#!/usr/bin/env python
from pyscf import gto, scf
from pyscf.tools import wfn_format
name = 'h2o'
mol = gto.Mole()
mol.atom = '''
O 0.0000 0.0000 0.1173
H 0.0000 0.7572 -0.4692
H 0.0000 -0.7572 -0.4692
'''
mol.basis = 'cc-pvdz'
mol.verbose = 4
mol.spin = 0
mol.symmetry = 1
mol.charge = 0
mol.build()
mf = scf.RHF(mol)
mf.kernel()
wfn_file = name + '.wfn'
nmo = mol.nelectron // 2
coef = mf.mo_coeff[:, :nmo]
occ = mf.mo_occ[:nmo]
ene = mf.mo_energy[:nmo]
with open(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, mol, coef, mo_occ=occ, mo_energy=ene)
eri_mo = eri_mo.reshape(nocc, nvir, nocc, nvir)
e_denom = 1.0 / (eo.reshape(-1, 1, 1, 1) - ev.reshape(-1, 1, 1) +
eo.reshape(-1, 1) - ev)
t2 = numpy.zeros((nocc, nvir, nocc, nvir))
t2 = 2.0 * lib.einsum('iajb,iajb->iajb', eri_mo, e_denom)
t2 -= lib.einsum('ibja,iajb->iajb', eri_mo, e_denom)
e_mp2 = numpy.einsum('iajb,iajb->', eri_mo, t2, optimize=True)
lib.logger.info(mf, "!*** E(MP2): %12.8f" % e_mp2)
lib.logger.info(mf, "!**** E(HF+MP2): %12.8f" % (e_mp2 + ehf))
wfn_file = name + '.wfn'
ao_loc = cell.ao_loc_nr()
fspt = open(wfn_file, 'w')
wfn_format.write_mo(fspt,
cell,
mf.mo_coeff,
mo_occ=mf.mo_occ,
mo_energy=mf.mo_energy)
fspt.write('MP2\n')
fspt.write('1-RDM:\n')
occup = 2.0
norb = cell.nelectron // 2
for i in range(norb):
fspt.write('%i %i %.8f\n' % ((i + 1), (i + 1), occup))
fspt.write('t2_iajb:\n')
for i in range(nocc):
for j in range(nvir):
for k in range(nocc):
for l in range(nvir):
if (abs(t2[i, j, k, l]) > 1e-8):
fspt.write('%i %i %i %i %.10f\n' % ((i+1+ncore), \
rdm1, rdm2 = mcscf.addons._make_rdm12_on_mo(rdm1, rdm2, mc.ncore, mc.ncas, nmo)
lib.logger.info(mf,'Write rdm1-rdm2 on MO basis to HDF5 file')
dic = {'rdm1':rdm1,
'rdm2':rdm2}
lib.chkfile.save(name+'.chk', 'pdm', dic)
natocc, natorb = numpy.linalg.eigh(-rdm1)
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
wfn_file = name + '.wfn'
with open(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, cell, natorb, mo_occ=natocc)
wfn_format.write_coeff(f2, cell, mc.mo_coeff[:,:nmo])
wfn_format.write_ci(f2, mc.ci, mc.ncas, mc.nelecas, ncore=mc.ncore)
#c = mc.mo_coeff[:,:nmo]
#s = cell.pbc_intor('cint1e_ovlp_sph')
#t = cell.pbc_intor('cint1e_kin_sph')
#h = mc.get_hcore()
#s = reduce(numpy.dot, (c.T,s,c))
#t = reduce(numpy.dot, (c.T,t,c))
#h = reduce(numpy.dot, (c.T,h,c))
#enuc = cell.energy_nuc()
#ekin = numpy.einsum('ij,ji->',t,rdm1)
#hcore = numpy.einsum('ij,ji->',h,rdm1)
#pop = numpy.einsum('ij,ji->',s,rdm1)
#print('Population : %s' % pop)
