Exemple #1
0
def dumpAct(fname, info, actlst, base=1):
    actlst2 = [i - base for i in actlst]
    mol, ova, fav, pT, nb, nalpha, nbeta, nc, na, nv, lmo, enorb, occ = info
    corb = set(range(nc))
    aorb = set(range(nc, nc + na))
    vorb = set(range(nc + na, nc + na + nv))
    print '[dumpAct]'
    print ' corb=', corb
    print ' aorb=', aorb
    print ' vorb=', vorb
    sorb = set(actlst2)
    rcorb = corb.difference(corb.intersection(sorb))
    #assuming act in actlst
    #raorb = aorb.difference(aorb.intersection(sorb))
    rvorb = vorb.difference(vorb.intersection(sorb))
    corb = list(rcorb)
    aorb = list(sorb)
    vorb = list(rvorb)
    print ' corb=', corb
    print ' aorb=', aorb
    print ' vorb=', vorb
    clmo = lmo[:, corb].copy()
    almo = lmo[:, aorb].copy()
    vlmo = lmo[:, vorb].copy()
    ierr, ua = pmloc.loc(mol, almo)
    almo = almo.dot(ua)
    #>>> DUMP <<<#
    # P-SORT
    mo_c = clmo
    mo_v = vlmo
    e_c = enorb[corb].copy()
    e_v = enorb[vorb].copy()
    n_c = occ[corb].copy()
    n_v = occ[vorb].copy()
    mo_o, n_o, e_o = ulocal.psort(ova, fav, pT, almo)
    lmo2 = numpy.hstack((mo_c, mo_o, mo_v))
    enorb = numpy.hstack([e_c, e_o, e_v])
    occ = numpy.hstack([n_c, n_o, n_v])
    assert len(enorb) == nb
    assert len(occ) == nb
    # CHECK
    diff = reduce(numpy.dot, (lmo2.T, ova, lmo2)) - numpy.identity(nb)
    print 'diff=', numpy.linalg.norm(diff)
    ulocal.lowdinPop(mol, lmo, ova, enorb, occ)
    ulocal.dumpLMO(mol, fname + '_new', lmo2)
    print 'nalpha,nbeta,mol.spin,nb:',\
           nalpha,nbeta,mol.spin,nb
    print 'diff(LMO2-LMO)=', numpy.linalg.norm(lmo2 - lmo)
    nc = len(e_c)
    na = len(e_o)
    nv = len(e_v)
    assert na == len(actlst)
    assert nc + na + nv == nb
    print 'nc,na,nv,nb=', nc, na, nv, nb
    return lmo2, nc, na, nv
Exemple #2
0
def dumpAct(fname,info,actlst,base=1):
   actlst2 = [i-base for i in actlst]
   mol,ova,fav,pT,nb,nalpha,nbeta,nc,na,nv,lmo,enorb,occ = info
   corb = set(range(nc))
   aorb = set(range(nc,nc+na))
   vorb = set(range(nc+na,nc+na+nv))
   print '[dumpAct]'
   print ' corb=',corb
   print ' aorb=',aorb
   print ' vorb=',vorb
   sorb = set(actlst2)
   rcorb = corb.difference(corb.intersection(sorb))
   #assuming act in actlst
   #raorb = aorb.difference(aorb.intersection(sorb))
   rvorb = vorb.difference(vorb.intersection(sorb))
   corb = list(rcorb)
   aorb = list(sorb)
   vorb = list(rvorb)
   print ' corb=',corb
   print ' aorb=',aorb
   print ' vorb=',vorb
   clmo = lmo[:,corb].copy() 
   almo = lmo[:,aorb].copy() 
   vlmo = lmo[:,vorb].copy() 
   ierr,ua = pmloc.loc(mol,almo)
   almo = almo.dot(ua)
   #>>> DUMP <<<#
   # P-SORT
   mo_c = clmo
   mo_v = vlmo
   e_c = enorb[corb].copy()
   e_v = enorb[vorb].copy()
   n_c = occ[corb].copy()
   n_v = occ[vorb].copy()
   mo_o,n_o,e_o = ulocal.psort(ova,fav,pT,almo)
   lmo2 = numpy.hstack((mo_c,mo_o,mo_v))
   enorb = numpy.hstack([e_c,e_o,e_v])
   occ = numpy.hstack([n_c,n_o,n_v])
   assert len(enorb)==nb
   assert len(occ)==nb
