typos and typos

examples/mcscf/14-project_init_guess.py

@@ -10,7 +10,7 @@
 Use project_init_guess function to format the CASSCF initial guess orbitals
 
 CASSCF solver can use any orbital as initial guess, no matter how and where
-you get the orbital coeffcients.  It can even be the orbitals of different
+you get the orbital coefficients.  It can even be the orbitals of different
 molecule.
 '''
 

examples/pbc/20-k_points_scf_ksymm.py

@@ -43,7 +43,7 @@
 
 #
 # The mean-field object with k-point symmetry can be converted back to
-# the correponding non-symmetric mean-field object
+# the corresponding non-symmetric mean-field object
 #
 
 kmf = kmf.to_khf()
@@ -64,7 +64,7 @@
 
 #
 # The mean-field object with k-point symmetry can be converted back to
-# the correponding non-symmetric mean-field object
+# the corresponding non-symmetric mean-field object
 #
 kumf = kumf.to_khf()
 kumf.kernel(kumf.make_rdm1())

examples/tddft/31-energy_transfer_coupling_matrix.py

@@ -31,7 +31,7 @@
 v_B = moB[:,mfB.mo_occ==0]
 tdB = mfB.TDA().run()
 
-# CIS coeffcients
+# CIS coefficients
 state_id = 2  # The third excited state
 t1_A = tdA.xy[state_id][0]
 t1_B = tdB.xy[state_id][0]

pyscf/dft/dks.py

@@ -46,7 +46,7 @@ def energy_elec(ks, dm=None, h1e=None, vhf=None):
         ks : an instance of DFT class
 
         dm : 2D ndarray
-            one-partical density matrix
+            one-particle density matrix
         h1e : 2D ndarray
             Core hamiltonian
 

pyscf/dft/numint.py

@@ -2633,7 +2633,7 @@ def get_rho(ni, mol, dm, grids, max_memory=2000):
 class LibXCMixin:
     libxc = libxc
 
-    omega = None  # RSH paramter
+    omega = None  # RSH parameter
 
 ####################
 # Overwrite following functions to use custom XC functional

pyscf/dft/rks.py

@@ -228,7 +228,7 @@ def energy_elec(ks, dm=None, h1e=None, vhf=None):
         ks : an instance of DFT class
 
         dm : 2D ndarray
-            one-partical density matrix
+            one-particle density matrix
         h1e : 2D ndarray
             Core hamiltonian
 

pyscf/fci/direct_nosym.py

@@ -204,11 +204,11 @@ def eig(self, op, x0=None, precond=None, **kwargs):
             return scipy.linalg.eigh(op)
 
         # TODO: check the hermitian of Hamiltonian then determine whether to
-        # call the non-hermitian diagonlization solver davidson_nosym1
+        # call the non-hermitian diagonalization solver davidson_nosym1
 
         warnings.warn('direct_nosym.kernel is not able to diagonalize '
                       'non-Hermitian Hamiltonian. If h1e and h2e is not '
-                      'hermtian, calling symmetric diagonlization in eig '
+                      'hermtian, calling symmetric diagonalization in eig '
                       'can lead to wrong results.')
 
         self.converged, e, ci = \

pyscf/fci/direct_spin1.py

@@ -511,8 +511,8 @@ def kernel_ms1(fci, h1e, eri, norb, nelec, ci0=None, link_index=None,
         nroots: int
             Number of states to solve
         davidson_only: bool
-            Whether to call subspace diagonlization (davidson solver) or do a
-            full diagonlization (lapack eigh) for small systems
+            Whether to call subspace diagonalization (davidson solver) or do a
+            full diagonalization (lapack eigh) for small systems
         pspace_size: int
             Number of determinants as the threshold of "small systems",
         hop: function(c) => array_like_c
@@ -669,7 +669,7 @@ class FCIBase(lib.StreamObject):
             problems being solved by Davidson subspace algorithm.  This flag
             should be enabled when initial guess is given or particular spin
             symmetry or point-group symmetry is required because the initial
-            guess or symmetry are completely ignored in the direct diagonlization.
+            guess or symmetry are completely ignored in the direct diagonalization.
         pspace_size : int
             The dimension of Hamiltonian matrix over which Davidson iteration
             algorithm will be used for the eigenvalue problem.  Default is 400.
@@ -716,8 +716,8 @@ class FCIBase(lib.StreamObject):
     # dependence basis in davidson diagonalization solver
     level_shift = getattr(__config__, 'fci_direct_spin1_FCI_level_shift', 1e-3)
 