diis_obj = scf.ADIIS()
diis_obj.diis_space = 24
diis_obj.diis_start_cycle = 14
# Guess
mf = scf.RHF(mol)
mf.verbose = 0
mf.kernel()
dm = mf.make_rdm1()
# Calc
mf = scf.RHF(mol) #.newton()
mf.conv_tol = 1e-6
mf.max_cycle = 120
mf.diis = diis_obj
old_get_fock = mf.get_fock
mf.get_fock = get_cfock
mf.kernel(dm)
mf.analyze(with_meta_lowdin=False)
dm = mf.make_rdm1()
for i in range(natm):
ia = atms[i]
pop = numpy.einsum('ij,ji->', saom[i], dm)
lib.logger.info(mol, 'Population atom %d : %f' % (ia, pop))
wfn_file = name + '.wfn'
idx = mf.mo_occ > 0
with open(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, mol, mf.mo_coeff[:,idx], \
mo_occ=mf.mo_occ[idx], mo_energy=mf.mo_energy[idx])
mol.symmetry = 0
mol.build()
mf = scf.RHF(mol)
mf.verbose = 4
mf.kernel()
mf.analyze(with_meta_lowdin=False)
dm = mf.make_rdm1()
multiplicadores = numpy.zeros(mol.natm)
multiplicadores = [0.0,0.2]
my_diis_obj = scf.ADIIS()
my_diis_obj.diis_space = 14
mf = scf.RHF(mol)
mf.conv_tol = 1e-6
mf.max_cycle = 120
mf.diis = my_diis_obj
old_get_fock = mf.get_fock
mf.get_fock = get_cfock
#mf.verbose = 3
mf.kernel(dm0=dm)
mf.analyze(with_meta_lowdin=False)
dm = mf.make_rdm1()
wfn_file = name + '.wfn'
with open(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, mol, mf.mo_coeff[:,mf.mo_occ>0], \
mo_occ=mf.mo_occ[mf.mo_occ>0], mo_energy=mf.mo_energy[mf.mo_occ>0])
f2.write('%i %i %.16f\n' % (i, j, rdm1[i,j]))
#
rdm2_xc = numpy.zeros((nmo,nmo,nmo,nmo))
for i in range(nmo):
for j in range(nmo):
rdm2_xc[i,j,j,i] -= 2
x, y, z, w = rdm2_xc.nonzero()
nonzero = zip(x,y,z,w)
ifile = name + '.rdm2_xc'
with open(ifile, 'w') as f2:
for i, j, k, l in nonzero:
f2.write('%i %i %i %i %.16f\n' % (i, j, k, l, rdm2_xc[i,j,k,l]))
wfn_file = name + '.wfn'
with open(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, mol, coeff, occ)
##############################################################################
s = mol.intor('cint1e_ovlp_sph')
s = reduce(numpy.dot, (coeff.T,s,coeff))
x, y = s.nonzero()
nonzero = zip(x,y)
ifile = name + '.overlap'
with open(ifile, 'w') as f2:
for i, j in nonzero:
f2.write('%i %i %.16f\n' % (i, j, s[i,j]))
#
t = mol.intor('cint1e_kin_sph')
t = reduce(numpy.dot, (coeff.T,t,coeff))
x, y = t.nonzero()
nonzero = zip(x,y)
10] # Tune PWs in MDF for performance/accuracy balance
mf = scf.addons.remove_linear_dep_(mf)
mf.kernel()
wfn_file = name + '.wfn'
fspt = open(wfn_file, 'w')
coeff = mf.mo_coeff[:, mf.mo_occ > 0]
occ = mf.mo_occ[mf.mo_occ > 0]
energy = mf.mo_energy[mf.mo_occ > 0]
