def molden(self,mo_coeff,fname='mocoeff'):
print '\n[iface.molden] dump MOcoeff into file = '+fname+'.molden'
from pyscf.tools import molden
with open(fname+'.molden','w') as thefile:
molden.header(self.mol,thefile)
molden.orbital_coeff(self.mol,thefile,mo_coeff,symm=['A']*mo_coeff.shape[1])
return 0
def dump_bath_orbs( self, filename, impnumber=0 ):
import qcdmet_paths
from pyscf import tools
from pyscf.tools import molden
with open( filename, 'w' ) as thefile:
molden.header( self.ints.mol, thefile )
molden.orbital_coeff( self.ints.mol, thefile, np.dot( self.ints.ao2loc, self.dmetOrbs[impnumber] ) )
def dump_bath_orbs( self, filename, impnumber=0 ):
import qcdmet_paths
from pyscf import tools
from pyscf.tools import molden
with open( filename, 'w' ) as thefile:
molden.header( self.ints.mol, thefile )
molden.orbital_coeff( self.ints.mol, thefile, np.dot( self.ints.ao2loc, self.dmetOrbs[impnumber] ) )
def dumpLMO(mol,fname,lmo):
print 'Dump into '+fname+'.h5'
f = h5py.File(fname+'.h5','w')
f.create_dataset("lmo",data=lmo)
f.close()
print 'Dump into '+fname+'_lmo.molden'
with open(fname+'_lmo.molden','w') as thefile:
molden.header(mol,thefile)
molden.orbital_coeff(mol,thefile,lmo)
return 0
def dumpLMO(mol,fname,lmo):
print 'Dump into '+fname+'.h5'
f = h5py.File(fname+'.h5','w')
f.create_dataset("lmo",data=lmo)
f.close()
print 'Dump into '+fname+'_lmo.molden'
with open(fname+'_lmo.molden','w') as thefile:
molden.header(mol,thefile)
molden.orbital_coeff(mol,thefile,lmo)
return 0
def submo_molden(self, mo_coeff, mo_occ, loc2sub, filename, mol=None):
if mol is None: mol = self.mol
dim = mo_coeff.shape[0]
mo_loc = np.dot(loc2sub[:, :dim], mo_coeff)
transfo = np.dot(self.ao2loc, mo_loc)
with open(filename, 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, transfo, occ=mo_occ)
def dump_molden(self, filename, orbital_coeff):
r'''Create a molden file to inspect a set of orbitals
Args:
filename : Filename of the molden file
orbital_coeff: Set of orthonormal orbitals, expressed in terms of the AO, for which a molden file should be created
'''
with open(filename, 'w') as thefile:
molden.header(self.themol, thefile)
molden.orbital_coeff(self.themol, thefile, orbital_coeff)
def dump_molden( self, filename, orbital_coeff ):
r'''Create a molden file to inspect a set of orbitals
Args:
filename : Filename of the molden file
orbital_coeff: Set of orthonormal orbitals, expressed in terms of the AO, for which a molden file should be created
'''
with open( filename, 'w' ) as thefile:
molden.header( self.themol, thefile )
molden.orbital_coeff( self.themol, thefile, orbital_coeff )
def make_frozen_orbs(self, norb=None):
mf = self.mf_full
mol = mf.mol
loc_method = self.loc_method
pop_method = self.pop_method
pm_exponent = self.pm_exponent
if (norb is None):
norb = mol.nelectron // 2
mo_lo = None
if (loc_method.upper() == 'PM'):
pm = lo.pipek.PM(mol)
pm.pop_method = pop_method
pm.exponent = pm_exponent
