Remove deprecated get method calls (#238)

* Removal of deprecated functions [skip actions]

* Add force constant [skip actions]

* NEB refactoring

* Fix units for div mul

* Update changelog

* PR suggestions

---------

Co-authored-by: Shoubhik Maiti <17470159+shoubhikraj@users.noreply.github.com>

.gitignore

@@ -11,7 +11,7 @@ autode\.egg-info/
 doc/_build/
 **.DS_Store
 **htmlcov/
-.coverage
+.coverage*
 coverage.xml
 tests/*.xyz
 **/tmp.xyz
@@ -20,3 +20,4 @@ tests/*.xyz
 *.inp
 *.pyc
 .autode_calculations
+tests/initial_path/*

autode/__init__.py

@@ -5,6 +5,7 @@
 from autode import neb
 from autode import mol_graphs
 from autode import hessians
+from autode.neb import NEB, CINEB
 from autode.reactions.reaction import Reaction
 from autode.reactions.multistep import MultiStepReaction
 from autode.transition_states.transition_state import TransitionState
@@ -61,6 +62,8 @@
     "NCIComplex",
     "Config",
     "Calculation",
+    "NEB",
+    "CINEB",
     "pes",
     "neb",
     "geom",

autode/calculations/calculation.py

@@ -3,12 +3,8 @@
 
 from copy import deepcopy
 from typing import Optional, List
-from autode.utils import deprecated
-from autode.atoms import Atoms
 from autode.point_charges import PointCharge
 from autode.log import logger
-from autode.hessians import Hessian
-from autode.values import PotentialEnergy, Gradient
 from autode.calculations.types import CalculationType
 from autode.calculations.executors import (
     CalculationExecutor,
@@ -305,47 +301,6 @@ def _check_properties_exist(self) -> None:
 
         return None
 
-    # ----------------- Deprecated functions ----------------------
-
-    @deprecated
-    def get_energy(self) -> PotentialEnergy:
-        self._executor.set_properties()
-        return self.molecule.energy
-
-    @deprecated
-    def optimisation_converged(self) -> bool:
-        self._executor.set_properties()
-        return self.optimiser.converged
-
-    @deprecated
-    def optimisation_nearly_converged(self) -> bool:
-        self._executor.set_properties()
-        tol = PotentialEnergy(0.1, units="kcal mol-1")
-        return (
-            not self.optimiser.converged
-            and self.optimiser.last_energy_change < tol
-        )
-
-    @deprecated
-    def get_final_atoms(self) -> Atoms:
-        self._executor.set_properties()
-        return self.molecule.atoms
-
-    @deprecated
-    def get_atomic_charges(self) -> List[float]:
-        self._executor.set_properties()
-        return self.molecule.partial_charges
-
-    @deprecated
-    def get_gradients(self) -> Gradient:
-        self._executor.set_properties()
-        return self.molecule.gradient
-
-    @deprecated
-    def get_hessian(self) -> Hessian:
-        self._executor.set_properties()
-        return self.molecule.hessian
-
 
 def _are_opt(keywords) -> bool:
     return isinstance(keywords, kws.OptKeywords)

autode/constraints.py

@@ -1,5 +1,7 @@
 from collections.abc import MutableMapping
 from typing import Optional, Dict, List
+from copy import deepcopy
+
 from autode.values import Distance
 from autode.log import logger
 
@@ -122,6 +124,9 @@ def update(
 
         return None
 
+    def copy(self) -> "Constraints":
+        return deepcopy(self)
+
 
 class DistanceConstraints(MutableMapping):
     def __init__(self, *args, **kwargs):
@@ -178,3 +183,6 @@ def __setitem__(self, key, value):
             )
 
         self._store[self._key_transform(key)] = Distance(value)
+
+    def copy(self) -> "DistanceConstraints":
+        return deepcopy(self)

autode/neb/ci.py

@@ -3,25 +3,26 @@
 https://doi.org/10.1063/1.1329672
 """
 import numpy as np
+from scipy.optimize import OptimizeResult
 from typing import Optional
 from autode.neb.original import NEB, Images, Image
 from autode.log import logger
 
 
 class CImage(Image):
-    def __init__(self, image):
+    def __init__(self, image: Image):
         """
         Construct a climbing image from a non-climbing one
 