-    # force the diagonlization use davidson iteration.  When the CI space
-    # is small, the solver exactly diagonlizes the Hamiltonian.  But this
+    # force the diagonalization use davidson iteration.  When the CI space
+    # is small, the solver exactly diagonalizes the Hamiltonian.  But this
     # solution will ignore the initial guess.  Setting davidson_only can
     # enforce the solution on the initial guess state
     davidson_only = getattr(__config__, 'fci_direct_spin1_FCI_davidson_only', False)

pyscf/gto/mole.py

@@ -2197,7 +2197,7 @@ class MoleBase(lib.StreamObject):
             subgroup
 
         atom : list or str
-            To define molecluar structure.  The internal format is
+            To define molecular structure.  The internal format is
 
             | atom = [[atom1, (x, y, z)],
             |         [atom2, (x, y, z)],
@@ -2473,7 +2473,7 @@ def build(self, dump_input=True, parse_arg=ARGPARSE,
             max_memory : int, float
                 Allowd memory in MB.  If given, overwrite :attr:`Mole.max_memory`
             atom : list or str
-                To define molecluar structure.
+                To define molecular structure.
             basis : dict or str
                 To define basis set.
             nucmod : dict or str
@@ -3748,7 +3748,7 @@ def __getattr__(self, key):
     def ao2mo(self, mo_coeffs, erifile=None, dataname='eri_mo', intor='int2e',
               **kwargs):
         '''Integral transformation for arbitrary orbitals and arbitrary
-        integrals.  See more detalied documentation in func:`ao2mo.kernel`.
+        integrals.  See more detailed documentation in func:`ao2mo.kernel`.
 
         Args:
             mo_coeffs (an np array or a list of arrays) : A matrix of orbital

pyscf/gw/gw_ac.py

@@ -20,7 +20,7 @@
 Spin-restricted G0W0 approximation with analytic continuation
 This implementation has N^4 scaling, and is faster than GW-CD (N^4)
 and analytic GW (N^6) methods.
-GW-AC is recommended for valence states only, and is inaccuarate for core states.
+GW-AC is recommended for valence states only, and is inaccurate for core states.
 
 Method:
     See T. Zhu and G.K.-L. Chan, arxiv:2007.03148 (2020) for details

pyscf/gw/ugw_ac.py

@@ -21,7 +21,7 @@
 
 This implementation has N^4 scaling, and is faster than GW-CD (N^4)
 and analytic GW (N^6) methods.
-GW-AC is recommended for valence states only, and is inaccuarate for core states.
+GW-AC is recommended for valence states only, and is inaccurate for core states.
 
 Method:
     See T. Zhu and G.K.-L. Chan, arxiv:2007.03148 (2020) for details

pyscf/lib/cc/ccsd_pack.c

@@ -106,7 +106,7 @@ void CCmake_021(double *out, double *v1, double *v2, int count, int m,
 /*
  * if matrix B is symmetric for the contraction A_ij B_ij,
  * Tr(AB) ~ A_ii B_ii + (A_ij + A_ji) B_ij where i > j
- * This function extract the A_ii and the lower triangluar part of A_ij + A_ji
+ * This function extract the A_ii and the lower triangular part of A_ij + A_ji
  */
 void CCprecontract(double *out, double *in, int count, int m, double diagfac)
 {

pyscf/lib/gto/autocode/parser.cl

@@ -25,7 +25,7 @@
 ;;;         (bra-ops ... p* |op| ket-ops)
 ;;; the p* in the bra (| will be evaluated with |op| or |ket-ops) (if they
 ;;; have cross or dot operators). Using the sticker symbol for p/nabla
-;;; to prevent p/nabla operators comutating with the next p/nabla operators
+;;; to prevent p/nabla operators commutating with the next p/nabla operators
 
