pyscf 2.6.2__py3-none-macosx_11_0_arm64.whl → 2.7.0__py3-none-macosx_11_0_arm64.whl

pyscf/mcscf/mc1step.py

@@ -188,8 +188,8 @@ def gen_g_hop(casscf, mo, u, casdm1, casdm2, eris):
         if ncore > 0:
             # Due to x1_rs [4(pq|sr) + 4(pq|rs) - 2(pr|sq) - 2(ps|rq)] for r>s p>q,
             #    == -x1_sr [4(pq|sr) + 4(pq|rs) - 2(pr|sq) - 2(ps|rq)] for r>s p>q,
-            # x2[:,:ncore] += H * x1[:,:ncore] => (becuase x1=-x1.T) =>
-            # x2[:,:ncore] += -H' * x1[:ncore] => (becuase x2-x2.T) =>
+            # x2[:,:ncore] += H * x1[:,:ncore] => (because x1=-x1.T) =>
+            # x2[:,:ncore] += -H' * x1[:ncore] => (because x2-x2.T) =>
             # x2[:ncore] += H' * x1[:ncore]
             va, vc = casscf.update_jk_in_ah(mo, x1, casdm1, eris)
             x2[ncore:nocc] += va
@@ -282,7 +282,7 @@ def rotate_orb_cc(casscf, mo, fcivec, fcasdm1, fcasdm2, eris, x0_guess=None,
                 break
 
             elif (ikf >= max(casscf.kf_interval, -numpy.log(norm_dr+1e-7)) or
-                  # Insert keyframe if the keyframe and the esitimated grad
+                  # Insert keyframe if the keyframe and the estimated grad
                   # are very different
                   norm_gorb < norm_gkf/casscf.kf_trust_region):
                 ikf = 0
@@ -341,6 +341,9 @@ def kernel(casscf, mo_coeff, tol=1e-7, conv_tol_grad=None,
     if callback is None:
         callback = casscf.callback
 
+    if ci0 is None:
+        ci0 = casscf.ci
+
     mo = mo_coeff
     nmo = mo_coeff.shape[1]
     ncore = casscf.ncore
@@ -464,7 +467,7 @@ def kernel(casscf, mo_coeff, tol=1e-7, conv_tol_grad=None,
                 (max_offdiag_u < casscf.small_rot_tol or casscf.small_rot_tol == 0)):
             conv = True
 
-        if dump_chk:
+        if dump_chk and casscf.chkfile:
             casscf.dump_chk(locals())
 
         if callable(callback):
@@ -496,7 +499,7 @@ def kernel(casscf, mo_coeff, tol=1e-7, conv_tol_grad=None,
                      'call to mc.cas_natorb_() is required')
         mo_energy = None
 
-    if dump_chk:
+    if dump_chk and casscf.chkfile:
         casscf.dump_chk(locals())
 
     log.timer('1-step CASSCF', *cput0)
@@ -583,8 +586,8 @@ def max_stepsize_scheduler(casscf, envs):
 # To extend CASSCF for certain CAS space solver, it can be done by assign an
 # object or a module to CASSCF.fcisolver.  The fcisolver object or module
 # should at least have three member functions "kernel" (wfn for given
-# hamiltonain), "make_rdm12" (1- and 2-pdm), "absorb_h1e" (effective
-# 2e-hamiltonain) in 1-step CASSCF solver, and two member functions "kernel"
+# hamiltonian), "make_rdm12" (1- and 2-pdm), "absorb_h1e" (effective
+# 2e-hamiltonian) in 1-step CASSCF solver, and two member functions "kernel"
 # and "make_rdm12" in 2-step CASSCF solver
 class CASSCF(casci.CASBase):
     __doc__ = casci.CASBase.__doc__ + '''
@@ -652,7 +655,7 @@ class CASSCF(casci.CASBase):
             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
-            envrionment.
+            environment.
         scale_restoration : float
             When a step of orbital rotation moves out of trust region, the
             orbital optimization will be restored to previous state and the
@@ -758,8 +761,6 @@ class CASSCF(casci.CASBase):
     def __init__(self, mf_or_mol, ncas=0, nelecas=0, ncore=None, frozen=None):
         casci.CASBase.__init__(self, mf_or_mol, ncas, nelecas, ncore)
         self.frozen = frozen
-
-        self.callback = None
         self.chkfile = self._scf.chkfile
 
         self.fcisolver.max_cycle = getattr(__config__,
@@ -777,6 +778,9 @@ class CASSCF(casci.CASBase):
         self.converged = False
         self._max_stepsize = None
 
