Add the shallow copy method in the base class StreamObject

Remove copy statements in mcscf modules

pyscf/agf2/ragf2.py

@@ -869,8 +869,7 @@ def density_fit(self, auxbasis=None, with_df=None):
             myagf2.with_df = with_df
 
         if auxbasis is not None and myagf2.with_df.auxbasis != auxbasis:
-            import copy
-            myagf2.with_df = copy.copy(myagf2.with_df)
+            myagf2.with_df = myagf2.with_df.copy()
             myagf2.with_df.auxbasis = auxbasis
 
         return myagf2

pyscf/agf2/uagf2.py

@@ -633,8 +633,7 @@ def density_fit(self, auxbasis=None, with_df=None):
             myagf2.with_df = with_df
 
         if auxbasis is not None and myagf2.with_df.auxbasis != auxbasis:
-            import copy
-            myagf2.with_df = copy.copy(myagf2.with_df)
+            myagf2.with_df = myagf2.with_df.copy()
             myagf2.with_df.auxbasis = auxbasis
 
         return myagf2

pyscf/cc/ccsd.py

@@ -1355,8 +1355,7 @@ def density_fit(self, auxbasis=None, with_df=None):
         if with_df is not None:
             mycc.with_df = with_df
         if mycc.with_df.auxbasis != auxbasis:
-            import copy
-            mycc.with_df = copy.copy(mycc.with_df)
+            mycc.with_df = mycc.with_df.copy()
             mycc.with_df.auxbasis = auxbasis
         return mycc
 

pyscf/cc/test/test_ccsd_lambda.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import copy
 import tempfile
 import unittest
 import numpy
@@ -114,7 +113,7 @@ def test_ccsd(self):
 
     def test_restart(self):
         ftmp = tempfile.NamedTemporaryFile()
-        cc1 = copy.copy(mycc)
+        cc1 = mycc.copy()
         cc1.max_cycle = 5
         cc1.solve_lambda()
         l1ref = cc1.l1

pyscf/cc/test/test_dfccsd.py

@@ -14,7 +14,6 @@
 # limitations under the License.
 
 import unittest
-import copy
 import numpy
 from functools import reduce
 
@@ -24,7 +23,7 @@
 from pyscf.cc import dfccsd, eom_rccsd
 
 def make_mycc1():
-    mf1 = copy.copy(mf)
+    mf1 = mf.copy()
     no = mol.nelectron // 2
     n = mol.nao_nr()
     nv = n - no

pyscf/cc/test/test_eom_gccsd.py

@@ -14,7 +14,6 @@
 # limitations under the License.
 
 import unittest
-import copy
 import numpy
 from functools import reduce
 

pyscf/cc/test/test_eom_rccsd.py

@@ -26,7 +26,7 @@
 from pyscf.cc import ccsd, rccsd, eom_rccsd, rintermediates, gintermediates
 
 def make_mycc1():
-    mf1 = copy.copy(mf)
+    mf1 = mf.copy()
     no = mol.nelectron // 2
     n = mol.nao_nr()
     nv = n - no
@@ -67,7 +67,7 @@ def setUpModule():
     mf1, mycc1, eris1 = make_mycc1()
     no, nv = mycc1.t1.shape
 
-    mycci = copy.copy(mycc1)
+    mycci = mycc1.copy()
     erisi = copy.copy(eris1)
     erisi.oooo = eris1.oooo + numpy.sin(eris1.oooo)*1j
     erisi.oooo = erisi.oooo + erisi.oooo.conj().transpose(1,0,3,2)

pyscf/cc/test/test_eom_uccsd.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import copy
 import unittest
 import numpy
 import numpy as np
@@ -47,7 +46,7 @@ def setUpModule():
     mol1.spin = 2
     mol1.build()
     mf0 = scf.UHF(mol1).run(conv_tol=1e-12)
-    mf1 = copy.copy(mf0)
+    mf1 = mf0.copy()
 
     nocca, noccb = mol1.nelec
     nmo = mol1.nao_nr()
@@ -218,7 +217,7 @@ def test_ucc_eomee_ccsd_matvec(self):
         self.assertAlmostEqual(float(abs(gr2-uee1.spatial2spin(r2, orbspin)).max()), 0, 9)
         self.assertAlmostEqual(lib.fp(vec1), 49.499911123484523, 9)
 
-        ucc2 = copy.copy(ucc1)
+        ucc2 = ucc1.copy()
         ucc2.direct = True
         uee1 = eom_uccsd.EOMEESpinKeep(ucc2)
         vec1 = uee1.matvec(vec)
@@ -293,7 +292,7 @@ def test_ucc_eomsf_ccsd_matvec(self):
         self.assertAlmostEqual(float(abs(gr1-myeom.spatial2spin(v1, orbspin)).max()), 0, 9)
         self.assertAlmostEqual(float(abs(gr2-myeom.spatial2spin(v2, orbspin)).max()), 0, 9)
 
-        ucc2 = copy.copy(ucc1)
+        ucc2 = ucc1.copy()
         ucc2.direct = True
         myeom = eom_uccsd.EOMEESpinFlip(ucc2)
         vec1 = myeom.matvec(vec)
@@ -322,7 +321,7 @@ def test_ucc_eomip_matvec(self):
         self.assertAlmostEqual(float(abs(gr1-myeom.spatial2spin(v1, orbspin)).max()), 0, 9)
         self.assertAlmostEqual(float(abs(gr2-myeom.spatial2spin(v2, orbspin)).max()), 0, 9)
 
-        ucc2 = copy.copy(ucc1)
+        ucc2 = ucc1.copy()
         ucc2.direct = True
         myeom = eom_uccsd.EOMIP(ucc2)
         vec1 = myeom.matvec(vec)
@@ -351,7 +350,7 @@ def test_ucc_eomea_matvec(self):
         self.assertAlmostEqual(float(abs(gr1-myeom.spatial2spin(v1, orbspin)).max()), 0, 9)
         self.assertAlmostEqual(float(abs(gr2-myeom.spatial2spin(v2, orbspin)).max()), 0, 9)
 
-        ucc2 = copy.copy(ucc1)
+        ucc2 = ucc1.copy()
         ucc2.direct = True
         myeom = eom_uccsd.EOMEA(ucc2)
         vec1 = myeom.matvec(vec)

pyscf/cc/test/test_gccsd_t.py

@@ -15,7 +15,6 @@
 
 import unittest
 import numpy
-import copy
 from functools import reduce
 
 from pyscf import gto, scf, lib, symm
@@ -36,7 +35,7 @@ def setUpModule():
     mol.basis = '3-21g'
     mol.symmetry = 'C2v'
     mol.build()
-    mol1 = copy.copy(mol)
+    mol1 = mol.copy()
     mol1.symmetry = False
 
     mf = scf.UHF(mol1).run(conv_tol=1e-14)
@@ -53,7 +52,7 @@ def test_gccsd_t_compare_uccsd_t(self):
         self.assertAlmostEqual(myucc.ccsd_t(), mygcc.ccsd_t(t1=None), 7)
 
     def test_gccsd_t(self):
-        mf1 = copy.copy(mf)
+        mf1 = mf.copy()
         nao, nmo = mf.mo_coeff[0].shape
         numpy.random.seed(10)
         mf1.mo_coeff = numpy.random.random((2,nao,nmo))

pyscf/cc/test/test_rccsd.py

@@ -112,7 +112,7 @@ def ao2mofn(mos):
         self.assertAlmostEqual(abs(eris1.vvvv.imag-eris.vvvv).max(), 0, 11)
 
