# 4-particle density matrix is explicitly computed. # Ref: S Guo, JCTC, ASAP # ################################################## # # Call mol.build function to redirect the output to another file. # mol.build(output='dmrg_nevpt2_slow.out') mc = mcscf.CASCI(m, 4, 4) # # Use DMRGCI as the active space solver. DMRGCI solver allows us to handle # ~ 50 active orbitals. # mc.fcisolver = dmrgscf.DMRGCI(mol, maxM=200) mc.fcisolver.nroots = 2 # # Passing mc_orb to CASCI kernel function so that the CASCI calculation is # carried out with the given orbitals. More examples refers to # pyscf/mcscf/62-make_init_guess # mc.kernel(mc_orb) # # The default DMRG-SC-NEVPT2 implementation is based on the 4-particle density matrix. # dmrg_nevpt_e1 = mrpt.NEVPT(mc, root=0).kernel() dmrg_nevpt_e2 = mrpt.NEVPT(mc, root=1).kernel() ##################################################
def test_mc2step_4o4e(self):
mc = mcscf.CASSCF(m, 4, 4)
mc.fcisolver = dmrgscf.DMRGCI(mol)
emc = mc.mc2step()[0]
self.assertAlmostEqual(emc, -108.913786407955, 7)
def kernel(self):
mol = self.mol
output = mol.output
fpre = output[:output.rfind('_')]
nobt, nocc = self.nobt, self.nocc
# lowTri = [0]*nobt
# for i in range(1, nobt): lowTri[i] = lowTri[i-1]+i
# pub.lowTri=lowTri; gvb.rgvb.i_lowTri=lowTri
pub.lT0 = pub.lowTri0(nobt)
nc = self.nc
nt, np = self.nt, self.np
thd, ncyc, xE = self.thd, self.ncyc, self.xE
# mo integral and repressive matrix
print('get mo integral and repressive matrix')
datfile = F'{fpre}_gvb_init.dat'
fchkfile = F'{datfile}.fchk'
from pyscf import scf, ao2mo
hcore = scf.hf.get_hcore(mol)
eri = mol.intor('int2e', aosym='s8')
#onp=18; gvbfile=F'{fpre}_gvb{onp}.out' # reload CI
#with open(gvbfile, 'r') as input:
# linel=input.readlines()
# linel=linel[pub.iis('GVB CI:\n', linel)+1:]
# linel=linel[:pub.iis('\n', linel)]
# from re import findall
# for p in range(self.np):
# p1=-p-1
# sl = findall(r"[-+]?\d+\.?\d*[eE]?[-+]?\d*", linel[p1].strip('\r\n'))
# self.ci[p1] = [float(sl[1]), float(sl[3])]
# print(F'{self.p[p1, 0] + 1:2d}({self.ci[p1, 0]:6f}) <-> {self.p[p1, 1] + 1:2d}({self.ci[p1, 1]:6f})')
#from gvb.rgvb import load_mo # reload mo
#load_mo(self, F'{fpre}_gvb{onp}.fchk')
obts = self.mo_coeff
self.h = reduce(numpy.dot, (obts.T, hcore, obts))
self.g = ao2mo.kernel(eri, obts)
from bccc.rep import rep
# from bcpt2 import gvbpt2
# ael_pt2, mcl_pt2 = gvbpt2.gvb_bcpt2(mol, datfile, fchkfile, fixed_core=nc)
# print(F'mcl_pt2.shape = {mcl_pt2.shape}')
nbs = 16
rl = [None] * nocc
# print( 'mcl = ')
for P in range(nocc):
