-from ruamel.yaml import YAML
+
+from bird.meshing._mesh_tools import parseYAMLFile
 
 
 class StirredTankReactor:
@@ -133,11 +134,6 @@ def __init__(
     def from_file(cls, yamlfile):
         if ".yaml" not in yamlfile:
             yamlfile += ".yaml"
-        if os.path.exists(yamlfile):
-            yamlpath = Path(yamlfile)
-        else:
-            raise FileNotFoundError(yamlfile)
-        yaml = YAML(typ="safe")
-        in_dict = yaml.load(yamlpath)
+        in_dict = parseYAMLFile(yamlfile)
         react_dict = {**in_dict["geometry"], **in_dict["mesh"]}
         return cls(**react_dict)

bird/meshing/block_cyl_mesh.py

@@ -1,10 +1,13 @@
+import logging
 import os
 import sys
 
 import numpy as np
 
 from bird.meshing._mesh_tools import *
 
+logger = logging.getLogger(__name__)
+
 
 def assemble_geom(input_file, topo_file):
     # inpt = parseJsonFile(input_file)
@@ -106,7 +109,6 @@ def assemble_mesh(input_file, geomDict):
                 ),
                 1,
             )
-    # print(NR)
     NS = [NR[0] * 2]
     # Now figure out grading of each block
     for ir in range(len(R)):
@@ -189,14 +191,14 @@ def assemble_mesh(input_file, geomDict):
         minCellR = np.amin(block_cell_length)
         maxCellR = np.amax(block_cell_length)
 
-    print("Vertical mesh:")
-    print(f"\tTotal NVert {sum(NVert)}")
-    print(f"\tNVert {NVert}")
-    print(f"\tsize min {minCellVert:.2f}mm max {maxCellVert:.2f}mm")
-    print("Radial mesh:")
-    print(f"\tTotal NR {sum(NR)}")
-    print(f"\tNR {NR}")
-    print(f"\tsize min {minCellR:.2f}mm max {maxCellR:.2f}mm")
+    logger.info("Vertical mesh:")
+    logger.info(f"\tTotal NVert {sum(NVert)}")
+    logger.info(f"\tNVert {NVert}")
+    logger.info(f"\tsize min {minCellVert:.2f}mm max {maxCellVert:.2f}mm")
+    logger.info("Radial mesh:")
+    logger.info(f"\tTotal NR {sum(NR)}")
+    logger.info(f"\tNR {NR}")
+    logger.info(f"\tsize min {minCellR:.2f}mm max {maxCellR:.2f}mm")
 
     return {
         "NR": NR,

bird/meshing/stirred_tank_mesh.py

@@ -314,9 +314,6 @@ def write_blocks(outfile, react):
 
     outfile.write(");\n")
 
-    # print "meshz:",meshz
-    # print "meshr:",meshr
-
 
 def write_patches(outfile, react):
     inhub_ci = react.inhub_circ