Adds a adapt+NEB+TS method (duartegroup#172)

* Allow partition with max delta

* Adaptive initial force constant

* Add adapt+NEB+TS method

* Add tests

* Add assert when no path

* Update changelog

autode/config.py

@@ -186,9 +186,9 @@ class ORCA:
 
         optts_block = ('\n%geom\n'
                        'Calc_Hess true\n' 
-                       'Recalc_Hess 30\n'
+                       'Recalc_Hess 20\n'
                        'Trust -0.1\n'
-                       'MaxIter 150\n'
+                       'MaxIter 100\n'
                        'end')
 
         keywords = KeywordsSet(

autode/hessians.py

@@ -11,7 +11,7 @@
 from autode.log import logger
 from autode.config import Config
 from autode.constants import Constants
-from autode.values import ValueArray, Frequency, Coordinates
+from autode.values import ValueArray, Frequency, Coordinates, Distance
 from autode.utils import work_in, hashable
 from autode.units import (Unit, wavenumber,
                           ha_per_ang_sq, ha_per_a0_sq, J_per_m_sq, J_per_ang_sq,
@@ -362,10 +362,10 @@ class NumericalHessianCalculator:
 
     def __init__(self,
                  species:   'autode.species.Species',
-                 method:    'autode.wrappers.base.Method',
+                 method:    'autode.wrappers.methods.Method',
                  keywords:  'autode.wrappers.keywords.GradientKeywords',
                  do_c_diff:  bool,
-                 shift:      'autode.values.Distance',
+                 shift:      Distance,
                  n_cores:    Optional[int] = None
                  ):
 

autode/input_output.py

@@ -1,9 +1,11 @@
 import os
-from typing import Collection
+
+from typing import Collection, List, Optional
 from autode.atoms import Atom, Atoms
 from autode.exceptions import XYZfileDidNotExist
 from autode.exceptions import XYZfileWrongFormat
 from autode.log import logger
+from autode.utils import StringDict
 
 
 def xyz_file_to_atoms(filename: str) -> Atoms:
@@ -19,14 +21,9 @@ def xyz_file_to_atoms(filename: str) -> Atoms:
     """
     logger.info(f'Getting atoms from {filename}')
 
+    _check_xyz_file_exists(filename)
     atoms = Atoms()
 
-    if not os.path.exists(filename):
-        raise XYZfileDidNotExist(f'{filename} did not exist')
-
-    if not filename.endswith('.xyz'):
-        raise XYZfileWrongFormat('xyz file must have a .xyz file extension')
-
     with open(filename, 'r') as xyz_file:
 
         try:
@@ -85,3 +82,69 @@ def atoms_to_xyz_file(atoms:      Collection[Atom],
             print(f'{atom.label:<3}{x:10.5f}{y:10.5f}{z:10.5f}',
                   file=xyz_file)
     return None
+
+
+def xyz_file_to_molecules(filename: str) -> List["autode.Molecule"]:
+    """
+    From a .xyz file containing potentially more than a single molecule
+    return a list of molecules from it.
+
+    ---------------------------------------------------------------------------
+    Arguments:
+        filename: Filename to open
+
+    Returns:
+        (list(autode.species.molecule.Molecule)): Molecules
+    """
+    from autode.species.molecule import Molecule  # prevents circular imports
+
+    _check_xyz_file_exists(filename)
+
+    lines = open(filename, "r").readlines()
+    n_atoms = int(lines[0].split()[0])
+    molecules = []
+
+    for i in range(0, len(lines), n_atoms + 2):
+
+        atoms = []
+        title_line = StringDict(lines[i + 1])
+        for j, line in enumerate(lines[i + 2:i + n_atoms + 2]):
+            symbol, x, y, z = line.split()[:4]
+            atoms.append(Atom(atomic_symbol=symbol, x=x, y=y, z=z))
+
+        molecule = Molecule(atoms=atoms,
+                            solvent_name=title_line.get("solvent", None))
+
+        _set_attr_from_title_line(molecule, "charge", title_line)
+        _set_attr_from_title_line(molecule, "mult", title_line)
+        _set_attr_from_title_line(molecule, "energy", title_line, "E")
+
+        molecules.append(molecule)
+
+    return molecules
+
+
+def _check_xyz_file_exists(filename: str) -> None:
+
+    if not os.path.exists(filename):
+        raise XYZfileDidNotExist(f'{filename} did not exist')
+
+    if not filename.endswith('.xyz'):
+        raise XYZfileWrongFormat('xyz file must have a .xyz file extension')
+
+    return None
+
+
+def _set_attr_from_title_line(species: "Species",
+                              attr: str,
+                              title_line: StringDict,
+                              key_in_line: Optional[str] = None) -> None:
+
+    if key_in_line is None:
+        key_in_line = attr  # Default to e.g. charge attribute is "charge = 0"
+    try:
+        setattr(species, attr, title_line[key_in_line])
+    except IndexError:
+        logger.warning(f"Failed to set the species {attr} from xyz file")
+
+    return None

