def test_mo_comps(self):
mol = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo = numpy.random.random((mol.nao_nr(), 15))
idx4d = [i for i,s in enumerate(mol.spheric_labels(1)) if '4d' in s]
c = mo_mapping.mo_comps(idx4d, mol, mo, cart=False)
self.assertAlmostEqual(abs(c).sum(), 0, 12)
mo = numpy.random.random((mol.nao_cart(), 15)) * .2
c = mo_mapping.mo_comps(lambda x: '3d' in x, mol, mo, cart=True)
self.assertAlmostEqual(abs(c).sum(), 1.0643140119943388, 9)
def test_mo_comps(self):
mol = gto.M(atom='''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo = numpy.random.random((mol.nao_nr(), 15))
idx4d = [i for i, s in enumerate(mol.spheric_labels(1)) if '4d' in s]
c = mo_mapping.mo_comps(idx4d, mol, mo, cart=False)
self.assertAlmostEqual(abs(c).sum(), 0, 12)
mo = numpy.random.random((mol.nao_cart(), 15)) * .2
c = mo_mapping.mo_comps(lambda x: '3d' in x, mol, mo, cart=True)
self.assertAlmostEqual(abs(c).sum(), 1.0643140119943388, 9)
def test_mo_comps(self):
mol = gto.M(atom='''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo = numpy.random.random((mol.nao_nr(), 15))
idx4d = [i for i, s in enumerate(mol.ao_labels()) if '4d' in s]
c = mo_mapping.mo_comps(idx4d, mol, mo, cart=False)
self.assertAlmostEqual(abs(c).sum(), 0, 12)
def test_mo_comps(self):
mol = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo = numpy.random.random((mol.nao_nr(), 15))
idx4d = [i for i,s in enumerate(mol.ao_labels()) if '4d' in s]
c = mo_mapping.mo_comps(idx4d, mol, mo, cart=False)
self.assertAlmostEqual(abs(c).sum(), 0, 12)
c -1.217739890298750 0.703062453466927 0.000000000000000
h -2.172991468538160 1.254577209307266 0.000000000000000
c -1.217739890298750 -0.703062453466927 0.000000000000000
h -2.172991468538160 -1.254577209307266 0.000000000000000
c 0.000000000000000 -1.406124906933854 0.000000000000000
h 0.000000000000000 -2.509154418614532 0.000000000000000
''',
basis=bas)
cpu0 = get_cpu_timings()
mf = mol.RHF().run()
cpu0 = log.timer('C6H6 %s RHF' % bas, *cpu0)
mymp2 = mf.MP2().run()
cpu0 = log.timer('C6H6 %s MP2' % bas, *cpu0)
mymc = mf.CASSCF(6, 6)
idx_2pz = mo_comps('2pz', mol, mf.mo_coeff).argsort()[-6:]
mo = mymc.sort_mo(idx_2pz, base=0)
mymc.kernel(mo)
cpu0 = log.timer('C6H6 %s CASSCF' % bas, *cpu0)
mycc = mf.CCSD().run()
cpu0 = log.timer('C6H6 %s CCSD' % bas, *cpu0)
mf = mol.RKS().run(xc='b3lyp')
cpu0 = log.timer('C6H6 %s B3LYP' % bas, *cpu0)
mf = mf.density_fit().run()
cpu0 = log.timer('C6H6 %s density-fit RHF' % bas, *cpu0)
mf.chkfile = 'benzene-631g.chk'
mf.kernel()
pz_idx = numpy.array([17, 20, 21, 22, 23, 30, 36, 41, 42, 47, 48, 49]) - 1
loc_orb = lo.Boys(mol, mf.mo_coeff[:, pz_idx]).kernel()
molden.from_mo(mol, 'benzene-631g-boys.molden', loc_orb)
import numpy
from pyscf import lib
from pyscf import tools
from pyscf.tools import mo_mapping
mol, mo_energy, mo_coeff, mo_occ, irrep_labels, spins = \
tools.molden.load('benzene-631g-boys.molden')
comp = mo_mapping.mo_comps(
'C.*2p[yz]', # regular expression
mol,
mo_coeff)
mol = lib.chkfile.load_mol('benzene-631g.chk')
mo = lib.chkfile.load('benzene-631g.chk', 'scf/mo_coeff')