# ael[P] = numpy.zeros(nbs)
# if nc<=P:
# ael[P][:15] = ael_pt2[P-nc]
# ael[P][:] = ael[P][[4, 5, 6, 7, 8, 9, 15, 0, 1, 2, 3, 10, 11, 12, 13, 14]]
# # mc = numpy.zeros(shape=(nbs, nbs))
# # mc[:15, :15] = mcl_pt2[P]; mc[15][15] = 1.
# # mc[:,:] = mc[[4, 5, 6, 7, 8, 9, 15, 0, 1, 2, 3, 10, 11, 12, 13, 14], :]
# # mc[:,:] = mc[:, [4, 6, 7, 5, 8, 9, 15, 0, 1, 2, 3, 10, 11, 12, 13, 14]]
# # mcl[P] = mc
# # rl[P] = mrfeqd(mc)
mc1 = numpy.identity(nbs)
if nc <= P:
# self.ci[P] = mcl_pt2[P-nc][4][4:6]
# mc1[0,0:2] = [mcl_pt2[P-nc][4,4], mcl_pt2[P-nc][4,5]]
mc1[0, 0:2] = self.ci[P]
mc1[1, 0:2] = [-mc1[0, 1], mc1[0, 0]]
a = 1 / math.sqrt(2.)
mc1[2, 2:4] = [a, -a]
mc1[3, 2:4] = [a, a]
# print(F'P = {P}')
# print(F' 0: {mc1[0][:4]}')
# print(F' 1: {mc1[1][:4]}')
# print(F' 2: {mc1[2][:4]}')
# print(F' 3: {mc1[3][:4]}')
# print(F' 7: {mc1[7][7:9]}')
# print(F' 8: {mc1[8][7:9]}')
# print(F' 9: {mc1[9][9:11]}')
# print(F' 10: {mc1[10][9:11]}')
# print(F' 11: {mc1[11][11:13]}')
# print(F' 12: {mc1[12][11:13]}')
# print(F' 13: {mc1[13][13:15]}')
# print(F' 14: {mc1[14][13:15]}')
rl[P] = rep(mc1)
print('\n\n\n\n')
# check GVB energy
print('check GVB energy')
from bcpt2.read_pair import read_eng_dat
E_gvb, e_nuc = read_eng_dat(datfile)
print(F'e_nuc = {e_nuc}')
print(F'E(GVB) = {E_gvb:.10f} (.dat)')
mf = self.ref
mf.h_mo, mf.g_mo = self.h, self.g
gvb.rgvb.lT0 = pub.lT0
mf.e_ele = mf.energy_elec()
E_gvb = mf.e_nuc + mf.e_ele
print(F'E(GVB) = {E_gvb:.10f} (Ref.)')
from bccc.hm.hm_ import hm_
h0d = hm_(rl, self.h, self.g, self.p, nc)[()]
# h0d = hm_(rl, self)[()]
E_gvb = self.e_nuc + h0d[()]
print(F'E(GVB) = {E_gvb:.10f}')
print('\n\n\n\n')
# BCPT2
print('check GVB-BCPT2 energy')
from bcpt2 import gvbpt2
ael_pt2, E_bcpt2 = gvbpt2.gvb_bcpt2(mol,
datfile,
fchkfile,
fixed_core=nc,
fixed_virt=self.nvir - self.np)
ael = [None] * nocc
for P in range(nocc):
ael[P] = numpy.zeros(nbs)
if nc <= P:
ael[P][:15] = ael_pt2[P - nc]
ael[P][:] = ael[P][[
4, 5, 6, 7, 8, 9, 15, 0, 1, 2, 3, 10, 11, 12, 13, 14
]]
print(F'E(GVB-BCPT2) = {E_bcpt2:.10f} (Ref.)')