a = cell.a
t = cell.get_lattice_Ls()
t = t[numpy.argsort(lib.norm(t, axis=1))]
kpts = numpy.asarray([0.0, 0.0, 0.0])
#expLk = numpy.exp(1j * numpy.asarray(numpy.dot(t, kpts.T), order='C'))
wfn_format.write_mo(fspt, cell, coeff, mo_energy=energy, mo_occ=occ)
fspt.write('CRYSTAL\n')
fspt.write('CELL\n')
fspt.write(' %11.8f %11.8f %11.8f\n' % (a[0][0], a[0][1], a[0][2]))
fspt.write(' %11.8f %11.8f %11.8f\n' % (a[1][0], a[1][1], a[1][2]))
fspt.write(' %11.8f %11.8f %11.8f\n' % (a[2][0], a[2][1], a[2][2]))
fspt.write('N-KPOINTS 1\n')
fspt.write(' %11.8f %11.8f %11.8f\n' % (kpts[0], kpts[1], kpts[2]))
fspt.write('T-VECTORS %3d\n' % len(t))
for i in range(len(t)):
fspt.write(' %11.8f %11.8f %11.8f\n' % (t[i][0], t[i][1], t[i][2]))
fspt.close()
dm = mf.make_rdm1()
s = cell.pbc_intor('int1e_ovlp')
def run(uparam, tparam):
s = overlap(nsites)
h1 = hop(tparam, nsites, pbc)
eri = onsite(uparam, nsites)
mol = gto.Mole()
mol.nelectron = nelectrons
mol.verbose = 0
mol.spin = spin
mol.symmetry = 0
mol.charge = 0
mol.incore_anyway = True
mol.build()
mf = scf.RHF(mol)
mf = scf.addons.frac_occ(mf)
mf.verbose = 0
mf.conv_tol = 1e-8
mf.max_cycle = 150
mf.diis = True
mf.diis_space = 12
mf.get_hcore = lambda *args: h1
mf.get_ovlp = lambda *args: s
mf._eri = ao2mo.restore(8, eri, nsites)
mf.kernel()
mc = mcscf.CASCI(mf, nsites, nelectrons)
mc.verbose = 4
efci = mc.kernel()[0]
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,
nsites)
fs.write('%.7f %.7f ' % (-1.0 * uparam / tparam, efci))
wfn_file = 'h4_%.4f.wfn' % (-1.0 * uparam / tparam)
aom_file = 'h4_%.4f.wfn.aom' % (-1.0 * uparam / tparam)
edf_file = 'h4_%.4f.edf' % (-1.0 * uparam / tparam)
den2_file = 'h4_%.4f_2.den' % (-1.0 * uparam / tparam)
den4_file = 'h4_%.4f_4.den' % (-1.0 * uparam / tparam)
atms = []
atms.append(('H', 0.0, 1.0, 0.0))
atms.append(('H', 1.0, 1.0, 0.0))
atms.append(('H', 1.0, 0.0, 0.0))
atms.append(('H', 0.0, 0.0, 0.0))
mol = gto.Mole()
mol.nelectron = nelectrons
mol.verbose = 0
mol.spin = spin
mol.symmetry = 0
mol.charge = 0
mol.basis = 'sto-1g'
mol.atom = atms
mol.build()
nmo = mc.ncore + mc.ncas
natocc, natorb = numpy.linalg.eigh(-rdm1)
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(wfn_file, 'w') as f2:
wfn_format.write_mo(f2, mol, natorb, mo_occ=natocc)
wfn_format.write_coeff(f2, mol, mc.mo_coeff[:, :nmo])
wfn_format.write_ci_hubbard(f2,
mc.ci,
mc.ncas,
mc.nelecas,
ncore=mc.ncore)
with open(edf_file, 'w') as f2:
f2.write('0\n')
f2.write('%s\n' % (aom_file))
f2.write('%s\n' % (wfn_file))