     def test_dump_chk(self):
-        cc1 = copy.copy(mycc)
+        cc1 = mycc.copy()
         cc1.nmo = mf.mo_energy.size
         cc1.nocc = mol.nelectron // 2
         cc1.dump_chk()
@@ -221,7 +221,7 @@ def test_vector_size(self):
         self.assertEqual(mycc.vector_size(), 860)
 
     def test_rccsd_frozen(self):
-        cc1 = copy.copy(mycc)
+        cc1 = mycc.copy()
         cc1.frozen = 1
         self.assertEqual(cc1.nmo, 12)
         self.assertEqual(cc1.nocc, 4)
@@ -383,7 +383,7 @@ def test_add_vvvv(self):
         nocc, nvir = t1.shape
         tau = t2 + numpy.einsum('ia,jb->ijab', t1, t1)
         eris1 = copy.copy(eris)
-        mycc1 = copy.copy(mycc)
+        mycc1 = mycc.copy()
         ovvv = eris1.get_ovvv()
         tmp = -numpy.einsum('ijcd,ka,kdcb->ijba', tau, t1, ovvv)
         t2a = tmp + tmp.transpose(1,0,3,2)

pyscf/cc/test/test_rccsd_lambda.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import copy
 import unittest
 import numpy
 import numpy as np
@@ -170,7 +169,7 @@ def test_rdm(self):
         self.assertAlmostEqual(e1, mycc.e_tot, 6)
 
         d1 = ccsd_rdm._gamma1_intermediates(mycc, mycc.t1, mycc.t2, mycc.l1, mycc.l2)
-        mycc1 = copy.copy(mycc)
+        mycc1 = mycc.copy()
         mycc1.max_memory = 0
         d2 = ccsd_rdm._gamma2_intermediates(mycc1, mycc.t1, mycc.t2, mycc.l1, mycc.l2, True)
         dm2 = ccsd_rdm._make_rdm2(mycc, d1, d2, with_dm1=True, with_frozen=True)

pyscf/cc/test/test_uccsd.py

@@ -187,7 +187,7 @@ def test_amplitudes_from_rccsd(self):
         self.assertAlmostEqual(abs(t2[2]-myucc.t2[2]).max(), 0, 5)
 
     def test_uccsd_frozen(self):
-        ucc1 = copy.copy(myucc)
+        ucc1 = myucc.copy()
         ucc1.frozen = 1
         self.assertEqual(ucc1.nmo, (12,12))
         self.assertEqual(ucc1.nocc, (4,4))

pyscf/cc/test/test_uccsd_t.py

@@ -15,7 +15,6 @@
 
 import unittest
 import numpy
-import copy
 from functools import reduce
 
 from pyscf import gto, scf, lib, symm
@@ -43,7 +42,7 @@ def setUpModule():
     mol.basis = '3-21g'
     mol.symmetry = 'C2v'
     mol.build()
-    mol1 = copy.copy(mol)
+    mol1 = mol.copy()
     mol1.symmetry = False
 
     mf = scf.UHF(mol1).run(conv_tol=1e-14)
@@ -58,7 +57,7 @@ def tearDownModule():
 
 class KnownValues(unittest.TestCase):
     def test_uccsd_t(self):
-        mf1 = copy.copy(mf)
+        mf1 = mf.copy()
         nao, nmo = mf.mo_coeff[0].shape
         numpy.random.seed(10)
         mf1.mo_coeff = numpy.random.random((2,nao,nmo)) - .5

pyscf/df/addons.py

@@ -17,7 +17,6 @@
 #
 
 import sys
-import copy
 import numpy
 from pyscf.lib import logger
 from pyscf import gto
@@ -204,7 +203,7 @@ def make_auxmol(mol, auxbasis=None):
 
     See also the paper JCTC, 13, 554 about generating auxiliary fitting basis.
     '''
-    pmol = copy.copy(mol)  # just need shallow copy
+    pmol = mol.copy(deep=False)
 
     if auxbasis is None:
         auxbasis = make_auxbasis(mol)

pyscf/df/df.py

@@ -21,7 +21,6 @@
 '''
 