from bccc.pub import bcpt2
corr_bcpt2 = bcpt2(ael, h0d)
print(F'corr(GVB-BCPT2) = {corr_bcpt2}')
E_bcpt2 = E_gvb + corr_bcpt2
print(F'E(GVB-BCPT2) = {E_bcpt2}')
print('\n\n\n\n')
# check FCI/MCSCF/DMRG
print('check FCI/MCSCF/DMRG', flush=True)
# from bccc.hm1.hm import hm
# print('From hm1')
#from bccc.hm.hm import hm
#t1 = datetime.datetime.now()
#mh = hm(rl, self.h, self.g, self.p, self.nt, nc)
#t2 = datetime.datetime.now()
#print(F'calculate H matrix {t2-t1}')
#nu=len(mh); id={u: i for i, u in enumerate(mh.keys())}
#mH = numpy.zeros(shape=(nu, nu))
#for bra,i in id.items():
# # print(F'bra = {bra}')
# for ket,j in id.items():
# mH[i,j] = mh[bra].get(ket, 0.0)
# # if abs(mH[i,j])>1.0e-6: print(F' ket = {ket}: {mH[i,j]}')
#eig,v = numpy.linalg.eigh(mH)
## print(F'eig = {eig}')
#E_fci = self.e_nuc+eig[0]
#print(F'E(FCI) = {E_fci}')
hf = scf.RHF(self.mol)
hf.max_cycle = 1
hf.kernel()
# gvb.rgvb.load_mo(hf, fchkfile)
# hf.mo_coeff[:,nc:nocc+np] = self.mo_coeff[:, list(range(nc, 2*nocc-nc, 2))+list(range(2*nocc-1-nc, nc, -2))]
hf.mo_coeff = self.mo_coeff
# FCI
# from pyscf import fci
# mc = fci.FCI(hf)
# mc.kernel()
# CASCI
from pyscf import mcscf
mc = mcscf.CASCI(hf, 2 * np, 2 * np, ncore=nc)
#mc.fcisolver.nroots = nu
mc.fcisolver.memory = 30 # GB
#e_fci,eig_fci,*_ = mc.kernel()
## print(F'eig_fci = {eig_fci}')
#E_fci = e_fci[0]
#print(F'E(FCI) = {E_fci} (Ref.)')
# CASSCF
# mc = mcscf.CASSCF(hf, 2*np, 2*np, ncore=nc)
mc.fix_spin_(ss=0.0)
mc.fcisolver.level_shift = 0.2
mc.fcisolver.pspace_size = 1200
if np > 6: # DMRG
from pyscf import dmrgscf
mc.fcisolver = dmrgscf.DMRGCI(mol, maxM=1000)
mc.fcisolver.block_extra_keyword = ['memory, 30, g']
mc.kernel()
#err = [abs(a-b) for a,b in zip(eig, eig_fci)]
#emax = max(err)
#print(F'max error = {emax}')
#emean = sum(err)/nu
#print(F'mean error = {emean}')
print('\n\n\n\n')
# initilize t
print('initialize t')
# from bccc.init import init
# t0 = init(nocc)
from bccc.hm.hm import hm
t1 = datetime.datetime.now()
mh = hm(rl, self.h, self.g, self.p, self.nt, nc)
# mh = hm(rl, self)
t2 = datetime.datetime.now()
print(F'calculate H matrix {t2-t1}')
from bccc.pub import bclcc
corr_bclcc, t0 = bclcc(nocc, mh, nt, nc)
print(F'corr(GVB-BCLCC{nt}) = {corr_bclcc}')
E_bclcc = E_gvb + corr_bclcc
print(F'E(GVB-BCLCC{nt}) = {E_bclcc}')
import gc
del mh
gc.collect()
#t0 = ddict(float)
#finit='C4H10_4_6-31g_bccc2b.out'
#print(F'finit = {finit}')
#with open(finit, 'r') as input:
# linel=input.readlines()
# linel=linel[pub.iis('t(final) =\n', linel)+1:]
# linel=linel[:pub.iis('\n', linel)]
# from re import findall
# for line in linel:
# sl = findall(r"[-+]?\d+\.?\d*[eE]?[-+]?\d*", line.strip('\r\n'))
# t0[tuple((int(sl[i]), int(sl[i+1])) for i in range(0,len(sl)-1,2))] = float(sl[-1])
#print('t(initial) =')
#for u,tu in t0.items():
# if abs(tu)>1.0e-6: print(F'u,tu = {u},{tu}')
print('\n\n\n\n')