         -----------------------------------------------------------------------
         Arguments:
             image (autode.neb.Image):
         """
-        super().__init__(image.name, image.k)
+        super().__init__(species=image, name=image.name, k=image.k)
         # Set all the current attributes from the regular image
         self.__dict__.update(image.__dict__)
 
-    def get_force(self, im_l, im_r) -> np.ndarray:
+    def get_force(self, im_l: Image, im_r: Image) -> np.ndarray:
         """
         Compute F_m
 
@@ -34,14 +35,13 @@ def get_force(self, im_l, im_r) -> np.ndarray:
         hat_tau, x_l, x, x_r = self._tau_xl_x_xr(im_l, im_r)
 
         # F_m = ∇V(x_m) + (2∇V(x_m).τ)τ
-        return -self.grad + 2.0 * np.dot(self.grad, hat_tau) * hat_tau
+        return -self.gradient + 2.0 * np.dot(self.gradient, hat_tau) * hat_tau
 
 
 class CImages(Images):
     def __init__(
         self,
         images: Images,
-        num: int = None,
         wait_iterations: int = 4,
         init_k: Optional[float] = None,
     ):
@@ -55,11 +55,10 @@ def __init__(
             wait_iterations (int): Number of iterations to wait before turning
                                   on the climbing image
 
-            init_k: Initial force constant
+            init_k: Initial force constant. Must be defined if the images are empty
         """
         super().__init__(
-            num=num if num is not None else len(images),
-            init_k=init_k if init_k is not None else images[0].k,
+            init_k=init_k if init_k is not None else images.init_k,
         )
 
         self.wait_iteration = wait_iterations
@@ -102,9 +101,7 @@ def __init__(self, *args, **kwargs):
 
         self.images = CImages(self.images)
 
-    def _minimise(
-        self, method, n_cores, etol, max_n=30
-    ) -> "scipy.optimize.OptimizeResult":
+    def _minimise(self, method, n_cores, etol, max_n=30) -> OptimizeResult:
         """Minimise th energy of every image in the NEB"""
         logger.info(f"Minimising to ∆E < {etol:.4f} Ha on all NEB coordinates")
         result = super()._minimise(method, n_cores, etol, max_n)

autode/neb/idpp.py

@@ -1,5 +1,10 @@
 import numpy as np
+
 from scipy.spatial import distance_matrix
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from autode.neb.original import Images, Image
 
 
 class IDPP:
@@ -17,7 +22,7 @@ class IDPP:
     as suggested in the paper.
     """
 
-    def __init__(self, images: "autode.neb.original.Images"):
+    def __init__(self, images: "Images"):
         """Initialise a IDPP potential from a set of NEB images"""
 
         if len(images) < 2:
@@ -29,7 +34,7 @@ def __init__(self, images: "autode.neb.original.Images"):
 
         self._set_distance_matrices(images)
 
-    def __call__(self, image: "autode.neb.original.Image") -> float:
+    def __call__(self, image: "Image") -> float:
         r"""
         Value of the IDPP objective function for a single image defined by,
 
@@ -52,7 +57,7 @@ def __call__(self, image: "autode.neb.original.Image") -> float:
 
         return 0.5 * np.sum(w * (r_k - r) ** 2)
 
-    def grad(self, image: "autode.neb.original.Image") -> np.ndarray:
+    def grad(self, image: "Image") -> np.ndarray:
         r"""
         Gradient of the potential with respect to displacement of
         the Cartesian components: :math:`\nabla S = (dS/dx_0, dS/dy_0, dS/dz_0,
@@ -75,7 +80,7 @@ def grad(self, image: "autode.neb.original.Image") -> np.ndarray:
             (np.ndarray): :math:`\nabla S`
         """
 