mo_lo = pm.kernel(mf.mo_coeff[:, :norb], verbose=4)
elif (loc_method.upper() == 'BOYS'):
boys = lo.boys.Boys(mol)
mo_lo = boys.kernel(mf.mo_coeff[:, :norb], verbose=4)
else:
raise NotImplementedError('loc_method %s' % loc_method)
s = mol.intor_symmetric('int1e_ovlp')
nbas = mol.nao_nr()
dm_lo = np.empty((norb, nbas, nbas))
for i in range(norb):
dm_lo[i] = np.outer(mo_lo[:, i], mo_lo[:, i])
pop = np.zeros((norb))
for i in range(norb):
for iatom, (b0, b1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
if (self.env[iatom] == 1):
pop[i] += np.trace(np.dot(dm_lo[i, p0:p1, :], s[:, p0:p1]))
#tools.VecPrint(pop,"Mulliken popupaltion")
ind = np.argsort(-pop)
pop = pop[ind]
mo_lo[:, :norb] = mo_lo[:, ind]
tools.VecPrint(pop,
"sorted Mulliken popupaltion: 1.0 for fully occupied")
with open('mo_lo.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, mo_lo)
self.mo_lo = mo_lo
self.pop_lo = pop
return (mo_lo, pop)
name = 'ceo'
atm = [0,1]
mol = lib.chkfile.load_mol(name+'.chk')
mo_coeff = lib.chkfile.load(name+'.chk', 'scf/mo_coeff')
nmo = mol.nelectron//2
mo_coeff = mo_coeff[:,0:nmo]
with h5py.File(name+'.chk.h5') as f:
idx = 'ovlp'+str(atm[0])
aom1 = f[idx+'/aom'].value
idx = 'ovlp'+str(atm[1])
aom2 = f[idx+'/aom'].value
delta = 4*numpy.einsum('ij,ji->', aom1, aom2)
log.info('Delta %f for pair %d %d' % (delta, atm[0], atm[1]))
dab = 4*numpy.einsum('ik,kj->ij', aom1, aom2)
dba = 4*numpy.einsum('ik,kj->ij', aom2, aom1)
d2c = (dab+dba)/2.0
from pyscf.tools import molden
natocc, natorb = numpy.linalg.eigh(d2c)
log.info('Occ for NADO %s', natocc)
log.info('Sum Occ for NADO %f', natocc.sum())
natorb = numpy.dot(mo_coeff, natorb)
with open(name+'_'+str(atm[0])+'-'+str(atm[1])+'_2c.molden', 'w') as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, natorb, occ=natocc)
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
def genEmbedBasis(mol,
mo_coeff,
selectionRule,
thresh=0.001,
lao='meta_lowdin',
debug=False,
ifplot=True):
print('\n[embed.genEmbedBasis] for unrestricted determinant')
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(' (CtSC-I)[a]', numpy.linalg.norm(diff))
diff = reduce(numpy.dot,
(mo_coeff[1].T, ova, mo_coeff[1])) - numpy.identity(nb)
print(' (CtSC-I)[b]', 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
print(' nalpha/nbeta = ', (nalpha, nbeta))
# Spin-averaged DM
ma_occ = ma[:, :nalpha]
mb_occ = mb[:, :nbeta]
pTa = numpy.dot(ma_occ, ma_occ.T)
pTb = numpy.dot(mb_occ, mb_occ.T)
pT = pTa + pTb
#------------------------------------
# OAO basis
#------------------------------------
# Due to optimization by segmentation,
# the lowdin here do not correspond to
# the idea lowdin OAO.
if lao == 'bad_lowdin':
s12 = sqrtm(ova)
s12inv = lowdin(ova)
# Better choice: Pbas*|chiANO>
elif lao == 'meta_lowdin':
from pyscf import lo
meta = lo.orth_ao(mol, method='meta_lowdin')
diff = reduce(numpy.dot, (meta.T, ova, meta)) - numpy.identity(nb)
s12inv = meta.copy()
s12 = numpy.linalg.inv(s12inv)