+    __getstate__, __setstate__ = lib.generate_pickle_methods(
+            excludes=('chkfile', 'callback'))
+
     def dump_flags(self, verbose=None):
         log = logger.new_logger(self, verbose)
         log.info('')
@@ -853,6 +857,9 @@ To enable the solvent model for CASSCF, the following code needs to be called
             self.mo_coeff = mo_coeff
         if callback is None: callback = self.callback
 
+        if ci0 is None:
+            ci0 = self.ci
+
         self.check_sanity()
         self.dump_flags()
 
@@ -966,7 +973,7 @@ To enable the solvent model for CASSCF, the following code needs to be called
     rotate_orb_cc = rotate_orb_cc
 
     def update_ao2mo(self, mo):
-        raise DeprecationWarning('update_ao2mo was obseleted since pyscf v1.0.  '
+        raise DeprecationWarning('update_ao2mo was obsoleted since pyscf v1.0.  '
                                  'Use .ao2mo method instead')
 
     def ao2mo(self, mo_coeff=None):
@@ -1171,38 +1178,55 @@ To enable the solvent model for CASSCF, the following code needs to be called
         paaa = lib.transpose(buf.reshape(ncas*ncas,-1), out=out)
         return paaa.reshape(nmo,ncas,ncas,ncas)
 
-    def dump_chk(self, envs):
-        if not self.chkfile:
-            return self
+    def dump_chk(self, envs_or_file):
+        '''Serialize the MCSCF object and save it to the specified chkfile.
 
-        if getattr(self.fcisolver, 'nevpt_intermediate', None):
-            civec = None
-        elif self.chk_ci:
-            civec = envs['fcivec']
+        Args:
+            envs_or_file:
+                If this argument is a file path, the serialized MCSCF object is
+                saved to the file specified by this argument.
+                If this attribute is a dict (created by locals()), the necessary
+                variables are saved to the file specified by the attribute .chkfile.
+        '''
+        if isinstance(envs_or_file, str):
+            envs = None
+            chk_file = envs_or_file
         else:
-            civec = None
+            envs = envs_or_file
+            chk_file = self.chkfile
+            if not chk_file:
+                return self
+
+        e_tot = mo_coeff = mo_occ = mo_energy = e_cas = civec = casdm1 = None
         ncore = self.ncore
         nocc = ncore + self.ncas
-        if 'mo' in envs:
-            mo_coeff = envs['mo']
-        else:
-            mo_coeff = envs['mo_coeff']
-        mo_occ = numpy.zeros(mo_coeff.shape[1])
-        mo_occ[:ncore] = 2
-        if self.natorb:
-            occ = self._eig(-envs['casdm1'], ncore, nocc)[0]
-            mo_occ[ncore:nocc] = -occ
-        else:
-            mo_occ[ncore:nocc] = envs['casdm1'].diagonal()
-# Note: mo_energy in active space =/= F_{ii}  (F is general Fock)
-        if 'mo_energy' in envs:
-            mo_energy = envs['mo_energy']
-        else:
-            mo_energy = 'None'
-        chkfile.dump_mcscf(self, self.chkfile, 'mcscf', envs['e_tot'],
+
+        if envs is not None:
+            if self.chk_ci:
+                civec = envs.get('fcivec', None)
+
+            e_tot = envs['e_tot']
+            e_cas = envs['e_cas']
+            casdm1 = envs['casdm1']
+            if 'mo' in envs:
+                mo_coeff = envs['mo']
+            else:
+                mo_coeff = envs['mo_coeff']
+            mo_occ = numpy.zeros(mo_coeff.shape[1])
+            mo_occ[:ncore] = 2
+            if self.natorb:
+                occ = self._eig(-casdm1, ncore, nocc)[0]
+                mo_occ[ncore:nocc] = -occ
+            else:
+                mo_occ[ncore:nocc] = casdm1.diagonal()
+            # Note: mo_energy in active space =/= F_{ii}  (F is general Fock)
+            if 'mo_energy' in envs:
+                mo_energy = envs['mo_energy']
+
+        chkfile.dump_mcscf(self, chk_file, 'mcscf', e_tot,
                            mo_coeff, ncore, self.ncas, mo_occ,
-                           mo_energy, envs['e_cas'], civec, envs['casdm1'],
-                           overwrite_mol=False)
+                           mo_energy, e_cas, civec, casdm1,
+                           overwrite_mol=(envs is None))
         return self
 
