示例#1
0
def pyq1_dft(atomtuples=[(2, (0, 0, 0))],
             basis='6-31G**',
             maxit=10,
             xcname='SVWN'):
    from PyQuante import Ints, settings, Molecule
    from PyQuante.dft import getXC
    from PyQuante.MG2 import MG2 as MolecularGrid
    from PyQuante.LA2 import mkdens, geigh, trace2
    from PyQuante.Ints import getJ

    print("PyQ1 DFT run")
    atoms = Molecule('Pyq1', atomlist=atomtuples)

    bfs = Ints.getbasis(atoms, basis=basis)
    S, h, Ints = Ints.getints(bfs, atoms)

    nclosed, nopen = nel // 2, nel % 2
    assert nopen == 0
    enuke = atoms.get_enuke()

    grid_nrad = settings.DFTGridRadii
    grid_fineness = settings.DFTGridFineness

    gr = MolecularGrid(atoms, grid_nrad, grid_fineness)
    gr.set_bf_amps(bfs)

    orbe, orbs = geigh(h, S)
    eold = 0

    for i in range(maxit):
        D = mkdens(orbs, 0, nclosed)
        gr.setdens(D)

        J = getJ(Ints, D)

        Exc, Vxc = getXC(gr, nel, functional=xcname)

        F = h + 2 * J + Vxc
        orbe, orbs = geigh(F, S)

        Ej = 2 * trace2(D, J)
        Eone = 2 * trace2(D, h)
        energy = Eone + Ej + Exc + enuke

        print(i, energy, Eone, Ej, Exc, enuke)
        if np.isclose(energy, eold):
            break
        eold = energy
    return energy
示例#2
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def pyq1_dft(atomtuples=[(2,(0,0,0))],basis = '6-31G**',maxit=10,
             xcname='SVWN'):
    from PyQuante import Ints,settings,Molecule
    from PyQuante.dft import getXC
    from PyQuante.MG2 import MG2 as MolecularGrid
    from PyQuante.LA2 import mkdens,geigh,trace2
    from PyQuante.Ints import getJ
    
    print ("PyQ1 DFT run")
    atoms = Molecule('Pyq1',atomlist=atomtuples)

    bfs = Ints.getbasis(atoms,basis=basis)
    S,h,Ints = Ints.getints(bfs,atoms)

    nclosed,nopen = nel//2,nel%2
    assert nopen==0
    enuke = atoms.get_enuke()

    grid_nrad = settings.DFTGridRadii
    grid_fineness = settings.DFTGridFineness

    gr = MolecularGrid(atoms,grid_nrad,grid_fineness) 
    gr.set_bf_amps(bfs)

    orbe,orbs = geigh(h,S)
    eold = 0

    for i in range(maxit):
        D = mkdens(orbs,0,nclosed)
        gr.setdens(D)

        J = getJ(Ints,D)

        Exc,Vxc = getXC(gr,nel,functional=xcname)

        F = h+2*J+Vxc
        orbe,orbs = geigh(F,S)
        
        Ej = 2*trace2(D,J)
        Eone = 2*trace2(D,h)
        energy = Eone + Ej + Exc + enuke
        
        print (i,energy,Eone,Ej,Exc,enuke)
        if np.isclose(energy,eold):
            break
        eold = energy
    return energy
示例#3
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文件: utils.py 项目: avirshup/dexter
def GetBasis(gaussResult, quiet=False):
    """Get PyQuante representation of a basis from a gaussian output file"""

    # Create representation of molecule within PyQuante
    PQMol = cclib.bridge.makepyquante(gaussResult.atomcoords[-1], gaussResult.atomnos)

    # Get PyQuante representation of basis set
    basis = Ints.getbasis(PQMol, gaussResult.basisname)

    # Check that PyQuante and g09 have the same basis set ordering
    nbasis = gaussResult.nbasis
    assert len(basis.bfs) == nbasis, (
        "Gaussian and PyQuante have " "different basis sets. Did you specify the same basis for each?"
    )
    overlap_py = np.array(Ints.getS(basis))
    maxdefect = 0.0
    if hasattr(gaussResult, "mocoeffs_sao"):
        sao = gaussResult.mocoeffs_sao
    else:
        sao = gaussResult.aooverlaps

