fixing a few typos

Author: fchapoton

pyscf/agf2/chkfile.py

@@ -111,7 +111,7 @@ def load_agf2(chkfile):
 def dump_agf2(agf2, chkfile=None, key='agf2',
               gf=None, se=None, frozen=None, nmom=None,
               mo_energy=None, mo_coeff=None, mo_occ=None):
-    ''' Save the AGF2 calculatuion to a chkfile.
+    ''' Save the AGF2 calculation to a chkfile.
     '''
 
     if mpi_helper.rank != 0:

pyscf/data/elements.py

@@ -827,7 +827,7 @@
     [14,36,40,28],     #118  Og
 ]
 
-# This is No. of shells, not the atomic configuations
+# This is No. of shells, not the atomic configurations
 #     core       core+valence
 # core+valence = lambda nuc, l: \
 #            int(numpy.ceil(pyscf.lib.parameters.ELEMENTS[nuc][2][l]/(4*l+2.)))

pyscf/df/df.py

@@ -166,7 +166,7 @@ def build(self):
                                      max_memory=max_memory, verbose=log)
             else:
                 # Store DF tensor in blocks. This is to reduce the
-                # initiailzation overhead
+                # initialization overhead
                 outcore.cholesky_eri_b(mol, cderi, dataname=self._dataname,
                                        int3c=int3c, int2c=int2c, auxmol=auxmol,
                                        max_memory=max_memory, verbose=log)

pyscf/dft/xcfun.py

@@ -833,7 +833,7 @@ def parse_token(token, suffix, search_xc_alias=False):
 
 def eval_xc(xc_code, rho, spin=0, relativity=0, deriv=1, omega=None, verbose=None):
     r'''Interface to call xcfun library to evaluate XC functional, potential
-    and functional derivatives. Return deriviates following libxc convention.
+    and functional derivatives. Return derivatives following libxc convention.
 
     See also :func:`pyscf.dft.libxc.eval_xc`
     '''

pyscf/eph/eph_fd.py

@@ -101,7 +101,7 @@ def kernel(mf, disp=1e-4, mo_rep=False, cutoff_frequency=CUTOFF_FREQUENCY, keep_
     omega, vec = get_mode(mf, cutoff_frequency, keep_imag_frequency)
     mass = mol.atom_mass_list() * MP_ME
     vec = rhf_eph._freq_mass_weighted_vec(vec, omega, mass)
-    mols_a, mols_b = gen_moles(mol, disp/2.0) # generate a bunch of molecules with disp/2 on each cartesion coord
+    mols_a, mols_b = gen_moles(mol, disp/2.0) # generate a bunch of molecules with disp/2 on each cartesian coord
     mfset = run_mfs(mf, mols_a, mols_b) # run mean field calculations on all these molecules
     vmat = get_vmat(mf, mfset, disp) # extracting <p|dV|q>/dR
     if mo_rep:

pyscf/fci/addons.py

@@ -224,7 +224,7 @@ def search_open_shell_det(occ_lst):
                     ci_1[addr_x_a,addr_y_b] = numpy.sqrt(.5)
                     ci_1[addr_y_a,addr_x_b] =-numpy.sqrt(.5)
             else:
-                # TODO: Other direct-product to direct-sum transofromation
+                # TODO: Other direct-product to direct-sum transformation
                 # which involves CG coefficients.
                 ci_1[addra,addrb] = 1
             ci0.append(ci_1.ravel())

pyscf/fci/cistring.py

@@ -200,7 +200,7 @@ def gen_linkstr_index(orb_list, nocc, strs=None, tril=False):
     For given string str0, index[str0] is (nocc+nocc*nvir) x 4 array.
     The first nocc rows [i(:occ),i(:occ),str0,sign] are occupied-occupied
     excitations, which do not change the string. The next nocc*nvir rows
-    [a(:vir),i(:occ),str1,sign] are occupied-virtual exciations, starting from
+    [a(:vir),i(:occ),str1,sign] are occupied-virtual excitations, starting from
     str0, annihilating i, creating a, to get str1.
     '''
     if strs is None:

pyscf/gto/mole.py

@@ -459,7 +459,7 @@ def format_basis(basis_tab, sort_basis=True):
         if len(_basis) == 0:
             raise BasisNotFoundError('Basis not found for  %s' % symb)
 
-        # Sort basis accroding to angular momentum. This is important for method
+        # Sort basis according to angular momentum. This is important for method
         # decontract_basis, which assumes that basis functions with the same
         # angular momentum are grouped together. Related to issue #1620 #1770
         if sort_basis:
@@ -2457,7 +2457,7 @@ def build(self, dump_input=True, parse_arg=ARGPARSE,
               atom=None, basis=None, unit=None, nucmod=None, ecp=None, pseudo=None,
               charge=None, spin=0, symmetry=None, symmetry_subgroup=None,
               cart=None, magmom=None):
-        '''Setup moleclue and initialize some control parameters.  Whenever you
+        '''Setup molecule and initialize some control parameters.  Whenever you
         change the value of the attributes of :class:`Mole`, you need call
         this function to refresh the internal data of Mole.
 
@@ -3800,7 +3800,7 @@ def ao2mo(self, mo_coeffs, erifile=None, dataname='eri_mo', intor='int2e',
         return ao2mo.kernel(self, mo_coeffs, erifile, dataname, intor, **kwargs)
 
     def to_cell(self, a, dimension=3):
-        '''Put a molecule in a cell with periodic boundary condictions
+        '''Put a molecule in a cell with periodic boundary conditions
 
         Args:
             a : (3,3) ndarray

pyscf/lib/dft/grid_common.c

@@ -242,7 +242,7 @@ int orth_components(double *xs_exp, int* bounds, double dx, double radius,
         }
     }
 
-    // add up contributions from all images to the referece image
+    // add up contributions from all images to the reference image
     if (ngridx >= nx_per_cell) {
         memset(xs_exp, 0, (topl+1)*nx_per_cell*sizeof(double));
         int ix, l, lb, ub, size_x;

pyscf/lib/dft/xcfun_itrf.c

@@ -102,7 +102,7 @@ int XCFUN_eval_xc(int nfn, int *fn_id, double *fac, double *omega,
                         rho = rho_u;
                         err = eval_xc(fun, deriv, XC_N, np, 1, outlen, rho, output);
                 }
-// xcfun computed rho*Exc[rho] for zeroth order deriviative instead of Exc[rho]
+// xcfun computed rho*Exc[rho] for zeroth order derivative instead of Exc[rho]
                 for (i = 0; i < np; i++) {
                         output[i*outlen] /= rho_u[i] + 1e-150;
                 }