     def update_from_chk(self, chkfile=None):

pyscf/mcscf/newton_casscf.py

@@ -366,8 +366,8 @@ def gen_g_hop(casscf, mo, ci0, eris, verbose=None):
             # part4, part5, part6
             # Due to x1_rs [4(pq|sr) + 4(pq|rs) - 2(pr|sq) - 2(ps|rq)] for r>s p>q,
             #    == -x1_sr [4(pq|sr) + 4(pq|rs) - 2(pr|sq) - 2(ps|rq)] for r>s p>q,
-            # x2[:,:ncore] += H * x1[:,:ncore] => (becuase x1=-x1.T) =>
-            # x2[:,:ncore] += -H' * x1[:ncore] => (becuase x2-x2.T) =>
+            # x2[:,:ncore] += H * x1[:,:ncore] => (because x1=-x1.T) =>
+            # x2[:,:ncore] += -H' * x1[:ncore] => (because x2-x2.T) =>
             # x2[:ncore] += H' * x1[:ncore]
             va, vc = casscf.update_jk_in_ah(mo, x1, casdm1, eris)
             x2[ncore:nocc] += va
@@ -501,7 +501,7 @@ def update_orb_ci(casscf, mo, ci0, eris, x0_guess=None,
                 break
 
             elif ((ikf >= max(casscf.kf_interval, casscf.kf_interval-numpy.log(norm_dr+1e-7)) or
-                   # Insert keyframe if the keyframe and the esitimated grad are too different
+                   # Insert keyframe if the keyframe and the estimated grad are too different
                    norm_gall < norm_gkf/casscf.kf_trust_region)):
                 ikf = 0
                 u, ci_kf = extract_rotation(casscf, dr, u, ci_kf)
@@ -705,7 +705,7 @@ class CASSCF(mc1step.CASSCF):
             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
-            envrionment.
+            environment.
 
     Saved results
 
@@ -852,7 +852,7 @@ class CASSCF(mc1step.CASSCF):
         return e_tot, e_cas, fcivec
 
     def update_ao2mo(self, mo):
-        raise DeprecationWarning('update_ao2mo was obseleted since pyscf v1.0.  '
+        raise DeprecationWarning('update_ao2mo was obsoleted since pyscf v1.0.  '
                                  'Use .ao2mo method instead')
 
 

pyscf/mcscf/ucasci.py

@@ -54,7 +54,7 @@ def extract_orbs(mo_coeff, ncas, nelecas, ncore):
     return mo_core, mo_cas, mo_vir
 
 def h1e_for_cas(casci, mo_coeff=None, ncas=None, ncore=None):
-    '''CAS sapce one-electron hamiltonian for UHF-CASCI or UHF-CASSCF
+    '''CAS space one-electron hamiltonian for UHF-CASCI or UHF-CASSCF
 
     Args:
         casci : a U-CASSCF/U-CASCI object or UHF object

pyscf/mcscf/umc1step.py

@@ -27,6 +27,7 @@ from functools import reduce
 import numpy
 import pyscf.gto
 import pyscf.scf
+from pyscf import lib
 from pyscf.lib import logger
 from pyscf.mcscf import ucasci
 from pyscf.mcscf.mc1step import expmat, rotate_orb_cc, max_stepsize_scheduler, as_scanner
@@ -399,6 +400,9 @@ class UCASSCF(ucasci.UCASBase):
         self.converged = False
         self._max_stepsize = None
 
+    __getstate__, __setstate__ = lib.generate_pickle_methods(
+            excludes=('chkfile', 'callback'))
+
     def dump_flags(self, verbose=None):
         log = logger.new_logger(self, verbose)
         log.info('')
@@ -732,39 +736,54 @@ class UCASSCF(ucasci.UCASBase):
                 ci1 += xs[i] * v[i,0]
         return ci1, g
 
-    def dump_chk(self, envs):
-        if not self.chkfile:
-            return self
+    def dump_chk(self, envs_or_file):
+        '''Serialize the MCSCF object and save it to the specified chkfile.
 
-        if self.chk_ci:
-            civec = envs['fcivec']
+        Args:
+            envs_or_file:
+                If this argument is a file path, the serialized MCSCF object is
+                saved to the file specified by this argument.
+                If this attribute is a dict (created by locals()), the necessary
+                variables are saved to the file specified by the attribute .chkfile.
+        '''
+        if isinstance(envs_or_file, str):
+            envs = None
+            chk_file = envs_or_file
         else:
-            civec = None
+            envs = envs_or_file
+            chk_file = self.chkfile
+            if not chk_file:
+                return self
+
+        e_tot = mo_coeff = mo_occ = mo_energy = e_cas = civec = casdm1 = None
         ncore = self.ncore
         ncas = self.ncas
         nocca = ncore[0] + ncas
         noccb = ncore[1] + ncas
-        if 'mo' in envs:
-            mo_coeff = envs['mo']
-        else:
-            mo_coeff = envs['mo']
-        mo_occ = numpy.zeros((2,envs['mo'][0].shape[1]))
-        mo_occ[0,:ncore[0]] = 1
-        mo_occ[1,:ncore[1]] = 1
-        if self.natorb:
-            occa, ucas = self._eig(-envs['casdm1'][0], ncore[0], nocca)
-            occb, ucas = self._eig(-envs['casdm1'][1], ncore[1], noccb)
-            mo_occ[0,ncore[0]:nocca] = -occa
-            mo_occ[1,ncore[1]:noccb] = -occb
-        else:
-            mo_occ[0,ncore[0]:nocca] = envs['casdm1'][0].diagonal()
-            mo_occ[1,ncore[1]:noccb] = envs['casdm1'][1].diagonal()
-        mo_energy = 'None'
 
-        chkfile.dump_mcscf(self, self.chkfile, 'mcscf', envs['e_tot'],
+        if envs is not None:
+            if self.chk_ci:
+                civec = envs['fcivec']
+            if 'mo' in envs:
+                mo_coeff = envs['mo']
+            else:
+                mo_coeff = envs['mo_coeff']
+            mo_occ = numpy.zeros((2,envs['mo'][0].shape[1]))
+            mo_occ[0,:ncore[0]] = 1
+            mo_occ[1,:ncore[1]] = 1
+            if self.natorb:
+                occa, ucas = self._eig(-casdm1[0], ncore[0], nocca)
+                occb, ucas = self._eig(-casdm1[1], ncore[1], noccb)
+                mo_occ[0,ncore[0]:nocca] = -occa
+                mo_occ[1,ncore[1]:noccb] = -occb
+            else:
+                mo_occ[0,ncore[0]:nocca] = casdm1[0].diagonal()
+                mo_occ[1,ncore[1]:noccb] = casdm1[1].diagonal()
+
+        chkfile.dump_mcscf(self, self.chkfile, 'mcscf', e_tot,
                            mo_coeff, ncore, ncas, mo_occ,
-                           mo_energy, envs['e_cas'], civec, envs['casdm1'],
-                           overwrite_mol=False)
+                           mo_energy, e_cas, civec, casdm1,
+                           overwrite_mol=(envs is None))
         return self
 
     def rotate_mo(self, mo, u, log=None):

pyscf/md/integrators.py

@@ -128,7 +128,7 @@ class _Integrator(lib.StreamObject):
         method : lib.GradScanner, rhf.GradientsBase instance, or
         has nuc_grad_method method.
             Method by which to compute the energy gradients and energies
-            in order to propogate the equations of motion. Realistically,
+            in order to propagate the equations of motion. Realistically,
             it can be any callable object such that it returns the energy
             and potential energy gradient when given a mol.
 
@@ -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

@@ -54,7 +54,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2, verbos
     emp2_ss = emp2_os = 0
     for i in range(nocc):
         if isinstance(eris.ovov, numpy.ndarray) and eris.ovov.ndim == 4:
-            # When mf._eri is a custom integrals wiht the shape (n,n,n,n), the
+            # When mf._eri is a custom integrals with the shape (n,n,n,n), the
             # ovov integrals might be in a 4-index tensor.
             gi = eris.ovov[i]
         else:
@@ -160,7 +160,7 @@ def make_rdm1(mp, t2=None, eris=None, ao_repr=False, with_frozen=True):
 
     Kwargs:
         ao_repr : boolean
-            Whether to transfrom 1-particle density matrix to AO
+            Whether to transform 1-particle density matrix to AO
             representation.
     '''
     from pyscf.cc import ccsd_rdm
@@ -248,7 +248,8 @@ def make_fno(mp, thresh=1e-6, pct_occ=None, nvir_act=None, t2=None):
         else:
             cumsum = numpy.cumsum(n/numpy.sum(n))
             logger.debug(mp, 'Sum(pct_occ): %s', cumsum)
-            nvir_keep = numpy.count_nonzero(cumsum<pct_occ)
+            nvir_keep = numpy.count_nonzero(
+                [c <= pct_occ or numpy.isclose(c, pct_occ) for c in cumsum])
     else:
         nvir_keep = min(nvir, nvir_act)
 
@@ -383,7 +384,7 @@ 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:
@@ -478,7 +479,7 @@ class MP2(lib.StreamObject):
             For non-canonical MP2, DIIS space size in MP2
             iterations.  Default is 6.
         level_shift : float
-            A shift on virtual orbital energies to stablize the MP2 iterations.
+            A shift on virtual orbital energies to stabilize the MP2 iterations.
         frozen : int or list
             If integer is given, the inner-most orbitals are excluded from MP2
             amplitudes.  Given the orbital indices (0-based) in a list, both

pyscf/mp/ump2.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 '''
-UMP2 with spatial integals
+UMP2 with spatial integrals
 '''
 
 
@@ -63,7 +63,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2, verbos
     emp2_ss = emp2_os = 0.0
     for i in range(nocca):
         if isinstance(eris.ovov, numpy.ndarray) and eris.ovov.ndim == 4:
-            # When mf._eri is a custom integrals wiht the shape (n,n,n,n), the
+            # When mf._eri is a custom integrals with the shape (n,n,n,n), the
             # ovov integrals might be in a 4-index tensor.
             eris_ovov = eris.ovov[i]
         else:
@@ -77,7 +77,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2, verbos
             t2aa[i] = t2i - t2i.transpose(0,2,1)
 
         if isinstance(eris.ovOV, numpy.ndarray) and eris.ovOV.ndim == 4:
-            # When mf._eri is a custom integrals wiht the shape (n,n,n,n), the
+            # When mf._eri is a custom integrals with the shape (n,n,n,n), the
             # ovov integrals might be in a 4-index tensor.
             eris_ovov = eris.ovOV[i]
         else:
@@ -90,7 +90,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2, verbos
 
     for i in range(noccb):
         if isinstance(eris.OVOV, numpy.ndarray) and eris.OVOV.ndim == 4:
-            # When mf._eri is a custom integrals wiht the shape (n,n,n,n), the
+            # When mf._eri is a custom integrals with the shape (n,n,n,n), the
             # ovov integrals might be in a 4-index tensor.
             eris_ovov = eris.OVOV[i]
         else:
@@ -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)
@@ -323,7 +323,8 @@ def make_fno(mp, thresh=1e-6, pct_occ=None, nvir_act=None, t2=None, eris=None):
             else:
                 cumsum = numpy.cumsum(n/numpy.sum(n))
                 logger.debug(mp, 'Sum(pct_occ): %s', cumsum)
-                nvir_keep = numpy.count_nonzero(cumsum<pct_occ)
+                nvir_keep = numpy.count_nonzero(
+                    [c <= pct_occ or numpy.isclose(c, pct_occ) for c in cumsum])
         else:
             nvir_keep = min(nvir, nvir_act[s])
 

pyscf/pbc/adc/kadc_rhf.py

@@ -44,7 +44,7 @@ from pyscf.lib.parameters import LOOSE_ZERO_TOL, LARGE_DENOM  # noqa
 import h5py
 import tempfile
 
-# Note : All interals are in Chemist's notation except for vvvv
+# Note : All integrals are in Chemist's notation except for vvvv
 #        Eg.of momentum conservation :
 #        Chemist's  oovv(ijab) : ki - kj + ka - kb
 #        Amplitudes t2(ijab)  : ki + kj - ka - kba

pyscf/pbc/adc/kadc_rhf_amplitudes.py

@@ -45,7 +45,7 @@ import h5py
 import tempfile
 
 
-# Note : All interals are in Chemist's notation except for vvvv
+# Note : All integrals are in Chemist's notation except for vvvv
 #        Eg.of momentum conservation :
 #        Chemist's  oovv(ijab) : ki - kj + ka - kb
 #        Amplitudes t2(ijab)  : ki + kj - ka - kba
@@ -281,7 +281,7 @@ def compute_amplitudes(myadc, eris):
         cput0 = log.timer_debug1("Completed t2_2 amplitude calculation", *cput0)
 
