Maintain examples (#405)

* maintain examples

* Update rsdf_builder.py

---------

Co-authored-by: Xiaojie Wu <wxj6000@gmail..com>

Author: wxj6000

examples/10-dft_with_ecp.py

@@ -25,13 +25,13 @@
 '''
 
 # def2-qzvpp contains ecp for heavy atoms
+# One needs to specify ecp separately
 mol = pyscf.M(atom=atom, basis='def2-qzvpp', ecp='def2-qzvpp')
 mf = rks.RKS(mol, xc='b3lyp').density_fit()
 mf.grids.level = 6   # more grids are needed for heavy atoms
 e_dft = mf.kernel()
 
-# gradient and Hessian of ECP are also supported
-# but ECP contributions are still calculated on CPU
+# ECP contributions are accelerated with GPU
 g = mf.nuc_grad_method()
 grad = g.kernel()
 

examples/11-dft_with_nlc.py

@@ -28,9 +28,7 @@
 '''
 
 start_time = time.time()
-mol = pyscf.M(
-    atom='Vitamin_C.xyz',
-    verbose=4)
+mol = pyscf.M(atom=atom, verbose=4)
 
 print(f'{mol.nao} atomic orbitals')
 mf = rks.RKS(mol, xc='HYB_MGGA_XC_WB97M_V').density_fit()
@@ -42,8 +40,11 @@
 end_time = time.time()
 print(f'Wallclock time: {end_time-start_time}')
 
-print('calculating gradient')
+# Compute gradient
 gobj = mf.nuc_grad_method()
 gobj.kernel()
 
-# Hessian for nlc is not supported
+# Compute Hessian
+h = mf.Hessian()
+h.auxbasis_response = 2
+h_dft = h.kernel()

examples/18-ccsd.py

@@ -26,5 +26,5 @@
     verbose=1)
 
 mf = mol.RHF().run()
-mf.with_df = None
+mf.with_df = None   # DF CCSD is not supported yet.
 e_tot = ccsd_incore.CCSD(mf).kernel()

examples/28-tddft_with_solvent.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 ###################################
-#  Example of TDDFT
+#  Example of TDDFT with solvent
 ###################################
 
 import pyscf

examples/33-tddft-excitedstate-opt.py examples/33-tddft_excitedstate_opt.pyexamples/33-tddft-excitedstate-opt.py renamed to examples/33-tddft_excitedstate_opt.py

@@ -437,7 +437,9 @@ class Grids(lib.StreamObject):
     level = getattr(__config__, 'dft_gen_grid_Grids_level', 3)
     alignment    = ALIGNMENT_UNIT
     cutoff       = CUTOFF
-    _keys        = gen_grid_cpu.Grids._keys
+    _keys        = gen_grid_cpu.Grids._keys.union({
+        'grid_sorting_index', 'atm_idx', 'padding'
+    })
 
     __init__   = gen_grid_cpu.Grids.__init__
     dump_flags = gen_grid_cpu.Grids.dump_flags

gpu4pyscf/dft/gen_grid.py

@@ -78,6 +78,8 @@ def contraction(
     mode_a = list(str_a)
     mode_b = list(str_b)
     mode_c = list(str_c)
+    if len(mode_c) != len(set(mode_c)):
+        raise ValueError('Output subscripts string includes the same subscript multiple times.')
 
     dtype = np.result_type(a.dtype, b.dtype)
     a = cupy.asarray(a, dtype=dtype)

gpu4pyscf/lib/cutensor.py

@@ -99,7 +99,6 @@ def qmmm_for_scf(method, mm_mol):
             method.mm_ewald_pot = None
             method.qm_ewald_hess = None
             method.e_nuc = None
-            method.h1_on_cpu = False
             return method
 
         cls = QMMMSCF
@@ -128,7 +127,6 @@ def __init__(self, method, mm_mol):
         self.mm_ewald_pot = None
         self.qm_ewald_hess = None
         self.e_nuc = None
-        self.h1_on_cpu = False
 
     def dump_flags(self, verbose=None):
         super().dump_flags(verbose)
@@ -540,7 +538,6 @@ def qmmm_grad_for_scf(scf_grad):
 
     scf_grad.de_ewald_mm = None
     scf_grad.de_nuc_mm = None
-    scf_grad.h1_on_cpu = False
     return scf_grad.view(lib.make_class((QMMMGrad, scf_grad.__class__)))
 
 class QMMMGrad: