Add empirical scale factor to read_gamess (#704)

strawberryfields/apps/qchem/utils.py

@@ -99,28 +99,30 @@ def duschinsky(
     return U, delta
 
 
-def read_gamess(file) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
+def read_gamess(
+    file, scale_factor: float = 1.0
+) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
     r"""Reads molecular data from the output file generated by the GAMESS quantum chemistry package
     :cite:`schmidt1993general`.
 
     This function extracts the atomic coordinates (r), atomic masses (m), vibrational frequencies
-    (w), and normal modes (l) of a molecule from the output file of a vibrational frequency
+    (w), and normal modes (n) of a molecule from the output file of a vibrational frequency
     calculation performed with the GAMESS quantum chemistry package. The output file must contain
     the results of a `RUNTYP=HESSIAN` calculation performed with GAMESS. We recommend checking the
     output of this function with the GAMESS results to assure that the GAMESS output file is parsed
-    correctly.
+    correctly. Please also check if the normal modes are mass-weighted.
 
     **Example usage:**
 
-    >>> r, m, w, l = read_gamess('../BH_data.out')
+    >>> r, m, w, n = read_gamess('../BH_data.out')
     >>> r # atomic coordinates
     array([[0.0000000, 0.0000000, 0.0000000],
            [1.2536039, 0.0000000, 0.0000000]])
     >>> m # atomic masses
     array([11.00931,  1.00782])
     >>> w # vibrational frequencies
     array([19.74, 19.73, 0.00, 0.00, 0.00, 2320.32])
-    >>> l # normal modes
+    >>> n # normal modes
     array([[-0.0000000e+00, -7.5322000e-04, -8.7276210e-02,  0.0000000e+00,
          8.2280900e-03,  9.5339055e-01],
        [-0.0000000e+00, -8.7276210e-02,  7.5322000e-04,  0.0000000e+00,
@@ -136,6 +138,7 @@ def read_gamess(file) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
 
     Args:
         file (str): path to the GAMESS output file
+        scale_factor: empirical scale factor for correcting the vibrational frequencies
 
     Returns:
         tuple[array, array, array, array]: atomic coordinates, atomic masses, normal mode
@@ -146,7 +149,7 @@ def read_gamess(file) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
         r = []
         m = []
         w = []
-        l = []
+        n = []
 
         for line in f:
 
@@ -172,7 +175,7 @@ def read_gamess(file) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
                 d = []
                 for _ in range(len(r) * 3):
                     d.append(f.readline().rstrip().split()[-n_mode:])
-                l.append(np.array(d, float).T)
+                n.append(np.array(d, float).T)
 
     if not r:
         raise ValueError("No atomic coordinates found in the output file")
@@ -186,8 +189,8 @@ def read_gamess(file) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
     return (
         np.concatenate(r).reshape(len(r), 3),
         np.concatenate(m),
-        np.concatenate(w),
-        np.concatenate(l),
+        np.concatenate(w) * scale_factor,
+        np.concatenate(n),
     )