Merge branch 'docs' into 'main'

Documentation and lint.

See merge request !7

README.md

@@ -39,7 +39,7 @@ The usage requires only four lines of code:
 ## Further options
 
 The behavior can be finely controlled by passing additional keyword arguments to the
-`gext.Extrapolator()` constructor. **Note: many options are not yet implemented.**
+`gext.Extrapolator()` constructor. **Note:** some options might be implemented in the future.
 
 This is an up to date list of available keyword options:
 
@@ -58,6 +58,6 @@ Some options can be piped to the fitting modules.
 
 This work is based on these papers:
 
-  1. F. Pes, È. Polack, P. Mazzeo, G. Dusson, B. Stamm, and F. Lipparini, “A Quasi Time-Reversible scheme based on density matrix extrapolation on the Grassmann manifold for Born-Oppenheimer Molecular Dynamics.” arXiv, 2023. doi: 10.48550/ARXIV.2307.05653.
+  1. F. Pes, É. Polack, P. Mazzeo, G. Dusson, B. Stamm, and F. Lipparini, “A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics,” The Journal of Physical Chemistry Letters, vol. 14, no. 43. American Chemical Society (ACS), pp. 9720–9726, Oct. 25, 2023. doi: 10.1021/acs.jpclett.3c02098.
   2. É. Polack, G. Dusson, B. Stamm, and F. Lipparini, “Grassmann Extrapolation of Density Matrices for Born–Oppenheimer Molecular Dynamics,” Journal of Chemical Theory and Computation, vol. 17, no. 11. American Chemical Society (ACS), pp. 6965–6973, Oct. 08, 2021. doi: 10.1021/acs.jctc.1c00751. 
   3. É. Polack, A. Mikhalev, G. Dusson, B. Stamm, and F. Lipparini, “An approximation strategy to compute accurate initial density matrices for repeated self-consistent field calculations at different geometries,” Molecular Physics, vol. 118, no. 19–20. Informa UK Limited, p. e1779834, Jun. 22, 2020. doi: 10.1080/00268976.2020.1779834.

gext/fitting.py

@@ -70,7 +70,7 @@ class LeastSquare(AbstractFitting):
 
 class QuasiTimeReversible(AbstractFitting):
 
-    """Quasi time reversible fitting scheme. Not yet implemented."""
+    """Quasi time reversible fitting scheme."""
 
     supported_options = {
         "regularization": 0.0,
@@ -85,7 +85,8 @@ class QuasiTimeReversible(AbstractFitting):
             raise ValueError("Unsupported value for regularization")
 
     def fit(self, vectors: List[np.ndarray], target: np.ndarray):
-        """Time reversible least square minimization fitting."""
+        """Given a set of vectors and a target return the fitting
+        coefficients in a quasi time reversible scheme."""
 
         past_target = vectors[0]
         matrix = np.array(vectors[1:]).T

gext/main.py

@@ -25,7 +25,8 @@ class Extrapolator:
 
     def __init__(self, nelectrons: int, nbasis: int, natoms: int, **kwargs):
 
-        if not (type(nelectrons) == int and type(nbasis) == int and type(natoms) == int):
+        if not (isinstance(nelectrons, int) and isinstance(nbasis, int) \
+                and isinstance(natoms, int)):
             raise ValueError("Dimensions are not integers")
 
         self.nelectrons = nelectrons
@@ -33,11 +34,13 @@ class Extrapolator:
         self.natoms = natoms
         self.set_options(**kwargs)
 
-        self.gammas = CircularBuffer(self.options["nsteps"], (self.nelectrons//2, self.nbasis))
+        self.gammas = CircularBuffer(self.options["nsteps"],
+            (self.nelectrons//2, self.nbasis))
         self.descriptors = CircularBuffer(self.options["nsteps"],
             ((self.natoms - 1)*self.natoms//2, ))
         if self.options["store_overlap"]:
-            self.overlaps = CircularBuffer(self.options["nsteps"], (self.nbasis, self.nbasis))
+            self.overlaps = CircularBuffer(self.options["nsteps"],
+                (self.nbasis, self.nbasis))
 
         self.tangent: Optional[np.ndarray] = None