#
# Psi = chiAO*C
# = (chiAO*Y)*(Yinv*C)
# DM in ortho basis = Yinv*C*n*C^T*Yinv^T
# Only in lowdin basis Y^T=Y.
#
pTOAO = reduce(numpy.dot, (s12, pT, s12.T))
#------------------------------------
# Define impurity
labels = mol.spheric_labels()
fragBasis = []
fragLabels = []
for idx, item in enumerate(labels):
ifselect = False
if selectionRule(item):
ifselect = True
if ifselect:
fragBasis.append(idx)
fragLabels.append(item)
print(' Define central fragment:')
print(' No. of totalBasis:', nb)
print(' No. of fragBasis :', len(fragBasis))
print(' Indices of fragBasis:', fragBasis)
print(' fragLabels:')
for idx, item in enumerate(fragLabels):
print(' idx = ', idx, ' fragBas=', item)
compBasis = list(set(range(nb)) - set(fragBasis))
nfrag = len(fragBasis)
ncomp = len(compBasis)
# Fragment
pTf = pTOAO[numpy.ix_(fragBasis, fragBasis)]
ef, u = scipy.linalg.eigh(-pTf)
ef = -ef
ne_f = sum(ef)
print(' Diag_values of pTf:\n', numpy.diag(pTf))
print(' Eigenvalues of pTf:\n', ef)
uf = numpy.zeros((nb, nfrag))
# Retain the locality for impurity
#uf[fragBasis,:] = u
uf[fragBasis, :] = numpy.identity(nfrag)
# Complementary
if ncomp > 0:
pTc = pTOAO[numpy.ix_(compBasis, compBasis)]
ec, v = scipy.linalg.eigh(-pTc)
ec = -ec
ne_c = sum(ec)
print(' Eigenvalues of pTc:\n', ec)
cindx = []
aindx = []
vindx = []
for i in range(ncomp):
if abs(ec[i] - 2.0) < thresh:
cindx.append(i)
elif abs(ec[i]) < thresh:
vindx.append(i)
else:
aindx.append(i)
ncStrict = len(numpy.argwhere(abs(ec - 2.0) < 1.e-6))
nvStrict = len(numpy.argwhere(abs(ec) < 1.e-6))
naStrict = ncomp - ncStrict - nvStrict
nc = len(cindx)
na = len(aindx)
nv = len(vindx)
vc = numpy.zeros((nb, nc))
va = numpy.zeros((nb, na))
vv = numpy.zeros((nb, nv))
vc[compBasis, :] = v[:, cindx]
va[compBasis, :] = v[:, aindx]
vv[compBasis, :] = v[:, vindx]
# Set up the proper ordering
ucoeff = numpy.hstack((uf, va, vc, vv))
print('-' * 70)
print(' Final results for classification of basis with thresh=',
thresh)
print('-' * 70)
print(' (nf,na,nc,nv) = ', nfrag, na, nc, nv)
print(' (ncomp,ncStrict,nvStrict,naStrict) =', ncomp, ncStrict,
nvStrict, naStrict)
print(' Eigen_na =\n', ec[aindx])
if ifplot:
import matplotlib.pyplot as plt
plt.plot(abs(ef), marker='o', linewidth=2.0)
plt.plot(abs(ec), marker='o', linewidth=2.0)
plt.show()
else:
ne_c = 0.0
ucoeff = uf.copy()
# Check
pTu = reduce(numpy.dot, (ucoeff.T, pTOAO, ucoeff))
print(' Nf =', ne_f, 'Nc =', ne_c, 'Nt =', ne_f + ne_c)
if debug:
print(' diagonal of pTu =')
print(numpy.diag(pTu))
print('ucoeff\n', ucoeff)
# Back to AO basis
basis = numpy.dot(s12inv, ucoeff)
# Dump
diff = reduce(numpy.dot, (basis.T, ova, basis)) - numpy.identity(nb)
print(' CtSC-I=', numpy.linalg.norm(diff))
with open('embas.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, basis)
with open('cmoA.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, ma)
with open('cmoB.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, mb)
