fixed ion implant table loading first pass

Author: jcdoll

AGENTS.md

@@ -14,7 +14,7 @@ PiezoD/
 │   │   ├── cantileverImplantation.m
 │   │   ├── cantileverPiezoelectric.m
 │   │   ├── cantileverPoly.m
-│   │   ├── lookupTable.mat      # Precomputed data
+│   │   ├── ionImplantLookupTable.mat  # Ion implant lookup data
 │   │   └── sensorSimulation.mdl # Simulink model
 │   └── sampleCode.m             # Usage example
 ├── python/                      # Python port (in progress)
@@ -24,8 +24,10 @@ PiezoD/
 │   │   ├── cantilever_epitaxy.py
 │   │   ├── cantilever_implantation.py
 │   │   ├── cantilever_piezoelectric.py
-│   │   └── cantilever_poly.py
-│   ├── tests/                   # Test suite (empty)
+│   │   ├── cantilever_poly.py
+│   │   └── data/                # Bundled data files
+│   │       └── ionImplantLookupTable.h5
+│   ├── tests/                   # Test suite
 │   ├── examples/                # Usage examples
 │   └── archive/                 # Legacy/experimental scripts
 ├── lookupTableGeneration/       # FLOOXS TCAD simulation (Docker)
@@ -34,7 +36,7 @@ PiezoD/
 │   ├── templates/               # FLOOXS simulation templates
 │   ├── simulations/             # Input/output directory
 │   ├── legacy/                  # TSUPREM-4 reference files
-│   └── lookupTable.mat          # Generated data
+│   └── lookupTable.mat          # Generated source data
 ├── Docs/                        # Website (jemdoc)
 │   ├── html/                    # Generated HTML
 │   └── cgi-bin/                 # Download scripts

lookupTableGeneration/Dockerfile

@@ -21,11 +21,11 @@ ENV FLXSHOME=/opt/flooxs
 ENV PL_LIBRARY=/usr/share/plplot5.15.0/tcl/
 
 # Build FLOOXS
-WORKDIR /opt/flooxs/src
-RUN mkdir -p release && cd release && cmake .. && make -j$(nproc)
+WORKDIR /opt/flooxs
+RUN cp src/License.pdf . && mkdir -p build && cd build && cmake .. && make -j$(nproc)
 
 # Create working directory for simulations
 WORKDIR /work
 
 # The built executable
-ENTRYPOINT ["/opt/flooxs/src/release/flooxs"]
+ENTRYPOINT ["/opt/flooxs/build/flooxs"]

matlab/PiezoD/cantileverImplantation.m

@@ -43,7 +43,7 @@
 
       % Load the lookup table
       try
-        data = open('lookupTable.mat');
+        data = open('ionImplantLookupTable.mat');
         self.lookupTableData = data;
       catch
         fprintf('Dopant type: %s\n', self.doping_type);

matlab/PiezoD/lookupTable.mat matlab/PiezoD/ionImplantLookupTable.matmatlab/PiezoD/lookupTable.mat renamed to matlab/PiezoD/ionImplantLookupTable.mat

@@ -10,10 +10,7 @@
 touch sensation in C. elegans.
 """
 
-from pathlib import Path
-
 import addcopyfighandler  # noqa: F401
-import scipy.io
 
 from piezod import CantileverImplantation
 
@@ -66,17 +63,6 @@
 c.fluid = "air"
 c.number_of_piezoresistors = 4  # Full bridge for temperature compensation
 
-# Load the lookup table for electrical calculations
-lookup_path = Path(__file__).parent.parent.parent / "matlab" / "PiezoD" / "lookupTable.mat"
-if lookup_path.exists():
-    mat_data = scipy.io.loadmat(str(lookup_path), squeeze_me=True)
-    c.load_lookup_table(mat_data)
-    lookup_loaded = True
-else:
-    print(f"Warning: Lookup table not found at {lookup_path}")
-    print("Electrical parameters requiring lookup table will not be available.")
-    lookup_loaded = False
-
 # Print design summary
 print("=== Ion-Implanted Cantilever Design ===")
 print("Based on Park et al. JMEMS 2010 (optimized for C. elegans force sensing)")
@@ -129,35 +115,34 @@ def print_row(name, model_str, paper_val, tol=0.15):
 print_row("Stiffness (mN/m)", f"{stiffness:.2f}", paper["stiffness_mN_m"])
 print_row("Resonant freq (kHz)", f"{freq:.2f}", paper["freq_kHz"])
 