comp = mo_mapping.mo_comps('C 2p', mol, mo)
#label = mol.ao_labels(True)
#tools.dump_mat.dump_rec(mol.stdout, mo_coeff, label, start=1)
print('rank MO-id components')
for i, j in enumerate(numpy.argsort(-comp)):
print('%3d %3d %.10f' % (i, j, comp[j]))
mf.chkfile = 'benzene-631g.chk'
mf.kernel()
pz_idx = numpy.array([17,20,21,22,23,30,36,41,42,47,48,49])-1
loc_orb = lo.Boys(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'benzene-631g-boys.molden', loc_orb)
import numpy
from pyscf import lib
from pyscf import tools
from pyscf.tools import mo_mapping
mol, mo_energy, mo_coeff, mo_occ, irrep_labels, spins = \
tools.molden.load('benzene-631g-boys.molden')
comp = mo_mapping.mo_comps('C.*2p[yz]', # regular expression
mol, mo_coeff)
mol = lib.chkfile.load_mol('benzene-631g.chk')
mo = lib.chkfile.load('benzene-631g.chk', 'scf/mo_coeff')
comp = mo_mapping.mo_comps('C 2p', mol, mo)
#label = mol.ao_labels()
#tools.dump_mat.dump_rec(mol.stdout, mo_coeff, label, start=1)
print('rank MO-id components')
for i,j in enumerate(numpy.argsort(-comp)):
print('%3d %3d %.10f' % (i, j, comp[j]))
log.note(line[:-1])
break
with open('/proc/meminfo') as f:
log.note(f.readline()[:-1])
log.note('OMP_NUM_THREADS=%s\n', os.environ.get('OMP_NUM_THREADS', None))
for bas in ('3-21g', '6-31g*', 'cc-pVTZ', 'ANO-Roos-TZ'):
mol = pyscf.M(atom='N 0 0 0; N 0 0 1.1', basis=bas)
cpu0 = time.clock(), time.time()
mf = mol.RHF().run()
cpu0 = log.timer('N2 %s RHF' % bas, *cpu0)
mymp2 = mf.MP2().run()
cpu0 = log.timer('N2 %s MP2' % bas, *cpu0)
mymc = mf.CASSCF(4, 4)
idx_2pz = mo_comps('2p[xy]', mol, mf.mo_coeff).argsort()[-4:]
mo = mymc.sort_mo(idx_2pz, base=0)
mymc.kernel(mo)
cpu0 = log.timer('N2 %s CASSCF' % bas, *cpu0)
mycc = mf.CCSD().run()
cpu0 = log.timer('N2 %s CCSD' % bas, *cpu0)
mf = mol.RKS().run(xc='b3lyp')
cpu0 = log.timer('N2 %s B3LYP' % bas, *cpu0)
mf = mf.density_fit().run()
cpu0 = log.timer('N2 %s density-fit RHF' % bas, *cpu0)
Read localized orbitals from molden, then find out C 2py and 2pz orbitals
'''
mol, mo_energy, mo_coeff, mo_occ, irrep_labels, spins = \
tools.molden.load('benzene-631g-boys.molden')
#
# Note mol._cart_gto is not a built-in attribute defined in Mole class. It is
# tagged in tools.molden.load function to indicate whether the orbitals read
# from molden file are based on cartesian gaussians (6d 10f).
#
if mol._cart_gto:
# If molden file does not have 5d,9g label, it's in Cartesian Gaussian
label = mol.cart_labels(True)
comp = mo_mapping.mo_comps(lambda x: re.search('C.*2p[yz]', x),
mol, mo_coeff, cart=True)
else:
label = mol.spheric_labels(True)
comp = mo_mapping.mo_comps(lambda x: re.search('C.*2p[yz]', x),
mol, mo_coeff)
#
# For orbitals generated by pyscf (or read from pyscf chkfile), the orbitals
# are all represented on spheric gaussians (5d 7f).
#
mol = lib.chkfile.load_mol('benzene-631g.chk')
mo = lib.chkfile.load('benzene-631g.chk', 'scf/mo_coeff')
label = mol.spheric_labels(True)
idx = [i for i,s in enumerate(labels) if 'C 2p' in s]
comp = mo_mapping.mo_comps(idx, mol, mo_coeff)
#tools.dump_mat.dump_rec(mol.stdout, mo_coeff, label, start=1)