ua = reduce(numpy.dot, (basis.T, ova, ma_occ))
ub = reduce(numpy.dot, (basis.T, ova, mb_occ))
if debug: print(' ua\n', ua)
if debug: print(' ub\n', ub)
ia = abs(reduce(numpy.dot, (ua.T, ua)))
ib = abs(reduce(numpy.dot, (ub.T, ub)))
print(' diffIa=', numpy.linalg.norm(ia - numpy.identity(nalpha)))
print(' diffIb=', numpy.linalg.norm(ib - numpy.identity(nbeta)))
return basis, ua, ub
#
rdm1 = mycc.make_rdm1()
rdm2 = mycc.make_rdm2()
eri_mo = ao2mo.kernel(mf._eri, coeff[:, :nmo], compact=False)
eri_mo = eri_mo.reshape(nmo, nmo, nmo, nmo)
h1 = reduce(numpy.dot, (coeff[:, :nmo].T, mf.get_hcore(), coeff[:, :nmo]))
ecc = (numpy.einsum('ij,ji->', h1, rdm1) +
numpy.einsum('ijkl,ijkl->', eri_mo, rdm2) * .5 + mf.mol.energy_nuc())
lib.logger.info(mycc, "* Energy with 1/2-RDM : %.8f" % ecc)
den_file = name + '.den'
fspt = open(den_file, 'w')
fspt.write('CCIQA\n')
fspt.write('1-RDM:\n')
for i in range(nmo):
for j in range(nmo):
fspt.write('%i %i %.10f\n' % ((i + 1), (j + 1), rdm1[i, j]))
fspt.write('2-RDM:\n')
for i in range(nmo):
for j in range(nmo):
for k in range(nmo):
for l in range(nmo):
if (abs(rdm2[i, j, k, l]) > 1e-8):
fspt.write('%i %i %i %i %.10f\n' % ((i+1), \
(j+1), (k+1), (l+1), rdm2[i,j,k,l]))
fspt.close()
with open(name + '.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, coeff[:, :nmo], occ=occ[:nmo])
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
#
from pyscf.tools import molden
with open(fname+'_uno.molden','w') as thefile:
molden.header(mol,thefile)
molden.orbital_coeff(mol,thefile,coeff)
#=============================
# local orbitals
#=============================
from pyscf.tools import molden,localizer
iflocal = False #True
if iflocal:
loc = localizer.localizer(mol,ma[:,:mol.nelectron/2],'boys')
loc.verbose = 10
new_coeff = loc.optimize()
loc = localizer.localizer(mol,ma[:,mol.nelectron/2:],'boys')
new_coeff2 = loc.optimize()
lmo = numpy.hstack([new_coeff,new_coeff2])
with open(fname+'lmo.molden','w') as thefile:
molden.header(mol,thefile)
def locmo_molden(self, mo_coeff, mo_occ, filename):
transfo = np.dot(self.ao2loc, mo_coeff)
with open(filename, 'w') as thefile:
molden.header(self.mol, thefile)
molden.orbital_coeff(self.mol, thefile, transfo, occ=mo_occ)
def molden( self, filename ):
with open( filename, 'w' ) as thefile:
molden.header( self.mol, thefile )
molden.orbital_coeff( self.mol, thefile, self.ao2loc )
fspt.write('%i %i %.16f\n' % ((i+1), (j+1), rdm1[i,j]))
fspt.write('La matriz d es:\n')
for i in range(nmo):
for j in range(nmo):
for k in range(nmo):
for l in range(nmo):
if (abs(rdm2[i,j,k,l]) > 1e-12):
fspt.write('%i %i %i %i %.16f\n' % ((i+1), (j+1), (k+1), (l+1), rdm2[i,j,k,l]))
fspt.close()
orbsym = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mc.mo_coeff[:,:nmo])
natocc, natorb = symm.eigh(-rdm1, orbsym)
for i, k in enumerate(numpy.argmax(abs(natorb), axis=0)):
if natorb[k,i] < 0:
natorb[:,i] *= -1
natorb = numpy.dot(mc.mo_coeff[:,:nmo], natorb)
natocc = -natocc
