removed spin ARG in bond()

- alpha/beta split is purely defined by `omods` ARG (evaluated in
`get_repr()`)

Author: YAY-C

qstack/spahm/rho/bond.py

@@ -10,7 +10,7 @@
 
 def bond(mols, dms,
          bpath=defaults.bpath, cutoff=defaults.cutoff, omods=defaults.omod,
-         spin=None, elements=None, only_m0=False, zeros=False, printlevel=0,
+         elements=None, only_m0=False, zeros=False, printlevel=0,
          pairfile=None, dump_and_exit=False, same_basis=False, only_z=[]):
     """ Computes SPAHM-b representations for a set of molecules.
 
@@ -20,7 +20,6 @@ def bond(mols, dms,
         - bpath (str): path to the directory containing bond-optimized basis-functions (.bas)
         - cutoff (float): the cutoff distance (angstrom) between atoms to be considered as bond
         - omods (list of str): the selected mode for open-shell computations
-        - spin (list of int): list of spins for each molecule
         - elements (list of str): list of all elements present in the set of molecules
         - only_m0 (bool): use only basis functions with `m=0`
         - zeros (bool): add zeros features for non-existing bond pairs
@@ -40,8 +39,6 @@ def bond(mols, dms,
     elements, mybasis, qqs0, qqs4q, idx, M = dmbb.read_basis_wrapper(mols, bpath, only_m0, printlevel,
                                                                      elements=elements, cutoff=cutoff,
                                                                      pairfile=pairfile, dump_and_exit=dump_and_exit, same_basis=same_basis)
-    if np.array(spin==None, ndmin=1).all():
-        omods = [None]
     qqs = qqs0 if zeros else qqs4q
     maxlen = max([dmbb.bonds_dict_init(qqs[q0], M)[1] for q0 in elements])
     if len(only_z) > 0:
@@ -116,10 +113,13 @@ def get_repr(mols, xyzlist, guess,  xc=defaults.xc, spin=None, readdm=None,
         all_atoms   = np.array([z for mol in mols for z in mol.elements if z in only_z], ndmin=2)
     else:
         all_atoms   = np.array([mol.elements for mol in mols])
+    spin = np.array(spin) ## a bit dirty but couldn't find a better way to ensure Iterable type!
+    if (spin == None).all():
+        omods = [None]
 
     allvec  = bond(mols, dms, bpath, cutoff, omods,
-                   spin=spin, elements=elements,
-                   only_m0=only_m0, zeros=zeros, printlevel=printlevel,
+                   elements=elements, only_m0=only_m0,
+                   zeros=zeros, printlevel=printlevel,
                    pairfile=pairfile, dump_and_exit=dump_and_exit, same_basis=same_basis, only_z=only_z)
     maxlen=allvec.shape[-1]
     natm = allvec.shape[-2]

qstack/spahm/rho/utils.py

@@ -60,7 +60,7 @@ def mols_guess(mols, xyzlist, guess, xc=defaults.xc, spin=None, readdm=False, pr
         if printlevel>0: print(xyzfile, flush=True)
         if not readdm:
             e, v = spahm.get_guess_orbitals(mol, guess, xc=xc)
-            dm   = guesses.get_dm(v, mol.nelec, mol.spin if spin is not None else None)
+            dm   = guesses.get_dm(v, mol.nelec, mol.spin if spin is not None else None) # mol.spin can not be `None`
         else:
             dm = np.load(readdm+'/'+os.path.basename(xyzfile)+'.npy')
             if spin and dm.ndim==2:

tests/test_spahm_b.py

@@ -9,7 +9,6 @@ def test_water():
     mols = utils.load_mols([xyz_in], [0], [0], 'minao')
     dms = utils.mols_guess(mols, [xyz_in], 'LB', spin=[0])
     X = bond.get_repr(mols, [xyz_in], 'LB', spin=[0], with_symbols=False, same_basis=False)
-    #X = np.hstack(X) # merging alpha-beta components for spin unrestricted representation #TODO: should be included into function not in main
     true_file = path+'/data/H2O_spahm_b.npy_alpha_beta.npy'
     X_true = np.load(true_file)
     assert(X_true.shape == X.shape)
@@ -21,7 +20,7 @@ def test_water_O_only():
     xyz_in = path+'/data/H2O.xyz'
     mols = utils.load_mols([xyz_in], [0], [0], 'minao')
     dms = utils.mols_guess(mols, [xyz_in], 'LB', spin=[0])
-    X = bond.bond(mols, dms, spin=[0], only_z=['O'])
+    X = bond.bond(mols, dms, only_z=['O'])
     X = np.squeeze(X) #contains a single elements but has shape (1,Nfeat)
     X = np.hstack(X) # merging alpha-beta components for spin unrestricted representation #TODO: should be included into function not in main
     true_file = path+'/data/H2O_spahm_b.npy_alpha_beta.npy'
@@ -36,7 +35,7 @@ def test_water_same_basis():
     xyz_in = path+'/data/H2O.xyz'
     mols = utils.load_mols([xyz_in], [0], [0], 'minao')
     dms = utils.mols_guess(mols, [xyz_in], 'LB', spin=[0])
-    X = bond.bond(mols, dms, spin=[0], same_basis=True)
+    X = bond.bond(mols, dms, same_basis=True)
     X = np.squeeze(X) #contains a single elements but has shape (1,Nfeat)
     X = np.hstack(X) # merging alpha-beta components for spin unrestricted representation #TODO: should be included into function not in main
     true_file = path+'/data/H2O_spahm_b_CCbas.npy_alpha_beta.npy'
@@ -50,7 +49,7 @@ def test_ecp():
     xyz_in = path+'/data/I2.xyz'
     mols = utils.load_mols([xyz_in], [0], [None], 'minao', ecp='def2-svp')
     dms = utils.mols_guess(mols, [xyz_in], 'LB', spin=[None])
-    X = bond.bond(mols, dms, spin=[None], same_basis=True)
+    X = bond.bond(mols, dms, same_basis=True)
     X = np.squeeze(X) #contains a single elements but has shape (1,Nfeat)
     X = np.hstack(X) # merging alpha-beta components for spin unrestricted representation #TODO: should be included into function not in main
     true_file = path+'/data/I2_spahm-b_minao-def2-svp_alpha-beta.npy'