GSOC 2025: Add electron density integration tools and BFit data processor

scripts/bfit_data_processor.py

@@ -0,0 +1,158 @@
+#!/usr/bin/env python3
+"""
+BFit Data Processor
+
+Processes promolecular coefficients and exponents from theochem/BFit
+data files for integration with Grid library.
+
+Note: This version handles s-type orbital data.
+"""
+
+import sys
+from pathlib import Path
+from dataclasses import dataclass
+from typing import Dict, Optional
+
+import numpy as np
+
+sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
+
+# Element symbol to atomic number mapping
+ELEMENT_TO_ATOMIC_NUMBER = {
+    "h": 1,
+    "he": 2,
+    "li": 3,
+    "be": 4,
+    "b": 5,
+    "c": 6,
+    "n": 7,
+    "o": 8,
+    "f": 9,
+    "ne": 10,
+    "na": 11,
+    "mg": 12,
+    "al": 13,
+    "si": 14,
+    "p": 15,
+    "s": 16,
+    "cl": 17,
+    "ar": 18,
+    "k": 19,
+    "ca": 20,
+    "sc": 21,
+    "ti": 22,
+    "v": 23,
+    "cr": 24,
+    "mn": 25,
+    "fe": 26,
+    "co": 27,
+    "ni": 28,
+    "cu": 29,
+    "zn": 30,
+    "ga": 31,
+    "ge": 32,
+    "as": 33,
+    "se": 34,
+    "br": 35,
+    "kr": 36,
+    "rb": 37,
+    "sr": 38,
+    "y": 39,
+    "zr": 40,
+    "nb": 41,
+    "mo": 42,
+    "tc": 43,
+    "ru": 44,
+    "rh": 45,
+    "pd": 46,
+    "ag": 47,
+    "cd": 48,
+    "in": 49,
+    "sn": 50,
+    "sb": 51,
+    "te": 52,
+    "i": 53,
+    "xe": 54,
+}
+
+
+@dataclass
+class BFitElementData:
+    """Store BFit data for a single element"""
+
+    symbol: str
+    atomic_number: int
+    coeffs: np.ndarray
+    exps: np.ndarray
+    num_s: int = 0
+    num_p: int = 0
+
+    @property
+    def coeffs_s(self) -> np.ndarray:
+        """S-type coefficients alias for compatibility"""
+        return self.coeffs
+
+    @property
+    def exps_s(self) -> np.ndarray:
+        """S-type exponents alias for compatibility"""
+        return self.exps
+
+
+class BFitDataProcessor:
+    """Process BFit data and convert to Grid library format"""
+
+    def __init__(self, data_file: Path):
+        self.data_file = data_file
+        self.raw_data: Optional[np.lib.npyio.NpzFile] = None
+        self.element_data: Dict[str, BFitElementData] = {}
+
+    def load_bfit_data(self) -> bool:
+        """Load BFit data file"""
+        try:
+            self.raw_data = np.load(self.data_file)
+            return True
+        except Exception as e:
+            print(f"Failed to load data file: {e}")
+            return False
+
+    def parse_element_data(self) -> Dict[str, BFitElementData]:
+        """Parse element data from BFit file"""
+        if self.raw_data is None:
+            print("Data not loaded, call load_bfit_data() first")
+            return {}
+
+        # Get all elements with coefficients
+        element_symbols = set()
+        for key in self.raw_data.files:
+            if "_coeffs_s" in key:
+                symbol = key.replace("_coeffs_s", "")
+                element_symbols.add(symbol)
+
+        for symbol in element_symbols:
+            try:
+                coeffs_key = f"{symbol}_coeffs_s"
+                exps_key = f"{symbol}_exps_s"
+
+                if coeffs_key not in self.raw_data or exps_key not in self.raw_data:
+                    print(f"Missing coefficient or exponent data for element {symbol}")
+                    continue
+
+                coeffs = self.raw_data[coeffs_key]
+                exps = self.raw_data[exps_key]
+                atomic_number = ELEMENT_TO_ATOMIC_NUMBER.get(symbol, 0)
+
+                element_data = BFitElementData(
+                    symbol=symbol,
+                    atomic_number=atomic_number,
+                    coeffs=coeffs,
+                    exps=exps,
+                    num_s=len(coeffs),
+                    num_p=0,
+                )
+
+                self.element_data[symbol] = element_data
+
+            except Exception as e:
+                print(f"Error parsing element {symbol}: {e}")
+
+        return self.element_data