with open('n2_cas.det', 'w') as f3:
write_ci(f3, mc.ci, mc.ncas, mc.nelecas, mc.ncore)
with open('n2_ref_nat.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, natorb, occ=natocc)
with open('n2_ref.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, mc.mo_coeff[:,:nmo], occ=mf.mo_occ[:nmo])
with open('n2_cas.wfn', 'w') as f2:
write_mo(f2, mol, natorb, mo_occ=natocc)
write_mo(f2, mol, mc.mo_coeff[:,:nmo])
with open('rdm_wfn.wfn', 'w') as f2:
write_mo(f2, mol, mc.mo_coeff[:,:nmo], mo_occ=mf.mo_occ[:nmo])
H 3.4870 0.0000 0.0197
H 1.0145 0.2578 0.0000
""",
basis="cc-pvdz",
symmetry=1,
)
mf = scf.RHF(mol)
mf.kernel()
#
# First method is to explicit call the functions provided by molden.py
#
with open("C6H6mo.molden", "w") as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
#
# Second method is to simply call from_mo function to write the orbitals
#
c_loc_orth = lo.orth.orth_ao(mol)
molden.from_mo(mol, "C6H6loc.molden", c_loc_orth)
#
# Molden format does not support high angular momentum basis. To handle the
# orbitals which have l>=5 functions, a hacky way is to call molden.remove_high_l
# function. However, the resultant orbitals may not be orthnormal.
#
mol = gto.M(atom="He 0 0 0", basis={"He": gto.expand_etbs(((0, 3, 1.0, 2.0), (5, 2, 1.0, 2.0)))})
mf = scf.RHF(mol).run()
m = scf.RHF(mol)
m.scf()
mc = mcscf.CASSCF(m, 4, 4)
mc.fcisolver = FCIQMCCI(mol)
mc.fcisolver.tau = 0.01
mc.fcisolver.RDMSamples = 1000
mc.max_cycle_macro = 10
# Return natural orbitals from mc2step in casscf_mo.
mc.natorb = True
emc_1, e_ci, fcivec, casscf_mo, mo_energy = mc.mc2step(m.mo_coeff)
# Write orbitals to molden output.
with open('output.molden', 'w') as fout:
molden.header(mol, fout)
molden.orbital_coeff(mol, fout, casscf_mo)
# Now, calculate the full RDMs for the full energy.
one_pdm, two_pdm = find_full_casscf_12rdm(mc.fcisolver, casscf_mo,
'spinfree_TwoRDM.1', 4, 4)
e = calc_energy_from_rdms(mol, casscf_mo, one_pdm, two_pdm)
print('Energy from rdms and CASSCF should be the same: ', e, emc_1)
mc = mcscf.CASCI(m, 4, 4)
mc.fcisolver = FCIQMCCI(mol)
mc.fcisolver.tau = 0.01
mc.fcisolver.RDMSamples = 1000
emc_0 = mc.casci()[0]
b = 1.4
mol = gto.Mole()
#######################
# Parse the input #
#######################
thebasis1 = 'cc-pvdz' # Basis set for H and C
thebasis2 = 'aug-cc-pvdz' # Basis set for Cl and Br
mol = sn2_structures.structure( thestructure, thebasis1, thebasis2 )
mf = scf.RHF( mol )
mf.verbose = 4
mf.scf()
if ( False ):
from pyscf.tools import molden, localizer
with open( 'sn2-mo.molden', 'w' ) as thefile:
molden.header( mol, thefile )
molden.orbital_coeff( mol, thefile, mf.mo_coeff )
if ( False ):
ccsolver = ccsd.CCSD( mf )
ccsolver.verbose = 5
ECORR, t1, t2 = ccsolver.ccsd()
ECCSD = mf.hf_energy + ECORR
print "ERHF for structure", thestructure, "=", mf.hf_energy
print "ECCSD for structure", thestructure, "=", ECCSD
if ( True ):