-        x = np.array(image.species.coordinates).flatten()
+        x = np.array(image.coordinates).flatten()
         grad = np.zeros_like(x)
 
         r = self._distance_matrix(image, unity_diagonal=True)
@@ -105,9 +110,9 @@ def grad(self, image: "autode.neb.original.Image") -> np.ndarray:
         grad[1::3] = np.sum(a * delta[1::3, 1::3], axis=1)  # y
         grad[2::3] = np.sum(a * delta[2::3, 2::3], axis=1)  # z
 
-        return grad
+        return grad.reshape((-1, 3))
 
-    def _set_distance_matrices(self, images) -> None:
+    def _set_distance_matrices(self, images: "Images") -> None:
         """
         For each image determine the optimum distance matrix using
 
@@ -130,22 +135,24 @@ def _set_distance_matrices(self, images) -> None:
         self._diagonal_distance_matrix_idxs = np.diag_indices_from(delta)
         return None
 
-    def _req_distance_matrix(self, image):
+    def _req_distance_matrix(self, image: "Image"):
         """Required distance matrix for an image, with elements r_{ij}^k"""
         return self._dists[image.name]
 
-    def _distance_matrix(self, image, unity_diagonal=False) -> np.ndarray:
+    def _distance_matrix(
+        self, image: "Image", unity_diagonal: bool = False
+    ) -> np.ndarray:
         """Distance matrix for an image"""
 
-        x = image.species.coordinates
+        x = image.coordinates
         r = distance_matrix(x, x)
 
         if unity_diagonal:
             r[self._diagonal_distance_matrix_idxs] = 1.0
 
         return r
 
-    def _weight_matrix(self, image) -> np.ndarray:
+    def _weight_matrix(self, image: "Image") -> np.ndarray:
         r"""
         Weight matrix with elements
 

autode/neb/neb.py

@@ -1,18 +1,25 @@
 import autode.exceptions as ex
+
 from autode.config import Config
 from autode.log import logger
 from autode.neb.ci import CINEB
 from autode.transition_states.ts_guess import TSguess
 from autode.utils import work_in
 
+from typing import TYPE_CHECKING, Optional
+
+if TYPE_CHECKING:
+    from autode.species.species import Species
+    from autode.wrappers.methods import Method
+
 
 def get_ts_guess_neb(
-    reactant: "autode.species.Species",
-    product: "autode.species.Species",
-    method: "autode.wrappers.methods.Method",
+    reactant: "Species",
+    product: "Species",
+    method: "Method",
     name: str = "neb",
     n: int = 10,
-):
+) -> Optional[TSguess]:
     """
     Get a transition state guess using a nudged elastic band calculation. The
     geometry of the reactant is used as the fixed initial point and the final
@@ -37,25 +44,21 @@ def get_ts_guess_neb(
     assert n is not None
     logger.info("Generating a TS guess using a nudged elastic band")
 
-    neb = CINEB(
-        initial_species=reactant.copy(), final_species=product.copy(), num=n
-    )
+    neb = CINEB.from_end_points(reactant, product, num=n)
 
-    # Calculate and generate the TS guess, in a unique directory
-    try:
-
-        @work_in(name)
-        def calculate():
-            return neb.calculate(method=method, n_cores=Config.n_cores)
+    @work_in(name)
+    def calculate():
+        return neb.calculate(method=method, n_cores=Config.n_cores)
 
+    try:
         calculate()
 
     except ex.CalculationException:
         logger.error("NEB failed - could not calculate")
         return None
 
     return TSguess(
-        atoms=neb.get_species_saddle_point().atoms,
+        atoms=neb.peak_species.atoms,
         reactant=reactant,
         product=product,
         name=name,