# GVB-BCCC
print('calculate GVB-BCCC energy')
# from bccc.ta1.ta import ta
# print('From ta1')
from bccc.iter import iter
# corr_bccc,t = ta(t0, mh, self.p, nt, nc)
corr_bccc, t = iter(t0, rl, self.h, self.g, self.p, nt, nc, thd, ncyc,
xE)
print(F'corr(GVB-BCCC{nt}) = {corr_bccc}')
E_bccc = E_gvb + corr_bccc
print(F'E(GVB-BCCC{nt}) = {E_bccc}')
print('t(final) =')
for u, tu in t.items():
if abs(tu) > 1.0e-6: print(F'u,tu = {u},{tu}')
print('\n\n\n\n')
['H', (1.435682, 2.309097, 0.0)],
['H', (1.435682, -0.163698, 0.0)],
['H', (-0.705820, -1.400095, 0.0)],
['H', (-2.847323, -0.163698, 0.0)],
['H', (-2.847323, 2.309097, 0.0)]],
basis=basisName,
output=outputName,
max_memory=16000)
# Hartree-Fock calculation
mf = scf.RHF(mol)
mf.kernel()
mf.analyze()
# Get active space for CASSCF calculation
n_orb_active_space, nelec_act_space, new_all_orbs = avas.kernel(mf, 'C 2pz')
# CASSCF
mc = dmrgscf.DMRGSCF(mf, n_orb_active_space, nelec_act_space)
mc.state_specific_(state=1)
mc.fcisolver.maxM = 500
mc.kernel(new_all_orbs)
mc_orbs = mc.mo_coeff
# CASCI
mc = mcscf.CASCI(mf, n_orb_active_space, nelec_act_space)
mc.fcisolver = dmrgscf.DMRGCI(mol)
mc.fcisolver.maxM = 1200
mc.fcisolver.nroots = 2
mc.kernel(mc_orbs)
# NEVPT2 correction
mps_nevpt_e2 = mrpt.NEVPT(mc, root=1).compress_approx(maxM=1200).kernel()
mc.analyze()
os.system('date > endTime')
def CAS(self, CAS, CAS_MO, Orbital_optimization = False, solver = 'FCI'):
'''
CASSCF with FCI or DMRG solver from BLOCK or CheMPS2
'''
Norb = self.Norb
Nimp = self.Nimp
FOCK = self.FOCK.copy()
if (self.chempot != 0.0):
for orb in range(Nimp):
FOCK[orb, orb] -= self.chempot
mol = gto.Mole()
mol.build(verbose = 0)
mol.atom.append(('C', (0, 0, 0)))
mol.nelectron = self.Nel
mol.incore_anyway = True
mf = scf.RHF( mol )
mf.get_hcore = lambda *args: FOCK
mf.get_ovlp = lambda *args: np.eye(Norb)
mf._eri = ao2mo.restore(8, self.TEI, Norb)
mf.scf(self.DMguess)
DMloc = np.dot(np.dot(mf.mo_coeff, np.diag(mf.mo_occ)), mf.mo_coeff.T)
if ( mf.converged == False ):
mf = rhf_newtonraphson.solve( mf, dm_guess=DMloc)
DMloc = np.dot(np.dot(mf.mo_coeff, np.diag(mf.mo_occ)), mf.mo_coeff.T)
if CAS == None:
CAS_nelec = self.Nel
CAS_norb = Norb
CAS = 'full'
else:
CAS_nelec = CAS[0]
CAS_norb = CAS[1]
print(" Active space: ", CAS)
# Replace FCI solver by DMRG solver in CheMPS2 or BLOCK
if Orbital_optimization == True:
mc = mcscf.CASSCF(mf, CAS_norb, CAS_nelec)
else:
mc = mcscf.CASCI(mf, CAS_norb, CAS_nelec)
if solver == 'CheMPS2':
mc.fcisolver = dmrgscf.CheMPS2(mol)
elif solver == 'Block':
mc.fcisolver = dmrgscf.DMRGCI(mol)
if CAS_MO is not None:
print(" Active space MOs: ", CAS_MO)
mo = mc.sort_mo(CAS_MO)
ECAS = mc.kernel(mo)[0]
else:
ECAS = mc.kernel()[0]
###### Get RDM1 + RDM2 #####
CAS_norb = mc.ncas
core_norb = mc.ncore
CAS_nelec = mc.nelecas
core_MO = mc.mo_coeff[:,:core_norb]
CAS_MO = mc.mo_coeff[:,core_norb:core_norb+CAS_norb]
