Import all pyscf modules in __all__.py. Implicit import pyscf modules…

… in gto.Mole class

examples/0-readme.py

@@ -6,11 +6,10 @@
 Before going throught the rest part, be sure the PySCF path is added in PYTHONPATH.
 '''
 
-from pyscf import gto
-from pyscf import scf
+import pyscf
 
 # mol is an object to hold molecule information.
-mol = gto.M(
+mol = pyscf.M(
     verbose = 4,
     output = 'out_h2o',
     atom = '''
@@ -26,22 +25,26 @@
 # control parameters.  The calculation can be executed by the kernel function.
 # Eg, to do Hartree-Fock, (1) create HF object, (2) call kernel function
 #
-mf = scf.RHF(mol)
+mf = mol.RHF()
 print('E=%.15g' % mf.kernel())
 
 
 
 #
 # The above code can be simplified using stream operations.
 # There are three stream functions ".set", ".run", ".apply" to pipe computing
-# streams.  Stream operations allows writing computing script in one line.
+# streams.  Stream operations allows writing multiple computing tasks in one
+# line.
 #
-mf = gto.M(
+mf = pyscf.M(
     atom = '''
       O     0    0       0
       h     0    -.757   .587
      1      0    .757    .587''',
     basis = '6-31g'
-).apply(scf.RHF).run()
+).RHF().run()
 print('E=%.15g' % mf.e_tot)
 
+
+mp2 = mol.RHF().run().MP2().run()
+print('E=%.15g' % mp2.e_tot)

examples/cc/00-simple_ccsd.py

@@ -7,14 +7,14 @@
 A simple example to run CCSD calculation.
 '''
 
-from pyscf import gto, scf, cc
+import pyscf
 
-mol = gto.M(
+mol = pyscf.M(
     atom = 'H 0 0 0; F 0 0 1.1',
     basis = 'ccpvdz')
 
-mf = scf.RHF(mol).run()
+mf = mol.RHF().run()
 
-mycc = cc.CCSD(mf).run()
+mycc = mf.CCSD().run()
 print('CCSD correlation energy', mycc.e_corr)
 

examples/cc/00-simple_ccsd_t.py

@@ -7,19 +7,19 @@
 A simple example to run CCSD(T) and UCCSD(T) calculation.
 '''
 
-from pyscf import gto, scf, cc
+import pyscf
 
-mol = gto.M(
+mol = pyscf.M(
     atom = 'H 0 0 0; F 0 0 1.1',
     basis = 'ccpvdz')
 
-mf = scf.RHF(mol).run()
-mycc = cc.CCSD(mf).run()
+mf = mol.RHF().run()
+mycc = mf.CCSD().run()
 et = mycc.ccsd_t()
 print('CCSD(T) correlation energy', mycc.e_corr + et)
 
-mf = scf.UHF(mol).run()
-mycc = cc.UCCSD(mf).run()
+mf = mol.UHF().run()
+mycc = mf.CCSD().run()
 et = mycc.ccsd_t()
 print('UCCSD(T) correlation energy', mycc.e_corr + et)
 

examples/ci/00-simple_cisd.py

@@ -7,17 +7,17 @@
 A simple example to run CISD calculation.
 '''
 
-from pyscf import gto, scf, ci
+import pyscf
 
-mol = gto.M(
+mol = pyscf.M(
     atom = 'H 0 0 0; F 0 0 1.1',
     basis = 'ccpvdz')
 
-mf = scf.RHF(mol).run()
-mycc = ci.CISD(mf).run()
+mf = mol.HF().run()
+mycc = mf.CISD().run()
 print('RCISD correlation energy', mycc.e_corr)
 
-mf = scf.UHF(mol).run()
-mycc = ci.CISD(mf).run()
+mf = mol.UHF().run()
+mycc = mf.CISD().run()
 print('UCISD correlation energy', mycc.e_corr)
 

examples/dft/00-simple_dft.py

@@ -3,7 +3,7 @@
 # Author: Qiming Sun <osirpt.sun@gmail.com>
 #
 
-from pyscf import gto, dft
+import pyscf
 
 '''
 A simple example to run DFT calculation.
@@ -12,14 +12,13 @@
 available XC functionals.
 '''
 
-mol = gto.Mole()
-mol.build(
+mol = pyscf.M(
     atom = 'H 0 0 0; F 0 0 1.1',  # in Angstrom
     basis = '631g',
     symmetry = True,
 )
 
-mf = dft.RKS(mol)
+mf = mol.KS()
 #mf.xc = 'svwn' # shorthand for slater,vwn
 #mf.xc = 'bp86' # shorthand for b88,p86
 #mf.xc = 'blyp' # shorthand for b88,lyp

examples/mcscf/00-simple_casci.py

@@ -7,20 +7,22 @@
 A simple example to run CASCI calculation.
 '''
 
-import numpy
-from pyscf import gto, scf, mcscf
+import pyscf
 
-mol = gto.M(
+mol = pyscf.M(
     atom = 'O 0 0 0; O 0 0 1.2',
     basis = 'ccpvdz',
     spin = 2)
 
-myhf = scf.RHF(mol)
-myhf.kernel()
+myhf = mol.RHF().run()
 
 # 6 orbitals, 8 electrons
-mycas = mcscf.CASCI(myhf, 6, 8)
-mycas.kernel()
+mycas = myhf.CASCI(6, 8).run()
+#
+# Note this mycas object can also be created using the APIs of mcscf module:
+#
+# from pyscf import mcscf
+# mycas = mcscf.CASCI(myhf, 6, 8).run()
 