   # CHECK
   diff = reduce(numpy.dot,(lmo2.T,ova,lmo2)) - numpy.identity(nb)
   print 'diff=',numpy.linalg.norm(diff)
   ulocal.lowdinPop(mol,lmo,ova,enorb,occ)
   ulocal.dumpLMO(mol,fname+'_new',lmo2)
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   print 'diff(LMO2-LMO)=',numpy.linalg.norm(lmo2-lmo)
   nc = len(e_c)
   na = len(e_o)
   nv = len(e_v)
   assert na == len(actlst)
   assert nc+na+nv == nb
   print 'nc,na,nv,nb=',nc,na,nv,nb
   return lmo2,nc,na,nv
Exemple #3
0
def dumpLocal(fname):
   chkfile = fname+'.chk'
   outfile = fname+'_cmo.molden'
   tools.molden.from_chkfile(outfile, chkfile)
   
   mol,mf = scf.chkfile.load_scf(chkfile)
   mo_coeff = mf["mo_coeff"]
   ova=mol.intor_symmetric("cint1e_ovlp_sph")
   nb = mo_coeff.shape[1]
   nalpha = (mol.nelectron+mol.spin)/2
   nbeta  = (mol.nelectron-mol.spin)/2
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   # UHF-alpha/beta
   ma = mo_coeff[0]
   mb = mo_coeff[1]
   
   #=============================
   # Localization
   #=============================
   ma_c = ma[:,:nalpha].copy()
   ma_v = ma[:,nalpha:].copy()
   #--------------------
   # Occupied space: PM
   #--------------------
   import pmloc
   ierr,uc = pmloc.loc(mol,ma_c)
   mc = numpy.dot(ma_c,uc)
   #--------------------
   # Virtual space: PAO
   #--------------------
   aux = lowdin(ova)
   mv = scdm(ma_v,ova,aux)
 
   # P[dm] 
   pa = numpy.dot(ma[:,:nalpha],ma[:,:nalpha].T)
   pb = numpy.dot(mb[:,:nbeta],mb[:,:nbeta].T)
   pT = 0.5*(pa+pb)
   # E-SORT
   enorb = mf["mo_energy"]
   fa = reduce(numpy.dot,(ma,numpy.diag(enorb[0]),ma.T))
   fb = reduce(numpy.dot,(mb,numpy.diag(enorb[1]),mb.T))
   fav = 0.5*(fa+fb)
   mc,occ_c,ec = psort(ova,fav,pT,mc)
   mv,occ_v,ev = psort(ova,fav,pT,mv)
   #---Check---
   tij = reduce(numpy.dot,(mc.T,ova,ma_c))
   sig = scipy.linalg.svd(tij,compute_uv=False)
   print 'nc=',nalpha,numpy.sum(sig**2)
   assert abs(nalpha-numpy.sum(sig**2))<1.e-8
   tij = reduce(numpy.dot,(mv.T,ova,ma_v))
   sig = scipy.linalg.svd(tij,compute_uv=False)
   print 'nv=',nb-nalpha,numpy.sum(sig**2)
   assert abs(nb-nalpha-numpy.sum(sig**2))<1.e-8

   lmo = numpy.hstack([mc,mv])
   enorb = numpy.hstack([ec,ev])
   occ = numpy.hstack([occ_c,occ_v])
   lowdinPop(mol,lmo,ova,enorb,occ)
   dumpLMO(mol,fname,lmo)
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   return 0
Exemple #4
0
def dumpLUNO(fname, thresh=0.01):
    chkfile = fname + '.chk'
    outfile = fname + '_cmo.molden'
    tools.molden.from_chkfile(outfile, chkfile)
    #=============================
    # Natural orbitals
    # Lowdin basis X=S{-1/2}
    # psi = chi * C
    #     = chi' * C'
    #     = chi*X*(X{-1}C')
    #=============================
    mol, mf = scf.chkfile.load_scf(chkfile)
    mo_coeff = mf["mo_coeff"]
    ova = mol.intor_symmetric("cint1e_ovlp_sph")
    nb = mo_coeff.shape[1]
    # Check overlap
    diff = reduce(numpy.dot,
                  (mo_coeff[0].T, ova, mo_coeff[0])) - numpy.identity(nb)
    print numpy.linalg.norm(diff)
    diff = reduce(numpy.dot,