 ;;; rscalar?
 (defparameter *intvar* '(p ip nabla px py pz

pyscf/lib/linalg_helper.py

@@ -453,7 +453,7 @@ def davidson1(aop, x0, precond, tol=1e-12, max_cycle=50, max_space=12,
             except IndexError:
                 raise LinearDependenceError('No linearly independent basis found '
                                             'by the diagonalization solver.')
-        if heff is None:  # Lazy initilize heff to determine the dtype
+        if heff is None:  # Lazy initialize heff to determine the dtype
             heff = numpy.empty((max_space+nroots,max_space+nroots), dtype=dtype)
         else:
             heff = numpy.asarray(heff, dtype=dtype)
@@ -826,7 +826,7 @@ def davidson_nosym1(aop, x0, precond, tol=1e-12, max_cycle=50, max_space=20,
                 dtype = numpy.result_type(axt[0], xt[0])
             except IndexError:
                 dtype = numpy.result_type(ax[0].dtype, xs[0].dtype)
-        if heff is None:  # Lazy initilize heff to determine the dtype
+        if heff is None:  # Lazy initialize heff to determine the dtype
             heff = numpy.empty((max_space+nroots,max_space+nroots), dtype=dtype)
         else:
             heff = numpy.asarray(heff, dtype=dtype)

pyscf/lib/mcscf/fci_contract.c

@@ -59,7 +59,7 @@
  */
 
 /* 
- * For given stra_id, spread alpah-strings (which can propagate to stra_id)
+ * For given stra_id, spread alpha-strings (which can propagate to stra_id)
  * into t1[:nstrb,nnorb] 
  *    str1-of-alpha -> create/annihilate -> str0-of-alpha
  * ci0[:nstra,:nstrb] is contiguous in beta-strings

pyscf/lib/misc.py

@@ -727,7 +727,7 @@ def fn1(self, *args, **kwargs):
 
     Using alias function instead of fn1 = fn because some methods may be
     overloaded in the child class. Using "alias" can make sure that the
-    overloaded mehods were called when calling the aliased method.
+    overloaded methods were called when calling the aliased method.
     '''
     name = fn.__name__
     if alias_name is None:
@@ -1015,7 +1015,7 @@ class call_in_background:
 
     Attributes:
         sync (bool): Whether to run in synchronized mode.  The default value
-            is False (asynchoronized mode).
+            is False (asynchronized mode).
 
     Examples:
 
@@ -1064,7 +1064,7 @@ def __enter__(self):
                 # import lock) bug in the threading module.  See also
                 # https://github.com/paramiko/paramiko/issues/104
                 # https://docs.python.org/2/library/threading.html#importing-in-threaded-code
-                # Disable the asynchoronous mode for safe importing
+                # Disable the asynchronous mode for safe importing
                 def def_async_fn(i):
                     return fns[i]
 

pyscf/lib/solvent/mnsol.F

@@ -44,8 +44,8 @@ SUBROUTINE CDSSET(ICDS,GCDS,AREACDS,NAT,C,IAN,DCDS,X,
 C     ICDS=1 FOR WATER
 C     ICDS=2 FOR ANY NONAQUEOUS SOLVENT
 C     IF ICDS=2 YOU NEED TO PROVIDE THE FOLLOWING SOLVENT DESCRIPTORS (see http://comp.chem.umn.edu/solvation/mnsddb.pdf):
-C       SOLA (Abraham's hydrogen-bond acidity paramerer),
-C       SOLB (Abraham's hydrogen-bond basicity paramerer),
+C       SOLA (Abraham's hydrogen-bond acidity parameter),
+C       SOLB (Abraham's hydrogen-bond basicity parameter),
 C       SOLC (carbon aromaticity),
 C       SOLG (macroscopic surface tension in cal/(mol A^2),
 C       SOLH (electronegative halogenicity),
@@ -306,8 +306,8 @@ SUBROUTINE SMD_CDS_NAQ(SIGMA,HSIGMA,CSSIGM,
       IMPLICIT DOUBLE PRECISION (A-H,O-Z)
 C
 C     YOU NEED TO PROVIDE THE FOLLOWING SOLVENT DESCRIPTORS (see http://comp.chem.umn.edu/solvation/mnsddb.pdf):
-C       SOLA (Abraham's hydrogen-bond acidity paramerer),
-C       SOLB (Abraham's hydrogen-bond basicity paramerer),
+C       SOLA (Abraham's hydrogen-bond acidity parameter),
+C       SOLB (Abraham's hydrogen-bond basicity parameter),
 C       SOLC (carbon aromaticity),
 C       SOLG (macroscopic surface tension in cal/(mol A^2),
 C       SOLH (electronegative halogenicity),