 # Natural occupancy in CAS space, Mulliken population etc.
 mycas.verbose = 4

examples/mcscf/00-simple_casscf.py

@@ -7,20 +7,22 @@
 A simple example to run CASSCF calculation.
 '''
 
-import numpy
-from pyscf import gto, scf, mcscf
+import pyscf
 
-mol = gto.M(
+mol = pyscf.M(
     atom = 'O 0 0 0; O 0 0 1.2',
     basis = 'ccpvdz',
     spin = 2)
 
-myhf = scf.RHF(mol)
-myhf.kernel()
+myhf = mol.RHF().run()
 
 # 6 orbitals, 8 electrons
-mycas = mcscf.CASSCF(myhf, 6, 8)
-mycas.kernel()
+mycas = myhf.CASSCF(6, 8).run()
+#
+# Note this mycas object can also be created using the APIs of mcscf module:
+#
+# from pyscf import mcscf
+# mycas = mcscf.CASSCF(myhf, 6, 8).run()
 
 # Natural occupancy in CAS space, Mulliken population etc.
 # See also 00-simple_casci.py for the instruction of the output of analyze()

examples/scf/00-simple_hf.py

@@ -10,17 +10,30 @@
 .analyze() function calls the Mulliken population analysis etc.
 '''
 
-from pyscf import gto, scf
+import pyscf
 
-mol = gto.Mole()
-mol.build(
+mol = pyscf.M(
     atom = 'H 0 0 0; F 0 0 1.1',  # in Angstrom
     basis = 'ccpvdz',
     symmetry = True,
 )
 
-myhf = scf.RHF(mol)
+myhf = mol.HF()
 myhf.kernel()
 
 # Orbital energies, Mulliken population etc.
 myhf.analyze()
+
+
+#
+# myhf object can also be created using the APIs of gto, scf module
+#
+from pyscf import gto, scf
+mol = gto.M(
+    atom = 'H 0 0 0; F 0 0 1.1',  # in Angstrom
+    basis = 'ccpvdz',
+    symmetry = True,
+)
+myhf = scf.HF(mol)
+myhf.kernel()
+

pyscf/__all__.py

@@ -0,0 +1,40 @@
+from . import post_scf
+from . import grad
+from . import gw
+from . import hci
+from . import hessian
+from . import lo
+from . import mrpt
+from . import prop
+from . import qmmm
+#from . import semiempirical
+from . import sgx
+from . import solvent
+from . import tools
+
+#from . import geomopt
+
+#try:
+#    from . import dftd3
+#except ImportError:
+#    pass
+#try:
+#    from . import dmrgscf
+#except ImportError:
+#    pass
+#try:
+#    from . import icmpspt
+#except ImportError:
+#    pass
+#try:
+#    from . import shciscf
+#except ImportError:
+#    pass
+#try:
+#    from . import cornell_shci
+#except ImportError:
+#    pass
+
+from .pbc import __all__
+del __all__
+

pyscf/__init__.py

@@ -35,7 +35,7 @@
 
 '''
 
-__version__ = '1.6.1'
+__version__ = '1.7.1'
 
 import os
 import sys
@@ -59,4 +59,12 @@
 
 DEBUG = __config__.DEBUG
 
+def M(**kwargs):
+    '''Main driver to create Molecule object (mol) or Material crystal object (cell)'''
+    if kwargs.get('a') is not None:  # a is crystal lattice parameter
+        from pyscf.pbc import gto as pgto
+        return pgto.M(**kwargs)
+    else:  # Molecule
+        return gto.M(**kwargs)
+
 del(os, sys, LooseVersion, numpy)

pyscf/cornell_shci/shci.py

@@ -52,7 +52,7 @@
     settings.MPIPREFIX = getattr(__config__, 'shci_MPIPREFIX', None)
     if settings.SHCIEXE is None:
         import sys
-        sys.stderr.write('settings.py not found.  Please create %s\n'
+        sys.stderr.write('settings.py not found for module cornell_shci.  Please create %s\n'
                          % os.path.join(os.path.dirname(__file__), 'settings.py'))
         raise ImportError('settings.py not found')
 

pyscf/dft/__init__.py

@@ -27,10 +27,12 @@
 
 try:
     from pyscf.dft import libxc
+    XC = libxc.XC
 except (ImportError, OSError):
     pass
 try:
     from pyscf.dft import xcfun
+    XC = xcfun.XC
 except (ImportError, OSError):
     pass
 #from pyscf.dft import xc

pyscf/dmrgscf/dmrgci.py

@@ -55,7 +55,7 @@
     settings.BLOCKVERSION = getattr(__config__, 'dmrgscf_BLOCKVERSION', None)
     if (settings.BLOCKEXE is None or settings.BLOCKSCRATCHDIR is None):
         import sys
-        sys.stderr.write('settings.py not found.  Please create %s\n'
+        sys.stderr.write('settings.py not found for module dmrgci.  Please create %s\n'
                          % os.path.join(os.path.dirname(__file__), 'settings.py'))
         raise ImportError('settings.py not found')
 

pyscf/fciqmcscf/fciqmc.py

@@ -31,7 +31,7 @@
 try:
     from pyscf.fciqmcscf import settings
 except ImportError:
-    msg = '''settings.py not found.  Please create %s
+    msg = '''settings.py not found for module fciqmcscf.  Please create %s
 ''' % os.path.join(os.path.dirname(__file__), 'settings.py')
     sys.stderr.write(msg)