    if not quiet:
        for i, vals in enumerate(zip(overlap_py.flat, sao.flat)):
            pq, g9 = vals
            x, y = np.unravel_index(i, (nbasis, nbasis))
            denom = max(pq, g9)
            if denom < 10 ** -13:
                continue
            if min(pq, g9) == 0:
                denom = 1.0
            defect = abs((pq - g9) / denom)
            if defect > maxdefect:
                maxdefect = defect
            if defect > 1e-3 and x <= y:
                print pq, g9, (x, y), 100 * abs(pq - g9) / denom

        print "Maximum error between G09 and PyQuante overlap matrices:", maxdefect
        if maxdefect > 1e-3:
            print "WARNING!!!! Calculated overlap matrix does not match basis set!"
            print "Basis sets might not match!\n\n\n"

    return nbasis, basis
示例#4
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文件: sdet.py 项目: freude/P2_bulk
    def comp_int(wf1, wf2, wf3, wf4):

        integral = 0

        for j1 in xrange(wf1.N):
            for j2 in xrange(wf2.N):
                for j3 in xrange(wf3.N):
                    for j4 in xrange(wf4.N):

                        over0 = overlap_int(wf1.gf[j1], wf2.gf[j2])
                        over1 = overlap_int(wf1.gf[j1], wf3.gf[j3])
                        over2 = overlap_int(wf1.gf[j1], wf4.gf[j4])
                        over3 = overlap_int(wf2.gf[j2], wf4.gf[j4])
                        over4 = overlap_int(wf3.gf[j3], wf4.gf[j4])
                        over5 = overlap_int(wf2.gf[j2], wf3.gf[j3])

                        if min([over0, over1, over2, over3, over4, over5]) >= 1.0:
                            integral += Ints.coulomb_repulsion(
                                (wf1.gf[j1][0], wf1.gf[j1][1], wf1.gf[j1][2]),
                                wf1.gf[j1][4],
                                (0, 0, 0),
                                wf1.gf[j1][3],
                                (wf2.gf[j2][0], wf2.gf[j2][1], wf2.gf[j2][2]),
                                wf2.gf[j2][4],
                                (0, 0, 0),
                                wf2.gf[j2][3],
                                (wf3.gf[j3][0], wf3.gf[j3][1], wf3.gf[j3][2]),
                                wf3.gf[j3][4],
                                (0, 0, 0),
                                wf3.gf[j3][3],
                                (wf4.gf[j4][0], wf4.gf[j4][1], wf4.gf[j4][2]),
                                wf4.gf[j4][4],
                                (0, 0, 0),
                                wf4.gf[j4][3],
                            )
                        else:
                            integral += 0

        return integral
示例#5
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def pyq1_rohf(atomtuples=[(2,(0,0,0))],basis = '6-31G**',maxit=10,mult=3):
    from PyQuante import Ints,settings,Molecule
    from PyQuante.hartree_fock import get_energy
    from PyQuante.MG2 import MG2 as MolecularGrid
    from PyQuante.LA2 import mkdens,geigh,trace2,simx
    from PyQuante.Ints import getJ,getK
    
    print ("PyQ1 ROHF run")
    atoms = Molecule('Pyq1',atomlist=atomtuples,multiplicity=mult)

    bfs = Ints.getbasis(atoms,basis=basis)
    S,h,I2e = Ints.getints(bfs,atoms)

    nbf = norbs = len(bfs)
    nel = atoms.get_nel()

    nalpha,nbeta = atoms.get_alphabeta()

    enuke = atoms.get_enuke()
    orbe,orbs = geigh(h,S)
    eold = 0

    for i in range(maxit):
        Da = mkdens(orbs,0,nalpha)
        Db = mkdens(orbs,0,nbeta)
        Ja = getJ(I2e,Da)
        Jb = getJ(I2e,Db)
        Ka = getK(I2e,Da)
        Kb = getK(I2e,Db)

        Fa = h+Ja+Jb-Ka
        Fb = h+Ja+Jb-Kb
        energya = get_energy(h,Fa,Da)
        energyb = get_energy(h,Fb,Db)
        eone = (trace2(Da,h) + trace2(Db,h))/2
        etwo = (trace2(Da,Fa) + trace2(Db,Fb))/2
        energy = (energya+energyb)/2 + enuke
        print (i,energy,eone,etwo,enuke)
        if abs(energy-eold) < 1e-5: break
        eold = energy

        Fa = simx(Fa,orbs)
        Fb = simx(Fb,orbs)
        # Building the approximate Fock matrices in the MO basis
        F = 0.5*(Fa+Fb)
        K = Fb-Fa

        # The Fock matrix now looks like
        #      F-K    |  F + K/2  |    F
        #   ---------------------------------
        #    F + K/2  |     F     |  F - K/2
        #   ---------------------------------
        #       F     |  F - K/2  |  F + K