# myInts = localintegrals.localintegrals( mf, range( mol.nao_nr() ), 'boys', localization_threshold=1e-5 )
# myInts = localintegrals.localintegrals( mf, range( mol.nao_nr() ), 'meta_lowdin' )
myInts = localintegrals.localintegrals( mf, range( mol.nao_nr() ), 'iao' )
myInts.molden( 'sn2-loc.molden' )
mc.kernel(loc_mo)
rdm1, rdm2 = mc.fcisolver.make_rdm12(mc.ci, norb, nelec)
rdm1, rdm2 = add_inactive_space_to_rdm(mol, mf.mo_coeff, rdm1, rdm2)
##########################################################################################
den_file = name + '.den'
fspt = open(den_file, 'w')
fspt.write(
'CCIQA ENERGY = 0.000000000000 THE VIRIAL(-V/T)= 2.00000000\n')
fspt.write('La matriz D es:\n')
for i in range(nmo):
for j in range(nmo):
fspt.write('%i %i %.16f\n' % ((i + 1), (j + 1), rdm1[i, j]))
fspt.write('La matriz d es:\n')
for i in range(nmo):
for j in range(nmo):
for k in range(nmo):
for l in range(nmo):
if (abs(rdm2[i, j, k, l]) > 1e-12):
fspt.write('%i %i %i %i %.16f\n' %
((i + 1), (j + 1), (k + 1),
(l + 1), rdm2[i, j, k, l]))
fspt.close()
##########################################################################################
with open(name + '.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, mc.mo_coeff, occ=mf.mo_occ)
cmd = '/home/jluis/bin/molden2aim ' + name
os.system(cmd)
cmd = 'cat ' + name + '.den ' + '>> ' + name + '.wfn'
os.system(cmd)
def sub_molden(self, loc2sub, filename, mo_occ=None):
transfo = np.dot(self.ao2loc, loc2sub)
with open(filename, 'w') as thefile:
molden.header(self.mol, thefile)
molden.orbital_coeff(self.mol, thefile, transfo, occ=mo_occ)
#===================this section is optional==============
# if you would like to check the generated orbitals
HF_en = mf.mo_energy
HF_MOcoeff = mf.mo_coeff
HF_occ = mf.mo_occ
ova = mol.intor_symmetric("cint1e_ovlp_sph")
e_d = numpy.diag(HF_en)
cect = numpy.dot(HF_MOcoeff, numpy.dot(e_d, HF_MOcoeff.T))
f = numpy.dot(ova, numpy.dot(cect, ova))
en = numpy.diag(numpy.dot(coeff.T, numpy.dot(f, coeff)))
fname = 'generated_AS_beforeCAS'
from pyscf.tools import molden
with open(fname + '.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, coeff, ene=en, occ=mf.mo_occ)
#==========================================================
mycas = mcscf.CASSCF(mf, norb, [nalpha, nbeta])
AS = range(N_Core, N_Core + N_Act)
mycas.chkfile = 'cas_FeCp2.chk' # it is useful to keep the chk file for CASSCF in case you want to run some subsequent CASCI and NEVPT2 calculations
mycas.fcisolver.nroots = 1
mycas.fix_spin_(
ss=0
) # in newer PYSCF it is better to specify ss which is usually your mol.spin
activeMO = mcscf.sort_mo(mycas, coeff, AS, base=0)
mycas.verbose = 5
mycas.max_cycle_macro = 150
mycas.kernel(activeMO)
mc = mcscf.CASCI(mf, norb, [nalpha, nbeta])
def molden( self, filename ):
with open( filename, 'w' ) as thefile:
molden.header( self.mol, thefile )
molden.orbital_coeff( self.mol, thefile, self.ao2loc )
m = scf.RHF(mol)
m.scf()
mc = mcscf.CASSCF(m, 4, 4)
mc.fcisolver = FCIQMCCI(mol)