f2.write('norecur\n')
f2.write('probcut 1d-3\n')
f2.write('ngroup 4\n')
f2.write('1 1\n')
f2.write('1 2\n')
f2.write('1 3\n')
f2.write('1 4\n')
f2.write('end\n')
with open(den2_file, 'w') as f2:
f2.write('0\n')
f2.write('%s\n' % (aom_file))
f2.write('%s\n' % (wfn_file))
f2.write('ngroup 2\n')
f2.write('1\n')
f2.write('2\n')
f2.write('end\n')
with open(den4_file, 'w') as f2:
f2.write('0\n')
f2.write('%s\n' % (aom_file))
f2.write('%s\n' % (wfn_file))
f2.write('ngroup 4\n')
f2.write('1\n')
f2.write('2\n')
f2.write('3\n')
f2.write('4\n')
f2.write('end\n')
with open(aom_file, 'w') as f2:
for k in range(nsites): # Over atoms == over primitives
f2.write("%5d <=== AOM within this center\n" % (k + 1))
ij = 0
for i in range(nsites):
for j in range(i + 1):
f2.write(' %16.10f' %
(mc.mo_coeff[k, i] * mc.mo_coeff[k, j]))
ij += 1
if (ij % 6 == 0):
f2.write("\n")
f2.write("\n")
rdm2 = rdm2 - numpy.einsum('ij,kl->ijkl', rdm1, rdm1)
rdm1 = reduce(numpy.dot, (mc.mo_coeff, rdm1, mc.mo_coeff.T))
rdm2 = numpy.dot(mc.mo_coeff, rdm2.reshape(nsites, -1))
rdm2 = numpy.dot(rdm2.reshape(-1, nsites), mc.mo_coeff.T)
rdm2 = rdm2.reshape(nsites, nsites, nsites, nsites).transpose(2, 3, 0, 1)
rdm2 = numpy.dot(mc.mo_coeff, rdm2.reshape(nsites, -1))
rdm2 = numpy.dot(rdm2.reshape(-1, nsites), mc.mo_coeff.T)
rdm2 = rdm2.reshape(nsites, nsites, nsites, nsites)
rdm2 = -rdm2
pairs2 = numpy.einsum('ijkl,ij,kl->ik', rdm2, s, s,
optimize=True) * 0.5 # XC
ia = 3
for ib in range(ia + 1):
if (ia == ib):
factor = 1.0
if (ia != ib):
factor = 2.0
fs.write('%.7f ' % (2 * factor * pairs2[ia, ib]))
fs.write('\n')
dm_u = mf.make_rdm1(mo0, occ)
# Apply mom occupation principle
mf = scf.addons.mom_occ(mf, mo0, occ)
# Start new SCF with new density matrix
mf.scf(dm_u)
coeffa = mf.mo_coeff[0][:,mf.mo_occ[0]>0]
energya = mf.mo_energy[0][mf.mo_occ[0]>0]
occa = mf.mo_occ[0][mf.mo_occ[0]>0]
coeffb = mf.mo_coeff[1][:,mf.mo_occ[1]>0]
energyb = mf.mo_energy[1][mf.mo_occ[1]>0]
occb = mf.mo_occ[1][mf.mo_occ[1]>0]
with open(name+'.wfn', 'w') as f2:
wfn_format.write_mo(f2, mol, coeffa, mo_energy=energya, mo_occ=occa)
wfn_format.write_mo(f2, mol, coeffb, mo_energy=energyb, mo_occ=occb)
norb = mf.mo_energy[0].size
nmoa = energya.size
nmob = energyb.size
rdm1a = numpy.zeros((nmoa,nmoa))
rdm1b = numpy.zeros((nmob,nmob))
rdm2a = numpy.zeros((nmoa,nmoa,nmoa,nmoa))
rdm2b = numpy.zeros((nmob,nmob,nmob,nmob))
rdm2ab = numpy.zeros((nmoa,nmoa,nmob,nmob))
rdm2ba = numpy.zeros((nmob,nmob,nmoa,nmoa))
for i in range(energya.size):