casdm1 = mc.fcisolver.make_rdm12(mc.ci, CAS_norb, CAS_nelec)[0] #in CAS space
# Transform the casdm1 (in CAS space) to casdm1ortho (orthonormal space).
casdm1ortho = np.einsum('ap,pq->aq', CAS_MO, casdm1)
casdm1ortho = np.einsum('bq,aq->ab', CAS_MO, casdm1ortho)
coredm1 = np.dot(core_MO, core_MO.T) * 2 #in localized space
RDM1 = coredm1 + casdm1ortho
casdm2 = mc.fcisolver.make_rdm12(mc.ci, CAS_norb, CAS_nelec)[1] #in CAS space
# Transform the casdm2 (in CAS space) to casdm2ortho (orthonormal space).
casdm2ortho = np.einsum('ap,pqrs->aqrs', CAS_MO, casdm2)
casdm2ortho = np.einsum('bq,aqrs->abrs', CAS_MO, casdm2ortho)
casdm2ortho = np.einsum('cr,abrs->abcs', CAS_MO, casdm2ortho)
casdm2ortho = np.einsum('ds,abcs->abcd', CAS_MO, casdm2ortho)
coredm2 = np.zeros([Norb, Norb, Norb, Norb]) #in AO
coredm2 += np.einsum('pq,rs-> pqrs',coredm1,coredm1)
coredm2 -= 0.5*np.einsum('ps,rq-> pqrs',coredm1,coredm1)
effdm2 = np.zeros([Norb, Norb, Norb, Norb]) #in AO
effdm2 += 2*np.einsum('pq,rs-> pqrs',casdm1ortho,coredm1)
effdm2 -= np.einsum('ps,rq-> pqrs',casdm1ortho,coredm1)
RDM2 = coredm2 + casdm2ortho + effdm2
ImpurityEnergy = 0.50 * np.einsum('ij,ij->', RDM1[:Nimp,:], FOCK[:Nimp,:] + self.OEI[:Nimp,:]) \
+ 0.125 * np.einsum('ijkl,ijkl->', RDM2[:Nimp,:,:,:], self.TEI[:Nimp,:,:,:]) \
+ 0.125 * np.einsum('ijkl,ijkl->', RDM2[:,:Nimp,:,:], self.TEI[:,:Nimp,:,:]) \
+ 0.125 * np.einsum('ijkl,ijkl->', RDM2[:,:,:Nimp,:], self.TEI[:,:,:Nimp,:]) \
+ 0.125 * np.einsum('ijkl,ijkl->', RDM2[:,:,:,:Nimp], self.TEI[:,:,:,:Nimp])
return (ImpurityEnergy, ECAS, RDM1)
def kernel(self):
mol = self.mol
output = mol.output
fpre = output[:output.rfind('_')]
nobt, nocc = self.nobt, self.nocc
pub.lT0 = pub.lowTri0(nobt)
nc = self.nc
nt, np = self.nt, self.np
thd, ncyc, xE = self.thd, self.ncyc, self.xE
# mo integral and repressive matrix
print('get mo integral and repressive matrix')
datfile = F'{fpre}_gvb_init.dat'
fchkfile = F'{datfile}.fchk'
from pyscf import scf, ao2mo
hcore = scf.hf.get_hcore(mol)
eri = mol.intor('int2e', aosym='s8')
obts = self.mo_coeff[:, :nobt]
self.h = reduce(numpy.dot, (obts.T, hcore, obts))
self.g = ao2mo.kernel(eri, obts)
from bccc.rep import rep
r = [None] * nocc
for P in range(nocc):
mc = numpy.identity(16)
if nc <= P:
mc[0, 0:2] = self.ci[P]
mc[1, 0:2] = [-mc[0, 1], mc[0, 0]]
a = 1 / math.sqrt(2.)