         if (myadc.method == "adc(3)" and myadc.approx_trans_moments is False):
-            raise NotImplementedError('3rd order singles amplitues not implemented')
+            raise NotImplementedError('3rd order singles amplitudes not implemented')
 
     t1 = (t1_2, t1_3)
     t2 = (t2_1, t2_2)

pyscf/pbc/ao2mo/eris.py

@@ -17,7 +17,7 @@
 #
 
 '''
-This ao2mo module is kept for backward compatiblity.  It's recommended to use
+This ao2mo module is kept for backward compatibility.  It's recommended to use
 pyscf.pbc.df module to get 2e MO integrals
 '''
 

pyscf/pbc/cc/kccsd_rhf.py

@@ -242,10 +242,10 @@ def _get_epq(pindices,qindices,fac=[1.0,1.0],large_num=LARGE_DENOM):
 
     Args:
         pindices (5-list of object):
-            A list of p0, p1, kp, orbital values, and non-zero indicess for the first
+            A list of p0, p1, kp, orbital values, and non-zero indices for the first
             denominator indices.
         qindices (5-list of object):
-            A list of q0, q1, kq, orbital values, and non-zero indicess for the second
+            A list of q0, q1, kq, orbital values, and non-zero indices for the second
             denominator element.
         fac (3-list of float):
             Factors to multiply the first and second denominator elements.
@@ -255,7 +255,7 @@ def _get_epq(pindices,qindices,fac=[1.0,1.0],large_num=LARGE_DENOM):
     def get_idx(x0,x1,kx,n0_p):
         return np.logical_and(n0_p[kx] >= x0, n0_p[kx] < x1)
 
-    assert (all([len(x) == 5 for x in [pindices,qindices]]))
+    assert (all(len(x) == 5 for x in [pindices,qindices]))
     p0,p1,kp,mo_e_p,nonzero_p = pindices
     q0,q1,kq,mo_e_q,nonzero_q = qindices
     fac_p, fac_q = fac

pyscf/pbc/cc/kccsd_t_rhf.py

@@ -117,7 +117,7 @@ def kernel(mycc, eris, t1=None, t2=None, max_memory=2000, verbose=logger.INFO):
     def get_w(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1):
         '''Wijkabc intermediate as described in Scuseria paper before Pijkabc acts
 
-        Uses tranposed eris for fast data access.'''
+        Uses transposed eris for fast data access.'''
         km = kconserv[kc, kk, kb]
         kf = kconserv[kk, kc, kj]
         out = einsum('cfjk,abif->abcijk', t2T[kc,kf,kj,c0:c1,:,:,:], eris_vvop[ka,kb,ki,a0:a1,b0:b1,:,nocc:])
@@ -579,7 +579,7 @@ def _get_epqr(pindices,qindices,rindices,fac=[1.0,1.0,1.0],large_num=LARGE_DENOM
     def get_idx(x0,x1,kx,n0_p):
         return np.logical_and(n0_p[kx] >= x0, n0_p[kx] < x1)
 
-    assert (all([len(x) == 5 for x in [pindices,qindices]]))
+    assert (all(len(x) == 5 for x in [pindices,qindices]))
     p0,p1,kp,mo_e_p,nonzero_p = pindices
     q0,q1,kq,mo_e_q,nonzero_q = qindices
     r0,r1,kr,mo_e_r,nonzero_r = rindices

pyscf/pbc/ci/kcis_rhf.py

@@ -126,7 +126,7 @@ def kernel(cis, nroots=1, eris=None, kptlist=None, **kargs):
     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
@@ -703,7 +703,7 @@ class AFTDF(lib.StreamObject, AFTDFMixin):
         cell = self.cell
         if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
             raise RuntimeError('ERIs of PBC-2D systems are not positive '
-                               'definite. Current API only supports postive '
+                               'definite. Current API only supports positive '
                                'definite ERIs.')
 
         if blksize is None:

pyscf/pbc/df/aft_ao2mo.py

@@ -222,7 +222,7 @@ def general(mydf, mo_coeffs, kpts=None,
 
 def get_ao_pairs_G(mydf, kpts=numpy.zeros((2,3)), q=None, shls_slice=None,
                    compact=getattr(__config__, 'pbc_df_ao_pairs_compact', False)):
-    '''Calculate forward Fourier tranform (G|ij) of all AO pairs.
+    '''Calculate forward Fourier transform (G|ij) of all AO pairs.
 
     Returns:
         ao_pairs_G : 2D complex array