Add initial NEB efforts.

architector/io_align_mol.py

@@ -198,6 +198,36 @@ def mirror_align(tarmol, srcmol, maxiter=1, tol=1e-6):
     srcmol_tmp.set_positions(newposits)
     rmsd, outr, msrcmol = permute_align(tarmol,srcmol_tmp,maxiter=maxiter,tol=tol)
     return rmsd, outr, msrcmol
+
+
+def neb_align(tarmol, srcmol, maxiter=1, tol=1e-6):
+    """neb_align 
+    Align for NEB including mirror images.
+
+    Parameters
+    ----------
+    tarmol : ase.atoms.Atoms
+        target molecule
+    srcmol : ase.atoms.Atoms
+        source molecule
+    maxiter : int, optional
+        how many times to try, by default 10
+    tol : float, optional
+        tolerance for convergence, by default 1e-2
+
+    Returns
+    -------
+    out : ase.atoms.Atoms
+        mirrored rotated version of the molecule.
+    """
+    normal, _, out = permute_align(tarmol, srcmol,
+                                     maxiter=maxiter, tol=tol, in_place=False)
+    mirror, _, out2 = mirror_align(tarmol, srcmol,
+                                     maxiter=maxiter, tol=tol)
+    if mirror < normal:
+        out = out2
+
+    return out
 
 
 def calc_rmsd(genMol, compareMol, coresize=2, maxiter=1, sample=300, atom_types=None,

architector/io_neb.py

@@ -0,0 +1,27 @@
+"""
+Routines for performing ASE NEB from two structures generated at different distances
+
+Developed by Michael Taylor
+"""
+
+from ase.neb import NEB
+from architector.io_align_mol import neb_align
+from architector.io_calc import CalcExecutor
+from architector.io_molecule import convert_io_molecule
+
+def NEB_setup(initial,final,nimages=8,neb_method='GFN2-xTB',interpolation='idpp',climb=True):
+    initial_mol = convert_io_molecule(initial)
+    final_mol = convert_io_molecule(final)
+    final_mol_ase = neb_align(initial_mol.ase_atoms,final_mol.ase_atoms)
+    final_mol.ase_atoms = final_mol_ase
+    images = [initial_mol.ase_atoms]
+    images += [initial_mol.ase_atoms.copy() for x in range(nimages-2)]
+    images += [final_mol.ase_atoms]
+    neb = NEB(images=images,climb=climb)
+    neb.interpolate(method=interpolation)
+    neb_images = []
+    for image in neb.images:
+        out = CalcExecutor(image,method=neb_method)
+        neb_images.append(out.mol.ase_atoms)
+    neb.images = neb_images
+    return neb