pyscf/mcscf/__init__.py

@@ -86,7 +86,7 @@
         The step size for orbital rotation.  Small step size is prefered.
         Default is 0.02.  
         (NOTE although the default step size is small enough for many systems,
-        it happens that the orbital optimizor crosses the barriar of local
+        it happens that the orbital optimizor crosses the barrier of local
         minimum and converge to the neighbour solution, e.g. the CAS(4,4) for
         C2H4 in the test files.  In these systems, adjusting max_stepsize,
         max_ci_stepsize and max_cycle_micro and ah_start_tol may be helpful)

pyscf/mcscf/apc.py

@@ -28,7 +28,7 @@ class Chooser():
         occ: 1D Numpy Array
             Orbital occupations for orbs (2,1,0); nactel will be set to the number of electrons in the selected orbitals
         entropies: 1D Numpy Array
-            Importance measurment used to rank the orbitals
+            Importance measurement used to rank the orbitals
         max_size: Int or Tuple
             Active space size constraint.
             If tuple, interpreted as (nelecas,ncas)

pyscf/md/integrators.py

@@ -179,8 +179,8 @@ class _Integrator(lib.StreamObject):
             Time of the last step during the simulation.
 
         callback : function(envs_dict) => None
-            Callback function takes one dict as the arugment which is
-            generaged by the builtin function :func:`locals`, so that the
+            Callback function takes one dict as the argument which is
+            generated by the builtin function :func:`locals`, so that the
             callback function can access all local variables in the current
             environment.
     '''

pyscf/mp/mp2.py

@@ -383,7 +383,7 @@ def get_frozen_mask(mp):
     '''Get boolean mask for the restricted reference orbitals.
 
     In the returned boolean (mask) array of frozen orbital indices, the
-    element is False if it corresonds to the frozen orbital.
+    element is False if it corresponds to the frozen orbital.
     '''
     moidx = numpy.ones(mp.mo_occ.size, dtype=bool)
     if mp._nmo is not None:

pyscf/mp/ump2.py

@@ -217,7 +217,7 @@ def get_frozen_mask(mp):
     '''Get boolean mask for the unrestricted reference orbitals.
 
     In the returned boolean (mask) array of frozen orbital indices, the
-    element is False if it corresonds to the frozen orbital.
+    element is False if it corresponds to the frozen orbital.
     '''
     moidxa = numpy.ones(mp.mo_occ[0].size, dtype=bool)
     moidxb = numpy.ones(mp.mo_occ[1].size, dtype=bool)

pyscf/pbc/ci/kcis_rhf.py

@@ -126,7 +126,7 @@ def precond(r, e0, x0):
     return evals, evecs
 
 def cis_matvec_singlet(cis, vector, kshift, eris=None):
-    """Compute matrix-vector product of the Hamiltonion matrix and a CIS c
+    """Compute matrix-vector product of the Hamiltonian matrix and a CIS c
     oefficient vector, in the space of single excitation.
 
     Arguments:
@@ -143,7 +143,7 @@ def cis_matvec_singlet(cis, vector, kshift, eris=None):
             electron repulsion integrals (default: {None})
 
     Returns:
-        1D array -- matrix-vector product of the Hamiltonion matrix and the
+        1D array -- matrix-vector product of the Hamiltonian matrix and the
             input vector.
     """
     if eris is None:

pyscf/pbc/df/aft.py

@@ -180,7 +180,7 @@ def _int_nuc_vloc(mydf, nuccell, kpts, intor='int3c2e', aosym='s2', comp=1):
     raise DeprecationWarning
 
 def get_pp(mydf, kpts=None):
-    '''Get the periodic pseudotential nuc-el AO matrix, with G=0 removed.
+    '''Get the periodic pseudopotential nuc-el AO matrix, with G=0 removed.
 