autode/methods.py

@@ -64,7 +64,7 @@ def get_hmethod() -> "autode.wrappers.methods.Method":
 
     ---------------------------------------------------------------------------
     Returns:
-        (autode.wrappers.base.ElectronicStructureMethod): High-level method
+        (autode.wrappers.methods.Method): High-level method
     """
 
     h_methods = [ORCA(), G09(), NWChem(), G16(), QChem()]
@@ -79,7 +79,7 @@ def get_lmethod() -> "autode.wrappers.methods.Method":
     """Get the 'low-level' electronic structure theory method to use
 
     Returns:
-        (autode.wrappers.base.ElectronicStructureMethod): Low-level method
+        (autode.wrappers.methods.Method): Low-level method
     """
 
     all_methods = [XTB(), MOPAC(), ORCA(), G16(), G09(), NWChem(), QChem()]
@@ -100,7 +100,7 @@ def get_first_available_method(possibilities) -> "autode.wrappers.methods.Method
         possibilities (list(autode.wrappers.base.ElectronicStructureMethod)):
 
     Returns:
-        (autode.wrappers.base.ElectronicStructureMethod): Method
+        (autode.wrappers.methods.Method): Method
 
     Raises:
         (autode.exceptions.MethodUnavailable):
@@ -123,7 +123,7 @@ def get_defined_method(name, possibilities) -> "autode.wrappers.methods.Method":
         possibilities (list(autode.wrappers.base.ElectronicStructureMethod)):
 
     Returns:
-        (autode.wrappers.base.ElectronicStructureMethod): Method
+        (autode.wrappers.methods.Method): Method
 
     Raises:
         (autode.exceptions.MethodUnavailable):

autode/neb/ci.py

@@ -3,6 +3,7 @@
 https://doi.org/10.1063/1.1329672
 """
 import numpy as np
+from typing import Optional
 from autode.neb.original import NEB, Images, Image
 from autode.log import logger
 
@@ -39,7 +40,11 @@ def get_force(self, im_l, im_r) -> np.ndarray:
 
 class CImages(Images):
 
-    def __init__(self, images, wait_iterations=4):
+    def __init__(self,
+                 images:          Images,
+                 num:             int = None,
+                 wait_iterations: int = 4,
+                 init_k:          Optional[float] = None):
         """
         Initialise a set of images
 
@@ -49,8 +54,11 @@ def __init__(self, images, wait_iterations=4):
 
             wait_iterations (int): Number of iterations to wait before turning
                                   on the climbing image
+
+            init_k: Initial force constant
         """
-        super().__init__(num=len(images), init_k=images[0].k)
+        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)
 
         self.wait_iteration = wait_iterations
         for i, image in enumerate(images):
@@ -83,6 +91,8 @@ def increment(self) -> None:
 
 class CINEB(NEB):
 
+    _images_type = CImages
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
@@ -104,9 +114,3 @@ def _minimise(self, method, n_cores, etol, max_n=30
         result = super()._minimise(method, n_cores, etol, max_n)
 
         return result
-
-    def partition(self, n: int) -> None:
-        """Partition a set of CI images"""
-        super().partition(n=n)
-        self.images = CImages(self.images)
-        return None

autode/neb/neb.py

@@ -8,7 +8,7 @@
 
 def get_ts_guess_neb(reactant: 'autode.species.Species',
                      product:  'autode.species.Species',
-                     method:   'autode.wrappers.base.Method',
+                     method:   'autode.wrappers.methods.Method',
                      name:     str = 'neb',
                      n:        int = 10):
     """
@@ -23,7 +23,7 @@ def get_ts_guess_neb(reactant: 'autode.species.Species',
 
         product (autode.species.Species):
 
-        method (autode.wrappers.base.Method):
+        method (autode.wrappers.methods.Method):
 
         name (str):