        # Make explicit slice objects to simplify this
        do = slice(0,nbeta)
        so = slice(nbeta,nalpha)
        uo = slice(nalpha,norbs)
        F[do,do] -= K[do,do]
        F[uo,uo] += K[uo,uo]
        F[do,so] += 0.5*K[do,so]
        F[so,do] += 0.5*K[so,do]
        F[so,uo] -= 0.5*K[so,uo]
        F[uo,so] -= 0.5*K[uo,so]

        orbe,mo_orbs = np.linalg.eigh(F)
        orbs = np.dot(orbs,mo_orbs)
    return energy,orbe,orbs
示例#6
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def pyq1_rohf(atomtuples=[(2, (0, 0, 0))], basis='6-31G**', maxit=10, mult=3):
    from PyQuante import Ints, settings, Molecule
    from PyQuante.hartree_fock import get_energy
    from PyQuante.MG2 import MG2 as MolecularGrid
    from PyQuante.LA2 import mkdens, geigh, trace2, simx
    from PyQuante.Ints import getJ, getK

    print("PyQ1 ROHF run")
    atoms = Molecule('Pyq1', atomlist=atomtuples, multiplicity=mult)

    bfs = Ints.getbasis(atoms, basis=basis)
    S, h, I2e = Ints.getints(bfs, atoms)

    nbf = norbs = len(bfs)
    nel = atoms.get_nel()

    nalpha, nbeta = atoms.get_alphabeta()

    enuke = atoms.get_enuke()
    orbe, orbs = geigh(h, S)
    eold = 0

    for i in range(maxit):
        Da = mkdens(orbs, 0, nalpha)
        Db = mkdens(orbs, 0, nbeta)
        Ja = getJ(I2e, Da)
        Jb = getJ(I2e, Db)
        Ka = getK(I2e, Da)
        Kb = getK(I2e, Db)

        Fa = h + Ja + Jb - Ka
        Fb = h + Ja + Jb - Kb
        energya = get_energy(h, Fa, Da)
        energyb = get_energy(h, Fb, Db)
        eone = (trace2(Da, h) + trace2(Db, h)) / 2
        etwo = (trace2(Da, Fa) + trace2(Db, Fb)) / 2
        energy = (energya + energyb) / 2 + enuke
        print(i, energy, eone, etwo, enuke)
        if abs(energy - eold) < 1e-5: break
        eold = energy

        Fa = simx(Fa, orbs)
        Fb = simx(Fb, orbs)
        # Building the approximate Fock matrices in the MO basis
        F = 0.5 * (Fa + Fb)
        K = Fb - Fa

        # The Fock matrix now looks like
        #      F-K    |  F + K/2  |    F
        #   ---------------------------------
        #    F + K/2  |     F     |  F - K/2
        #   ---------------------------------
        #       F     |  F - K/2  |  F + K

        # Make explicit slice objects to simplify this
        do = slice(0, nbeta)
        so = slice(nbeta, nalpha)
        uo = slice(nalpha, norbs)
        F[do, do] -= K[do, do]
        F[uo, uo] += K[uo, uo]
        F[do, so] += 0.5 * K[do, so]
        F[so, do] += 0.5 * K[so, do]
        F[so, uo] -= 0.5 * K[so, uo]
        F[uo, so] -= 0.5 * K[uo, so]

        orbe, mo_orbs = np.linalg.eigh(F)
        orbs = np.dot(orbs, mo_orbs)
    return energy, orbe, orbs
示例#7
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#Each numbered section refers to coressponding step in Szabo QM Textbook on page 161

from PyQuante import Molecule, Ints
from PyQuante import LA2 as linalg
from PyQuante.NumWrap import eigh, matrixmultiply
from PyQuante import hartree_fock as HF

#Global Variables############################
convergenceLimit = 1.0 * pow(10, -6)
maxCycle = 50

#Section 1############################
#specify a molecule
molecule = Molecule("H2", [(1, (0, 0, 0)), (1, (0, 0, 1)), (8, (-1, 0, 0))])

basisSet = Ints.getbasis(molecule, "sto-3g")

#Section 2############################
#Overlap Matrix
S = Ints.getS(basisSet)

#Follwing Two matrices compose the core Hamiltonian
#KE Matrix
KE = Ints.getT(basisSet)

#External Potential, Nuclear - Electron Attraction
Vext = Ints.getV(basisSet, molecule)

#Form Hcore
Hcore = KE + Vext