                  (mo_coeff[1].T, ova, mo_coeff[1])) - numpy.identity(nb)
    print numpy.linalg.norm(diff)
    # UHF-alpha/beta
    ma = mo_coeff[0]
    mb = mo_coeff[1]
    nalpha = (mol.nelectron + mol.spin) / 2
    nbeta = (mol.nelectron - mol.spin) / 2
    # Spin-averaged DM
    pTa = numpy.dot(ma[:, :nalpha], ma[:, :nalpha].T)
    pTb = numpy.dot(mb[:, :nbeta], mb[:, :nbeta].T)
    pT = 0.5 * (pTa + pTb)
    # Lowdin basis
    s12 = sqrtm(ova)
    s12inv = lowdin(ova)
    pTOAO = reduce(numpy.dot, (s12, pT, s12))
    eig, coeff = scipy.linalg.eigh(-pTOAO)
    eig = -2.0 * eig
    eig[eig < 0.0] = 0.0
    eig[abs(eig) < 1.e-14] = 0.0
    ifplot = False  #True
    if ifplot:
        import matplotlib.pyplot as plt
        plt.plot(range(nb), eig, 'ro')
        plt.show()
    # Back to AO basis
    coeff = numpy.dot(s12inv, coeff)
    diff = reduce(numpy.dot, (coeff.T, ova, coeff)) - numpy.identity(nb)
    print 'CtSC-I', numpy.linalg.norm(diff)
    #
    # Averaged Fock
    #
    enorb = mf["mo_energy"]
    fa = reduce(numpy.dot, (ma, numpy.diag(enorb[0]), ma.T))
    fb = reduce(numpy.dot, (mb, numpy.diag(enorb[1]), mb.T))
    # Non-orthogonal cases: FC=SCE
    # Fao = SC*e*C{-1} = S*C*e*Ct*S
    fav = 0.5 * (fa + fb)
    # Expectation value of natural orbitals <i|F|i>
    fexpt = reduce(numpy.dot, (coeff.T, ova, fav, ova, coeff))
    enorb = numpy.diag(fexpt)
    nocc = eig.copy()
    #
    # Reordering and define active space according to thresh
    #
    idx = 0
    active = []
    for i in range(nb):
        if nocc[i] <= 2.0 - thresh and nocc[i] >= thresh:
            active.append(True)
        else:
            active.append(False)
    print '\nNatural orbitals:'
    for i in range(nb):
        print 'orb:', i, active[i], nocc[i], enorb[i]
    active = numpy.array(active)
    actIndices = list(numpy.argwhere(active == True).flatten())
    cOrbs = coeff[:, :actIndices[0]]
    aOrbs = coeff[:, actIndices]
    vOrbs = coeff[:, actIndices[-1] + 1:]
    nb = cOrbs.shape[0]
    nc = cOrbs.shape[1]
    na = aOrbs.shape[1]
    nv = vOrbs.shape[1]
    print 'core orbs:', cOrbs.shape
    print 'act  orbs:', aOrbs.shape
    print 'vir  orbs:', vOrbs.shape
    assert nc + na + nv == nb
    # dump UNO
    with open(fname + '_uno.molden', 'w') as thefile:
        molden.header(mol, thefile)
        molden.orbital_coeff(mol, thefile, coeff)
    #=====================
    # Population analysis
    #=====================
    from pyscf import lo
    aux = lo.orth_ao(mol, method='meta_lowdin')
    #clmo = ulocal.scdm(cOrbs,ova,aux)
    #almo = ulocal.scdm(aOrbs,ova,aux)
    clmo = cOrbs
    almo = aOrbs
    ierr, uc = pmloc.loc(mol, clmo)
    ierr, ua = pmloc.loc(mol, almo)
    clmo = clmo.dot(uc)
    almo = almo.dot(ua)
    vlmo = ulocal.scdm(vOrbs, ova, aux)
    # P-SORT
    mo_c, n_c, e_c = ulocal.psort(ova, fav, pT, clmo)
    mo_o, n_o, e_o = ulocal.psort(ova, fav, pT, almo)
    mo_v, n_v, e_v = ulocal.psort(ova, fav, pT, vlmo)
    lmo = numpy.hstack((mo_c, mo_o, mo_v)).copy()
    enorb = numpy.hstack([e_c, e_o, e_v])