mc.fcisolver.tau = 0.01
mc.fcisolver.RDMSamples = 1000
mc.max_cycle_macro = 10
# Return natural orbitals from mc2step in casscf_mo.
mc.natorb = True
emc_1, e_ci, fcivec, casscf_mo = mc.mc2step(m.mo_coeff)
# Write orbitals to molden output.
with open( 'output.molden', 'w' ) as fout:
molden.header(mol, fout)
molden.orbital_coeff(mol, fout, casscf_mo)
# Now, calculate the full RDMs for the full energy.
one_pdm, two_pdm = find_full_casscf_12rdm(mc.fcisolver, casscf_mo,
'spinfree_TwoRDM.1', 4, 4)
e = calc_energy_from_rdms(mol, casscf_mo, one_pdm, two_pdm)
print('Energy from rdms and CASSCF should be the same: ',e,emc_1)
mc = mcscf.CASCI(m, 4, 4)
mc.fcisolver = FCIQMCCI(mol)
mc.fcisolver.tau = 0.01
mc.fcisolver.RDMSamples = 1000
emc_0 = mc.casci()[0]
b = 1.4
mol = gto.Mole()
def mo_molden(mol,mo_coeff,filename):
with open( filename, 'w' ) as thefile:
molden.header( mol, thefile )
molden.orbital_coeff( mol, thefile, mo_coeff )
h1a = reduce(numpy.dot, (mo_a.T.conj(), hcore, mo_a))
h1b = reduce(numpy.dot, (mo_b.T.conj(), hcore, mo_b))
e1 = einsum('ij,ji', h1a, rdm1a)
e1 += einsum('ij,ji', h1b, rdm1b)
e1 += einsum('ijkl,ijkl', eriaa, rdm2aa) * 0.5
e1 += einsum('ijkl,ijkl', eriab, rdm2ab)
e1 += einsum('ijkl,ijkl', eribb, rdm2bb) * 0.5
e1 += mol.energy_nuc()
lib.logger.info(pt2, "* Excited state Energy with 1/2-RDM : %.8f" % e1)
####### This can be removed ######
coeff = numpy.hstack([mo_a, mo_b])
occ = numpy.hstack([occ_a, occ_b])
with open(name + '.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, coeff, occ=occ)
# Aqui cuidado para hacer una prueba rapida los bucles
# Se recorren en alpha por ejemplo porque hay el mismo
# numero de alpha y beta congelados, si fuese distinto
# habria que cabiar
nmo = nmoa
den_file = name + '.den'
fspt = open(den_file, 'w')
fspt.write('CCIQA\n')
fspt.write('1-RDM:\n')
for i in range(nmo):
for j in range(nmo):
fspt.write('%i %i %.10f\n' % ((i + 1), (j + 1), rdm1a[i, j]))
fspt.write('%i %i %.10f\n' % ((i + 1 + nmo),
(j + 1 + nmo), rdm1b[i, j]))
C 3.2883 3.3891 0.2345
C 1.9047 3.5333 0.2237
C 3.8560 2.1213 0.1612
C 1.0888 2.4099 0.1396
C 3.0401 0.9977 0.0771
C 1.6565 1.1421 0.0663
H 3.9303 4.2734 0.3007
H 1.4582 4.5312 0.2815
H 4.9448 2.0077 0.1699
H 0.0000 2.5234 0.1311
H 3.4870 0.0000 0.0197
H 1.0145 0.2578 0.0000
''',
basis = 'cc-pvdz',
symmetry = 1)
mf = scf.RHF(mol)
mf.scf()
with open('C6H6mo.molden', 'w') as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
c_loc_orth = lo.orth.orth_ao(mol, 'meta_lowdin', lo.orth.pre_orth_ao(mol))
with open('C6H6loc.molden', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, c_loc_orth)
