Python project_mo_nr2r Examples

Example #1

File: test_addons.py Project: verena-neufeld/pyscf

    def test_project_mo_nr2r(self):
        numpy.random.seed(15)
        nao = mol.nao_nr()
        mo1 = numpy.random.random((nao, nao))
        mo2 = addons.project_mo_nr2r(mol, [mo1, mo1], mol_dz)
        self.assertAlmostEqual(abs(mo2[0]).sum(), 172.66468850263556, 11)
        self.assertAlmostEqual(abs(mo2[1]).sum(), 172.66468850263556, 11)

        mo2 = addons.project_mo_nr2r(mol, mo1, mol_dz)
        self.assertAlmostEqual(abs(mo2).sum(), 172.66468850263556, 11)

Example #2

File: test_addons.py Project: chrinide/pyscf

    def test_project_mo_nr2r(self):
        numpy.random.seed(15)
        nao = mol.nao_nr()
        mo1 = numpy.random.random((nao,nao))
        mo2 = addons.project_mo_nr2r(mol, [mo1,mo1], mol_dz)
        self.assertAlmostEqual(abs(mo2[0]).sum(), 172.66468850263556, 11)
        self.assertAlmostEqual(abs(mo2[1]).sum(), 172.66468850263556, 11)

        mo2 = addons.project_mo_nr2r(mol, mo1, mol_dz)
        self.assertAlmostEqual(abs(mo2).sum(), 172.66468850263556, 11)

Example #3

File: x2c.py Project: raybrad/pyscf

def _proj_dmll(mol_nr, dm_nr, mol):
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, 1, mol)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr*.5, proj.T.conj()))
    dm_ll = (dm_ll + dhf.time_reversal_matrix(mol, dm_ll)) * .5
    return dm_ll

Example #4

File: x2c.py Project: zzy2014/pyscf

def _proj_dmll(mol_nr, dm_nr, mol):
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, numpy.eye(mol_nr.nao_nr()), mol)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr * .5, proj.T.conj()))
    dm_ll = (dm_ll + dhf.time_reversal_matrix(mol, dm_ll)) * .5
    return dm_ll

Example #5

File: dhf.py Project: pengdl/pyscf

def _proj_dmll(mol_nr, dm_nr, mol):
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, 1, mol)

    n2c = proj.shape[0]
    n4c = n2c * 2
    dm = numpy.zeros((n4c,n4c), dtype=complex)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr*.5, proj.T.conj()))
    dm[:n2c,:n2c] = (dm_ll + time_reversal_matrix(mol, dm_ll)) * .5
    return dm

Example #6

File: dhf.py Project: armunoz/pyscf

def _proj_dmll(mol_nr, dm_nr, mol):
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, 1, mol)

    n2c = proj.shape[0]
    n4c = n2c * 2
    dm = numpy.zeros((n4c, n4c), dtype=complex)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr * .5, proj.T.conj()))
    dm[:n2c, :n2c] = (dm_ll + time_reversal_matrix(mol, dm_ll)) * .5
    return dm

Example #7

def _proj_dmll(mol_nr, dm_nr, mol):
    '''Project non-relativistic atomic density matrix to large component spinor
    representation
    '''
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, numpy.eye(mol_nr.nao_nr()), mol)

    n2c = proj.shape[0]
    n4c = n2c * 2
    dm = numpy.zeros((n4c, n4c), dtype=complex)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr * .5, proj.T.conj()))
    dm[:n2c, :n2c] = (dm_ll + time_reversal_matrix(mol, dm_ll)) * .5
    return dm

Example #8

File: dhf.py Project: chrinide/pyscf

def _proj_dmll(mol_nr, dm_nr, mol):
    '''Project non-relativistic atomic density matrix to large component spinor
    representation
    '''
    from pyscf.scf import addons
    proj = addons.project_mo_nr2r(mol_nr, numpy.eye(mol_nr.nao_nr()), mol)

    n2c = proj.shape[0]
    n4c = n2c * 2
    dm = numpy.zeros((n4c,n4c), dtype=complex)
    # *.5 because alpha and beta are summed in project_mo_nr2r
    dm_ll = reduce(numpy.dot, (proj, dm_nr*.5, proj.T.conj()))
    dm[:n2c,:n2c] = (dm_ll + time_reversal_matrix(mol, dm_ll)) * .5
    return dm

Example #9

    def test_project_dm_nr2r(self):
        numpy.random.seed(15)
        nao = mol.nao_nr()
        mo = numpy.random.random((nao,10))
        mo1 = addons.project_mo_nr2r(mol, mo, mol_dz)
        dm = numpy.dot(mo, mo.T.conj())
        dmref = numpy.dot(mo1, mo1.T.conj())
        dm1 = addons.project_dm_nr2r(mol, [dm,dm], mol_dz)

        self.assertAlmostEqual(abs(dmref-dm1[0]).max(), 0, 11)
        self.assertAlmostEqual(abs(dmref-dm1[1]).max(), 0, 11)
        self.assertAlmostEqual(lib.finger(dm1[0]), -13.580612999088892-20.209297457056557j, 11)

        dm1 = addons.project_dm_nr2r(mol, dm, mol_dz)
        self.assertAlmostEqual(abs(dmref-dm1).max(), 0, 11)