    occ = numpy.hstack([n_c, n_o, n_v])
    # CHECK
    diff = reduce(numpy.dot, (lmo.T, ova, lmo)) - numpy.identity(nb)
    print 'diff=', numpy.linalg.norm(diff)
    ulocal.lowdinPop(mol, lmo, ova, enorb, occ)
    ulocal.dumpLMO(mol, fname, lmo)
    print 'nalpha,nbeta,mol.spin,nb:',\
           nalpha,nbeta,mol.spin,nb
    return mol, ova, fav, pT, nb, nalpha, nbeta, nc, na, nv, lmo, enorb, occ
Exemple #5
0
def dumpLocal(fname):
   chkfile = fname+'.chk'
   outfile = fname+'_cmo.molden'
   tools.molden.from_chkfile(outfile, chkfile)
   
   mol,mf = scf.chkfile.load_scf(chkfile)
   mo_coeff = mf["mo_coeff"]
   ova=mol.intor_symmetric("cint1e_ovlp_sph")
   nb = mo_coeff.shape[1]
   nalpha = (mol.nelectron+mol.spin)/2
   nbeta  = (mol.nelectron-mol.spin)/2
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   # UHF-alpha/beta
   ma = mo_coeff[0]
   mb = mo_coeff[1]
   
   #=============================
   # Localization
   #=============================
   ma_c = ma[:,:nalpha].copy()
   ma_v = ma[:,nalpha:].copy()
   #--------------------
   # Occupied space: PM
   #--------------------
   import pmloc
   ierr,uc = pmloc.loc(mol,ma_c)
   mc = numpy.dot(ma_c,uc)
   #--------------------
   # Virtual space: PAO
   #--------------------
   from pyscf import lo
   aux = lo.orth_ao(mol,method='meta_lowdin')
   mv = scdm(ma_v,ova,aux)
 
   # P[dm] 
   pa = numpy.dot(ma[:,:nalpha],ma[:,:nalpha].T)
   pb = numpy.dot(mb[:,:nbeta],mb[:,:nbeta].T)
   pT = 0.5*(pa+pb)
   # E-SORT
   enorb = mf["mo_energy"]
   fa = reduce(numpy.dot,(ma,numpy.diag(enorb[0]),ma.T))
   fb = reduce(numpy.dot,(mb,numpy.diag(enorb[1]),mb.T))
   fav = 0.5*(fa+fb)
   mc,occ_c,ec = psort(ova,fav,pT,mc)
   mv,occ_v,ev = psort(ova,fav,pT,mv)
   #---Check---
   tij = reduce(numpy.dot,(mc.T,ova,ma_c))
   sig = scipy.linalg.svd(tij,compute_uv=False)
   print 'nc=',nalpha,numpy.sum(sig**2)
   assert abs(nalpha-numpy.sum(sig**2))<1.e-8
   tij = reduce(numpy.dot,(mv.T,ova,ma_v))
   sig = scipy.linalg.svd(tij,compute_uv=False)
   print 'nv=',nb-nalpha,numpy.sum(sig**2)
   assert abs(nb-nalpha-numpy.sum(sig**2))<1.e-8

   lmo = numpy.hstack([mc,mv])
   enorb = numpy.hstack([ec,ev])
   occ = numpy.hstack([occ_c,occ_v])
   lowdinPop(mol,lmo,ova,enorb,occ)
   dumpLMO(mol,fname,lmo)
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   return 0
Exemple #6
0
def dumpLUNO(fname,thresh=0.01):
   chkfile = fname+'.chk'
   outfile = fname+'_cmo.molden'
   tools.molden.from_chkfile(outfile, chkfile)
   #=============================
   # Natural orbitals
   # Lowdin basis X=S{-1/2}
   # psi = chi * C 
   #     = chi' * C'
   #     = chi*X*(X{-1}C')
   #=============================
   mol,mf = scf.chkfile.load_scf(chkfile)
   mo_coeff = mf["mo_coeff"]
   ova=mol.intor_symmetric("cint1e_ovlp_sph")
   nb = mo_coeff.shape[1]
   # Check overlap
   diff = reduce(numpy.dot,(mo_coeff[0].T,ova,mo_coeff[0])) - numpy.identity(nb)
   print numpy.linalg.norm(diff)
   diff = reduce(numpy.dot,(mo_coeff[1].T,ova,mo_coeff[1])) - numpy.identity(nb)
   print numpy.linalg.norm(diff)
