Add utils directory with script for fixing molden files with incorrect orbital normalization (#5)

Author: JMorado

utils/README.md

@@ -0,0 +1,23 @@
+# Utilities
+
+## fix_molden_normalization.py
+
+`orca_2mkl` seems to have a bug where certain molecules get written with incorrect orbital normalization. 
+
+When you hit an error like:
+
+```
+Error loading wavefunction file: Could not correct the data read from orca.molden.input. The molden or mkl file you are trying to load contains errors. Please report this problem to Toon.Verstraelen@UGent.be, so he can fix it.
+```
+
+Use this script to fix the normalization:
+
+```bash
+python utils/fix_molden_normalization.py orca.molden.input
+```
+
+This creates `fixed_orca.molden.input` with properly normalized orbitals that PyXDM can process.
+
+### Technical details
+
+HORTON tries 4 automatic fixes (ORCA-specific, PSI4, Turbomole, general renormalization), but all fail for this bug. The issue requires both fixing the basis set contractions (ORCA fix) AND renormalizing the MO coefficients. HORTON only attempts basis fixes but checks the final orbital normalization, which still fails. This script applies HORTON's ORCA basis fix first, then renormalizes each orbital coefficient against the corrected overlap matrix.

utils/fix_molden_normalization.py

@@ -0,0 +1,150 @@
+"""
+Fix molden files with incorrect orbital normalization.
+
+orca_2mkl seems to have a bug where certain molecules get written with
+incorrect basis set normalization AND orbital coefficient scaling.
+This causes HORTON to fail with "Could not correct the data read from..." errors.
+
+This script applies ORCA basis fix then renormalizes MO coefficients.
+"""
+
+import sys
+from pathlib import Path
+
+import numpy as np
+
+try:
+    import horton.io.molden as molden_module
+    from horton import IOData
+except ImportError:
+    print("Error: HORTON not installed")
+    sys.exit(1)
+
+
+def fix_molden_file(input_file, output_file=None):
+    """
+    Load molden file, apply ORCA basis fix, renormalize orbitals, and save.
+
+    Parameters
+    ----------
+    input_file : str
+        Path to input molden file
+    output_file : str, optional
+        Path to output molden file. Defaults to fixed_input_file
+
+    Returns
+    -------
+    str
+        Path to the output file
+    """
+    if output_file is None:
+        output_file = "fixed_" + input_file
+
+    print(f"Loading {input_file}...")
+
+    # Temporarily patch HORTON to not raise errors on bad normalization
+    original_fix = molden_module._fix_molden_from_buggy_codes
+
+    def patched_fix(result, filename):
+        try:
+            original_fix(result, filename)
+        except IOError:
+            print("  [Note: HORTON's automatic fixes failed, proceeding to manual fix...]")
+            # Apply ORCA basis fix manually
+            from horton import GOBasis
+
+            obasis = result["obasis"]
+            orca_con_coeffs = molden_module._get_fixed_con_coeffs(obasis, "orca")
+            if orca_con_coeffs is not None:
+                orca_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims, obasis.shell_types, obasis.alphas, orca_con_coeffs)
+                result["obasis"] = orca_obasis
+                print("  Applied ORCA basis set fix")
+
+    molden_module._fix_molden_from_buggy_codes = patched_fix
+
+    try:
+        result = molden_module.load_molden(input_file)
+    finally:
+        molden_module._fix_molden_from_buggy_codes = original_fix
+
+    obasis = result["obasis"]
+    orb_alpha = result["orb_alpha"]
+    orb_beta = result.get("orb_beta")
+
+    print(f"  {obasis.nbasis} basis functions, {orb_alpha.nfn} alpha orbitals")
+
+    # Compute overlap matrix
+    olp = obasis.compute_overlap()
+
+    # Renormalize alpha orbitals
+    print("  Renormalizing alpha orbitals...")
+    max_norm = 0.0
+    for i in range(orb_alpha.nfn):
+        c = orb_alpha._coeffs[:, i]
+        norm_sq = np.dot(c, np.dot(olp, c))
+        norm = np.sqrt(norm_sq)
+        max_norm = max(max_norm, norm)
+        orb_alpha._coeffs[:, i] /= norm
+
+    print(f"    Max initial norm: {max_norm:.6f} (should be ~1.0 for correct files)")
+
+    # Renormalize beta orbitals if present
+    if orb_beta is not None:
+        print("  Renormalizing beta orbitals...")
+        for i in range(orb_beta.nfn):
+            c = orb_beta._coeffs[:, i]
+            norm_sq = np.dot(c, np.dot(olp, c))
+            norm = np.sqrt(norm_sq)
+            orb_beta._coeffs[:, i] /= norm
+
+    # Verify correction
+    print("  Verifying normalization...")
+    max_error = 0.0
+    for i in range(orb_alpha.nfn):
+        c = orb_alpha._coeffs[:, i]
+        norm = np.dot(c, np.dot(olp, c))
+        error = abs(norm - 1.0)
+        max_error = max(max_error, error)
+
+    print(f"    Max error: {max_error:.2e} (target: < 1e-4)")
+
+    # Save corrected molden file
+    print(f"\nSaving to {output_file}...")
+
+    kwargs = {
+        "coordinates": result["coordinates"],
+        "numbers": result["numbers"],
+        "obasis": result["obasis"],
+        "orb_alpha": orb_alpha,
+    }
+
+    if orb_beta is not None:
+        kwargs["orb_beta"] = orb_beta
+
+    iodata = IOData(**kwargs)
+
+    # Add optional fields
+    if "energy" in result:
+        iodata.energy = result["energy"]
+    if "permutation" in result:
+        iodata.permutation = result["permutation"]
+
+    iodata.to_file(output_file)
+
+    print("Done. Use the fixed file:")
+    print(f"  pyxdm {output_file} --scheme mbis")
+
+    return output_file
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python fix_molden_normalization.py <input> [output]")
+        print("\nExample:")
+        print("  python fix_molden_normalization.py orca.molden.input")
+        sys.exit(1)
+
+    input_file = sys.argv[1]
+    output_file = sys.argv[2] if len(sys.argv) > 2 else None
+
+    fix_molden_file(input_file, output_file)