 
-import copy
 import tempfile
 import contextlib
 import numpy
@@ -277,7 +276,7 @@ def range_coulomb(self, omega):
         if key in self._rsh_df:
             rsh_df = self._rsh_df[key]
         else:
-            rsh_df = self._rsh_df[key] = copy.copy(self).reset()
+            rsh_df = self._rsh_df[key] = self.copy().reset()
             if hasattr(self, '_dataname'):
                 rsh_df._dataname = f'{self._dataname}/lr/{key}'
             logger.info(self, 'Create RSH-DF object %s for omega=%s', rsh_df, omega)

pyscf/df/df_jk.py

@@ -16,8 +16,6 @@
 # Author: Qiming Sun <[email protected]>
 #
 
-import copy
-
 import ctypes
 import numpy
 import scipy.linalg
@@ -83,7 +81,7 @@ def density_fit(mf, auxbasis=None, with_df=None, only_dfj=False):
             mf.with_df = with_df
         elif getattr(mf.with_df, 'auxbasis', None) != auxbasis:
             #logger.warn(mf, 'DF might have been initialized twice.')
-            mf = copy.copy(mf)
+            mf = mf.copy()
             mf.with_df = with_df
             mf.only_dfj = only_dfj
         return mf

pyscf/df/grad/sacasscf.py

@@ -17,7 +17,6 @@
 #
 
 import numpy as np
-import copy
 import time
 import gc
 from functools import reduce

pyscf/dft/dks.py

@@ -21,7 +21,6 @@
 '''
 
 
-import copy
 import numpy
 from pyscf import lib
 from pyscf.lib import logger
@@ -118,7 +117,7 @@ def to_dhf(self):
 
     def to_dks(self, xc=None):
         if xc is not None and xc != self.xc:
-            mf = copy.copy(self)
+            mf = self.copy()
             mf.xc = xc
             mf.converged = False
         return self

pyscf/dft/libxc.py

@@ -24,7 +24,6 @@
 
 import sys
 import warnings
-import copy
 import ctypes
 import math
 import numpy
@@ -1661,5 +1660,5 @@ def define_xc_(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):
     return ni
 
 def define_xc(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):
-    return define_xc_(copy.copy(ni), description, xctype, hyb, rsh)
+    return define_xc_(ni.copy(), description, xctype, hyb, rsh)
 define_xc.__doc__ = define_xc_.__doc__

pyscf/dft/xcfun.py

@@ -22,7 +22,6 @@
 U. Ekstrom et al, J. Chem. Theory Comput., 6, 1971
 '''
 
-import copy
 import ctypes
 from functools import lru_cache
 import math
@@ -1080,5 +1079,5 @@ def define_xc_(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):
     return ni
 
 def define_xc(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):
-    return define_xc_(copy.copy(ni), description, xctype, hyb, rsh)
+    return define_xc_(ni.copy(), description, xctype, hyb, rsh)
 define_xc.__doc__ = define_xc_.__doc__

pyscf/eph/eph_fd.py

@@ -20,7 +20,6 @@
 electron-phonon matrix from finite difference
 '''
 
-import copy
 import numpy as np
 from pyscf import scf, dft, gto, hessian
 from pyscf.eph import rhf as rhf_eph
@@ -35,9 +34,9 @@ def run_mfs(mf, mols_a, mols_b):
     dm0 = mf.make_rdm1()
     mflist = []
     for i in range(nconfigs):
-        mf1 = copy.copy(mf)
+        mf1 = mf.copy()
         mf1.reset(mols_a[i])
-        mf2 = copy.copy(mf)
+        mf2 = mf.copy()
         mf2.reset(mols_b[i])
         mf1.kernel(dm0=dm0)
         mf2.kernel(dm0=dm0)