     Kwargs:
         mesh: custom mesh grids. By default mesh is determined by the

pyscf/pbc/df/df.py

@@ -66,7 +66,7 @@
 
 def make_modrho_basis(cell, auxbasis=None, drop_eta=None):
     r'''Generate a cell object using the density fitting auxbasis as
-    the basis set. The normalization coeffcients of the auxiliary cell are
+    the basis set. The normalization coefficients of the auxiliary cell are
     different to the regular (square-norm) convention. To simplify the
     compensated charge algorithm, they are normalized against
     \int (r^l e^{-ar^2} r^2 dr
@@ -378,7 +378,7 @@ def load(aux_slice):
                     LpqR = LpqI = None
 
     def get_pp(self, kpts=None):
-        '''Get the periodic pseudotential nuc-el AO matrix, with G=0 removed.
+        '''Get the periodic pseudopotential nuc-el AO matrix, with G=0 removed.
         '''
         cell = self.cell
         kpts, is_single_kpt = _check_kpts(self, kpts)

pyscf/pbc/df/fft.py

@@ -63,7 +63,7 @@ def get_nuc(mydf, kpts=None):
     return numpy.asarray(vne)
 
 def get_pp(mydf, kpts=None):
-    '''Get the periodic pseudotential nuc-el AO matrix, with G=0 removed.
+    '''Get the periodic pseudopotential nuc-el AO matrix, with G=0 removed.
     '''
     from pyscf.pbc.dft import gen_grid
     kpts, is_single_kpt = _check_kpts(mydf, kpts)

pyscf/pbc/df/gdf_builder.py

@@ -750,7 +750,7 @@ def auxbar(fused_cell):
             if es.size == 1:
                 vbar[aux_loc[i]] = -1/es[0]
             else:
-                # Remove the normalization to get the primitive contraction coeffcients
+                # Remove the normalization to get the primitive contraction coefficients
                 norms = half_sph_norm/gto.gaussian_int(2, es)
                 cs = np.einsum('i,ij->ij', 1/norms, fused_cell._libcint_ctr_coeff(i))
                 vbar[aux_loc[i]:aux_loc[i+1]] = np.einsum('in,i->n', cs, -1/es)

pyscf/pbc/df/mdf.py

@@ -98,7 +98,7 @@ def build(self, j_only=None, with_j3c=True, kpts_band=None):
         df.GDF.build(self, j_only, with_j3c, kpts_band)
         cell = self.cell
         if any(x % 2 == 0 for x in self.mesh[:cell.dimension]):
-            # Even number in mesh can produce planewaves without couterparts
+            # Even number in mesh can produce planewaves without counterparts
             # (see np.fft.fftfreq). MDF mesh is typically not enough to capture
             # all basis. The singular planewaves can break the symmetry in
             # potential (leads to non-real density) and thereby break the

pyscf/pbc/df/rsdf.py

@@ -32,7 +32,7 @@
 In RSGDF, the two-center and three-center Coulomb integrals are calculated in two pars:
     j2c = j2c_SR(omega) + j2c_LR(omega)
     j3c = j3c_SR(omega) + j3c_LR(omega)
-where the SR and LR integrals correpond to using the following potentials
+where the SR and LR integrals correspond to using the following potentials
     g_SR(r_12;omega) = erfc(omega * r_12) / r_12
     g_LR(r_12;omega) = erf(omega * r_12) / r_12
 The SR integrals are evaluated in real space using a lattice summation, while

pyscf/pbc/df/rsdf_builder.py

@@ -1014,7 +1014,7 @@ def get_nuc(nuc_builder):
     return nuc
 
 def get_pp(nuc_builder):
-    '''get the periodic pseudotential nuc-el ao matrix, with g=0 removed.
+    '''get the periodic pseudopotential nuc-el ao matrix, with g=0 removed.
 
     kwargs:
         mesh: custom mesh grids. by default mesh is determined by the
@@ -1401,7 +1401,7 @@ def _round_off_to_odd_mesh(mesh):
     # the conjugation symmetry between the k-points k and -k.
     # When building the DF integral tensor in function _make_j3c, the symmetry
     # between k and -k is used (function conj_j2c) to overcome the error
-    # caused by auxiliary basis linear dependency. More detalis of this
+    # caused by auxiliary basis linear dependency. More details of this
     # problem can be found in function _make_j3c.
     if isinstance(mesh, (int, np.integer)):
         return (mesh // 2) * 2 + 1