improve mix and from_frag

.github/workflows/release.yml

@@ -43,4 +43,4 @@ jobs:
           repo_token: "${{ secrets.GITHUB_TOKEN }}"
           prerelease: true
           files: |
-            ./dist/pyAutoMR-$VERSION-py3-none-any.whl
+            ./dist/pyAutoMR-v*-py3-none-any.whl

CHANGELOG

@@ -1,4 +1,8 @@
 
+version 0.3.0-rc9 (Nov 16, 2022)
+--------------------------
+* GitHub Actions for auto-release and pypi upload
+
 version 0.3.0-rc1 (Nov 16, 2022)
 --------------------------
 Features

automr/guess.py

@@ -145,10 +145,14 @@ def _mix(mol,
     print('**** generating mix guess ****')
     mo_mix = mf.mo_coeff
     nocc = mol.nelectron//2
+    print('RHF MO energy and HOMO-3~LUMO+3 before mixing')
     print('mo_e', mf.mo_energy[nocc-4:nocc+4])
     dump_mat.dump_mo(mol, mo_mix[:,nocc-4:nocc+4], ncol=8)
+    if not isinstance(hl[0], list):
+        hl = [hl]
     for hlitem in hl:
         dm_mix, mo_mix = init_guess_mixed(mo_mix, mf.mo_occ, ho=hlitem[0], lu=hlitem[1], mix_param=mix_param)
+    print('After mixing')
     dump_mat.dump_mo(mol, mo_mix[0][:,nocc-4:nocc+4], ncol=8)
     dump_mat.dump_mo(mol, mo_mix[1][:,nocc-4:nocc+4], ncol=8)
     if xc is None:
@@ -172,21 +176,22 @@ def _mix(mol,
         mf_mix.level_shift = level_shift
         mf_mix.max_cycle = 100
     mf_mix.kernel(dm0=dm_mix)
-    if not mf_mix.converged and conv == 'tight':
+    mf_mix = postscf_check(mf_mix, conv, skipstb, newton)
+
+    t2 = time.time()
+    print('time for guess: %.3f' % (t2-t1))
+    return mf_mix
+
+def postscf_check(mf, conv, skipstb, newton):
+    if not mf.converged and conv == 'tight':
         raise RuntimeError('UHF not converged')
-    ss, s = mf_mix.spin_square()
+    ss, s = mf.spin_square()
     if s < 0.1:
         print('Warning: S too small, symmetry breaking may be failed')
 
     if conv == 'tight' and not skipstb:
-        mf_mix = check_stab(mf_mix, newton)
-
-    t2 = time.time()
-    print('time for guess: %.3f' % (t2-t1))
-    #dm = mf.make_rdm1()
-    #mf.max_cycle = 0
-    #mf_mix.kernel(dm)
-    return mf_mix
+        mf = check_stab(mf, newton)
+    return mf
 
 def apply_field(mf, f):
     h2 = mf.get_hcore() + np.einsum('x,xij->ij', f, mf.mol.intor('int1e_r', comp=3))
@@ -274,7 +279,9 @@ def from_frag(xyz, bas, frags, chgs, spins, **kwargs):
     return _from_frag(mol, frags, chgs, spins, **kwargs) 
 
 
-def _from_frag(mol_or_mf, frags, chgs, spins, cycle=2, xc=None, verbose=4, rmdegen=False, bgchg=None):
+def _from_frag(mol_or_mf, frags, chgs, spins, 
+               conv='loose', cycle=2, level_shift=0.0, 
+               skipstb=False, xc=None, newton=False, verbose=4, rmdegen=False, bgchg=None):
 
     t1 = time.time() 
     dm, mo, occ = guess_frag(mol_or_mf, frags, chgs, spins, rmdegen=rmdegen, bgchg=bgchg)
@@ -296,12 +303,14 @@ def _from_frag(mol_or_mf, frags, chgs, spins, cycle=2, xc=None, verbose=4, rmdeg
         mf.xc = xc
     mf.mo_coeff = mo
     mf.verbose = verbose
-    #mf.conv_tol = 1e-2
-    mf.max_cycle = cycle
+    if conv == 'loose':
+        mf.conv_tol = 1e-3
+        mf.max_cycle = cycle
+    elif conv == 'tight':
+        mf.level_shift = level_shift
+        mf.max_cycle = 100
     mf.kernel(dm0 = dm)
-    ss, s = mf.spin_square()
-    if s < 0.1:
-        print('Warning: S too small, symmetry breaking may be failed')
+    mf = postscf_check(mf, conv, skipstb, newton)
     t2 = time.time()
     print('time for guess: %.3f' % (t2-t1))
     return mf

examples/tutorial/01-mix_adv.py

@@ -0,0 +1,7 @@
+from automr import guess
+
+xyz = '''F 0.0 0.0 0.0; F 0.0 0.0 1.5'''
+bas = 'def2-svp'
+
+mf = guess.mix_tight(xyz, bas) # end up no polarized spin
+mf = guess.mix_tight(xyz, bas, hl=[-2,0]) # correct polarized spin

examples/tutorial/03-from_frag_adv.py

@@ -0,0 +1,11 @@
+from automr import guess
+
+xyz = '''F 0.0 0.0 0.0; F 0.0 0.0 4.0'''
+bas = 'cc-pvtz'
+mf = guess.from_frag_tight(xyz, bas, [[0],[1]], [0,0], [1,-1])
+
+mf0 = guess.gen('''F 0.0 0.0 0.0''', bas, 0, 1)
+mf0 = guess.apply_field(mf0, (0.01,0.01,0.0).run()
+#mf0.analyze()
+#mf = guess._from_frag(xyz, bas, [[0],[1]], [0,0], [1,-1])
+#

examples/tutorial/03-from_frag_manually.py

@@ -0,0 +1,13 @@
+from automr import guess
+
+xyz = '''H 0.0 0.0 0.0; F 0.0 0.0 2.0'''
+bas = 'def2-svp'
+mf = guess.from_frag_tight(xyz, bas, [[0],[1]], [0,0], [1,-1])
+
+mf0 = guess.gen('''H 0.0 0.0 0.0''', bas, 0, 1)
+#mf0 = guess.apply_field(mf0, (0.0,0.0,0.01)).run() # add field in z direction
+#mf0.mulliken_pop() # check odd electron on pz
+mf1 = guess.gen('''F 0.0 0.0 2.0''', bas, 0, -1).set(max_cycle=5)
+mf1 = guess.apply_field(mf1, (0.0,0.01,0.02)).run() # add field in z direction
+mf1.mulliken_pop() # check odd electron on pz
+mf = guess._from_frag([mf0, mf1], None, None, None, conv='tight')