mc.fix_spin_(shift=.5, ss=0)
#mc.__dict__.update(scf.chkfile.load(name+'.chk', 'mcscf'))
#mo = lib.chkfile.load(name+'.chk', 'mcscf/mo_coeff')
mc.kernel(mo)
nmo = mc.ncore + mc.ncas
rdm1, rdm2 = mc.fcisolver.make_rdm12(mc.ci, mc.ncas, mc.nelecas)
rdm1, rdm2 = mcscf.addons._make_rdm12_on_mo(rdm1, rdm2, mc.ncore, mc.ncas, nmo)
den_file = name + '.den'
fspt = open(den_file,'w')
fspt.write('CCIQA\n')
fspt.write('1-RDM:\n')
for i in range(nmo):
for j in range(nmo):
fspt.write('%i %i %.10f\n' % ((i+1), (j+1), rdm1[i,j]))
fspt.write('2-RDM:\n')
for i in range(nmo):
for j in range(nmo):
for k in range(nmo):
for l in range(nmo):
if (abs(rdm2[i,j,k,l]) > 1e-8):
fspt.write('%i %i %i %i %.10f\n' % ((i+1), \
(j+1), (k+1), (l+1), rdm2[i,j,k,l]))
fspt.close()
with open(name+'.mol', 'w') as f2:
molden.header(mol, f2)
molden.orbital_coeff(mol, f2, mc.mo_coeff[:,:nmo], occ=mf.mo_occ[:nmo])
['N', map(lambda x: x * fac, [0.0, 1.653532, 0.0])],
['O', map(lambda x: x * fac, [-2.050381, -2.530377, 0.0])],
['O', map(lambda x: x * fac, [2.050381, -2.530377, 0.0])],
['O', map(lambda x: x * fac, [-2.050381, 2.530377, 0.0])],
['O', map(lambda x: x * fac, [2.050381, 2.530377, 0.0])]]
mol.basis = 'aug-cc-pvdz'
mol.charge = 0
mol.spin = 0
mol.build()
mf = scf.RHF(mol)
mf.init_guess = 'atom'
mf.level_shift = 0.0
mf.max_cycle = 100
mf.conv_tol = 1.e-20
ehf = mf.scf()
nocc = mol.nelectron / 2
ierr, uo = loc(mol, mf.mo_coeff[:, :nocc], iop=0)
ierr, uv = loc(mol, mf.mo_coeff[:, nocc:], iop=0)
u = scipy.linalg.block_diag(uo, uv)
lmo = numpy.dot(mf.mo_coeff, u)
fname = 'n2o4'
with open(fname + '_cmo.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, mf.mo_coeff)
with open(fname + '_lmo.molden', 'w') as thefile:
molden.header(mol, thefile)
molden.orbital_coeff(mol, thefile, lmo)
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
H 0.0000 2.5234 0.1311
H 3.4870 0.0000 0.0197
H 1.0145 0.2578 0.0000
''',
basis = 'cc-pvdz',
symmetry = 1)
mf = scf.RHF(mol)
mf.kernel()
#
# First method is to explicit call the functions provided by molden.py
#
with open('C6H6mo.molden', 'w') as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
#
# Second method is to simply call from_mo function to write the orbitals
#
c_loc_orth = lo.orth.orth_ao(mol)
molden.from_mo(mol, 'C6H6loc.molden', c_loc_orth)
#
# Molden format does not support high angular momentum basis. To handle the
# orbitals which have l>=5 functions, a hacky way is to call molden.remove_high_l
# function. However, the resultant orbitals may not be orthnormal.
#
mol = gto.M(
atom = 'He 0 0 0',