   # UHF-alpha/beta
   ma = mo_coeff[0]
   mb = mo_coeff[1]
   nalpha = (mol.nelectron+mol.spin)/2
   nbeta  = (mol.nelectron-mol.spin)/2
   # Spin-averaged DM
   pTa = numpy.dot(ma[:,:nalpha],ma[:,:nalpha].T)
   pTb = numpy.dot(mb[:,:nbeta],mb[:,:nbeta].T)
   pT = 0.5*(pTa+pTb)
   # Lowdin basis
   s12 = sqrtm(ova)
   s12inv = lowdin(ova)
   pTOAO = reduce(numpy.dot,(s12,pT,s12))
   eig,coeff = scipy.linalg.eigh(-pTOAO)
   eig = -2.0*eig
   eig[eig<0.0]=0.0
   eig[abs(eig)<1.e-14]=0.0
   ifplot = False #True
   if ifplot:
      import matplotlib.pyplot as plt
      plt.plot(range(nb),eig,'ro')
      plt.show()
   # Back to AO basis
   coeff = numpy.dot(s12inv,coeff)
   diff = reduce(numpy.dot,(coeff.T,ova,coeff)) - numpy.identity(nb)
   print 'CtSC-I',numpy.linalg.norm(diff)
   # 
   # Averaged Fock
   #
   enorb = mf["mo_energy"]
   fa = reduce(numpy.dot,(ma,numpy.diag(enorb[0]),ma.T))
   fb = reduce(numpy.dot,(mb,numpy.diag(enorb[1]),mb.T))
   # Non-orthogonal cases: FC=SCE
   # Fao = SC*e*C{-1} = S*C*e*Ct*S
   fav = 0.5*(fa+fb)
   # Expectation value of natural orbitals <i|F|i>
   fexpt = reduce(numpy.dot,(coeff.T,ova,fav,ova,coeff))
   enorb = numpy.diag(fexpt)
   nocc = eig.copy()
   #
   # Reordering and define active space according to thresh
   #
   idx = 0
   active=[]
   for i in range(nb):
      if nocc[i]<=2.0-thresh and nocc[i]>=thresh:
         active.append(True)
      else:
         active.append(False)
   print '\nNatural orbitals:'
   for i in range(nb):
      print 'orb:',i,active[i],nocc[i],enorb[i]
   active = numpy.array(active)
   actIndices = list(numpy.argwhere(active==True).flatten())
   cOrbs = coeff[:,:actIndices[0]]
   aOrbs = coeff[:,actIndices]
   vOrbs = coeff[:,actIndices[-1]+1:]
   nb = cOrbs.shape[0]
   nc = cOrbs.shape[1]
   na = aOrbs.shape[1]
   nv = vOrbs.shape[1]
   print 'core orbs:',cOrbs.shape
   print 'act  orbs:',aOrbs.shape
   print 'vir  orbs:',vOrbs.shape
   assert nc+na+nv == nb
   # dump UNO
   with open(fname+'_uno.molden','w') as thefile:
       molden.header(mol,thefile)
       molden.orbital_coeff(mol,thefile,coeff)
   #=====================
   # Population analysis
   #=====================
   aux = s12inv
   #clmo = ulocal.scdm(cOrbs,ova,aux)
   #almo = ulocal.scdm(aOrbs,ova,aux)
   clmo = cOrbs
   almo = aOrbs
   ierr,uc = pmloc.loc(mol,clmo)
   ierr,ua = pmloc.loc(mol,almo)
   clmo = clmo.dot(uc)
   almo = almo.dot(ua)
   vlmo = ulocal.scdm(vOrbs,ova,aux)
   # P-SORT
   mo_c,n_c,e_c = ulocal.psort(ova,fav,pT,clmo)
   mo_o,n_o,e_o = ulocal.psort(ova,fav,pT,almo)
   mo_v,n_v,e_v = ulocal.psort(ova,fav,pT,vlmo)
   lmo = numpy.hstack((mo_c,mo_o,mo_v)).copy()
   enorb = numpy.hstack([e_c,e_o,e_v])
   occ = numpy.hstack([n_c,n_o,n_v])
   # CHECK
   diff = reduce(numpy.dot,(lmo.T,ova,lmo)) - numpy.identity(nb)
   print 'diff=',numpy.linalg.norm(diff)
   ulocal.lowdinPop(mol,lmo,ova,enorb,occ)
   ulocal.dumpLMO(mol,fname,lmo)
   print 'nalpha,nbeta,mol.spin,nb:',\
          nalpha,nbeta,mol.spin,nb
   return mol,ova,fav,pT,nb,nalpha,nbeta,nc,na,nv,lmo,enorb,occ