-# Electrical properties (require lookup table)
-if lookup_loaded:
-    Rs = c.sheet_resistance()
-    beta = c.beta()
-    Xj = c.junction_depth * 1e6  # um
-    resistance = c.resistance()
-    power = c.power_dissipation() * 1e3  # mW
-    sqrt_Dt = c.diffusion_length * 1e4  # um
-
-    print_row("Junction depth t_p (um)", f"{Xj:.2f}", paper["junction_depth_um"], tol=0.25)
-    print_row("Resistance R_piezo (Ohm)", f"{resistance:.0f}", paper["resistance_ohm"], tol=0.25)
-    print_row("Beta* (efficiency)", f"{beta:.2f}", paper["beta_star"])
-    print_row("sqrt(Dt) (um)", f"{sqrt_Dt:.4f}", paper["sqrt_Dt_um"])
-    print_row("Power dissipation (mW)", f"{power:.2f}", paper["power_mW"])
-
-    # Performance metrics
-    print("-" * 62)
-    force_sensitivity = c.force_sensitivity()
-    force_res = c.force_resolution() * 1e12  # pN
-
-    print_row("Sensitivity S_FV (V/N)", f"{force_sensitivity:.0f}", paper["sensitivity_V_N"])
-    print_row("Force resolution (pN)", f"{force_res:.1f}", paper["force_resolution_pN"])
-
-    # Additional derived parameters
-    print("-" * 62)
-    print("  Additional Parameters:")
-    print(f"    Sheet resistance: {Rs:.1f} Ohm/sq")
-    print(f"    Hooge parameter alpha: {c.alpha():.2e}")
-    print(f"    Number of squares: {c.number_of_squares():.1f}")
-    print(f"    Piezoresistor width: {c.w_pr() * 1e6:.1f} um")
+# Electrical properties (from bundled lookup table)
+Rs = c.sheet_resistance()
+beta = c.beta()
+Xj = c.junction_depth * 1e6  # um
+resistance = c.resistance()
+power = c.power_dissipation() * 1e3  # mW
+sqrt_Dt = c.diffusion_length * 1e4  # um
+
+print_row("Junction depth t_p (um)", f"{Xj:.2f}", paper["junction_depth_um"], tol=0.25)
+print_row("Resistance R_piezo (Ohm)", f"{resistance:.0f}", paper["resistance_ohm"], tol=0.25)
+print_row("Beta* (efficiency)", f"{beta:.2f}", paper["beta_star"])
+print_row("sqrt(Dt) (um)", f"{sqrt_Dt:.4f}", paper["sqrt_Dt_um"])
+print_row("Power dissipation (mW)", f"{power:.2f}", paper["power_mW"])
+
+# Performance metrics
+print("-" * 62)
+force_sensitivity = c.force_sensitivity()
+force_res = c.force_resolution() * 1e12  # pN
+
+print_row("Sensitivity S_FV (V/N)", f"{force_sensitivity:.0f}", paper["sensitivity_V_N"])
+print_row("Force resolution (pN)", f"{force_res:.1f}", paper["force_resolution_pN"])
+
+# Additional derived parameters
+print("-" * 62)
+print("  Additional Parameters:")
+print(f"    Sheet resistance: {Rs:.1f} Ohm/sq")
+print(f"    Hooge parameter alpha: {c.alpha():.2e}")
+print(f"    Number of squares: {c.number_of_squares():.1f}")
+print(f"    Piezoresistor width: {c.w_pr() * 1e6:.1f} um")
 
 print("=" * 62)

python/examples/ion_implantation.py

@@ -9,13 +9,13 @@
 import addcopyfighandler  # noqa: F401
 import matplotlib.pyplot as plt
 import numpy as np
-import scipy.io
+
+from piezod.cantilever_implantation import _load_lookup_table
 
 plt.style.use("piezod.default")
 
-# Load lookup table
-lookup_path = Path(__file__).parent.parent.parent / "matlab" / "PiezoD" / "lookupTable.mat"
-mat_data = scipy.io.loadmat(str(lookup_path), squeeze_me=True)
+# Load bundled lookup table
+mat_data = _load_lookup_table()
 
 # Available parameter ranges from lookup table
 DOSES = mat_data["ImplantDoses"]  # [2e14, 2e15, 2e16]

python/examples/ion_implantation_figures.py

@@ -27,6 +27,7 @@ dependencies = [
     "scipy>=1.7.0",
     "matplotlib>=3.4.0",
     "addcopyfighandler>=2.0.0",
+    "h5py>=3.0.0",
 ]
 
 [project.optional-dependencies]