mc[2, 2:4] = [a, -a]
mc[3, 2:4] = [a, a]
r[P] = rep(mc)
self.r = r
print('\n\n\n\n')
# check GVB energy
print('check GVB energy')
from bcpt2.read_pair import read_eng_dat
E_gvb, e_nuc = read_eng_dat(datfile)
print(F'e_nuc = {e_nuc}')
print(F'E(GVB) = {E_gvb:.10f} (.dat)')
mf = self.ref
mf.h_mo, mf.g_mo = self.h, self.g
gvb.rgvb.lT0 = pub.lT0
mf.e_ele = mf.energy_elec()
E_gvb = mf.e_nuc + mf.e_ele
print(F'E(GVB) = {E_gvb:.10f} (Ref.)')
from bccc.hm.hm_ import hm_
h0d = hm_(r, self.h, self.g, self.p, nc)[()]
# h0d = hm_(self)[()]
E_gvb = self.e_nuc + h0d[()]
print(F'E(GVB) = {E_gvb:.10f}')
print('\n\n\n\n')
# BCPT2
print('check GVB-BCPT2 energy')
from bcpt2 import gvbpt2
ael_pt2, E_bcpt2 = gvbpt2.gvb_bcpt2(mol,
datfile,
fchkfile,
fixed_core=nc,
fixed_virt=self.nvir - self.np)
ael = [None] * nocc
for P in range(nocc):
ael[P] = numpy.zeros(16)
if nc <= P:
ael[P][:15] = ael_pt2[P - nc]
ael[P][:] = ael[P][[
4, 5, 6, 7, 8, 9, 15, 0, 1, 2, 3, 10, 11, 12, 13, 14
]]
print(F'E(GVB-BCPT2) = {E_bcpt2:.10f} (Ref.)')
from bccc.pub import bcpt2
corr_bcpt2 = bcpt2(ael, h0d)
print(F'corr(GVB-BCPT2) = {corr_bcpt2}')
E_bcpt2 = E_gvb + corr_bcpt2
print(F'E(GVB-BCPT2) = {E_bcpt2}')
print('\n\n\n\n')
# check FCI/MCSCF/DMRG
print('check FCI/MCSCF/DMRG', flush=True)
hf = scf.RHF(self.mol)
hf.max_cycle = 1
hf.kernel()
hf.mo_coeff = self.mo_coeff
from pyscf import mcscf
mc = mcscf.CASCI(hf, 2 * np, 2 * np, ncore=nc)
#mc.fcisolver.nroots = nu
mc.fcisolver.memory = 30 # GB
mc.fix_spin_(ss=0.0)
#mc.fcisolver.level_shift = 0.2
#mc.fcisolver.pspace_size = 1200
if np > 6: # DMRG
from pyscf import dmrgscf
mc.fcisolver = dmrgscf.DMRGCI(mol, maxM=1000)
mc.fcisolver.block_extra_keyword = ['memory, 30, g']
#mc.kernel()
print('\n\n\n\n')
# initilize t
print('initialize t')
t = self.t
if t is None:
print('t0 from GVB-LBCCC')
from bccc.hm.hm import hm
t1 = datetime.datetime.now()
mh = hm(r, self.h, self.g, self.p, nt, nc)
# mh = hm(self)
t2 = datetime.datetime.now()
print(F'calculate H matrix {t2-t1}')
from bccc.pub import bclcc
corr_bclcc, t = bclcc(nocc, mh, nt, nc)
print(F'corr(GVB-BCLCC{nt}) = {corr_bclcc}')
E_bclcc = E_gvb + corr_bclcc
print(F'E(GVB-BCLCC{nt}) = {E_bclcc}')
import gc
del mh
gc.collect()
else:
finit = t # initial t0 file
print(F't0 from {finit}')
t = ddict(float)
with open(finit, 'r') as input:
linel = input.readlines()
linel = linel[pub.iis('t(final) =\n', linel) + 1:]
linel = linel[:pub.iis('\n', linel)]
from re import findall
for line in linel:
sl = findall(r"[-+]?\d+\.?\d*[eE]?[-+]?\d*",
line.strip('\r\n'))
t[tuple((int(sl[i]), int(sl[i + 1]))
for i in range(0,
len(sl) - 1, 2))] = float(sl[-1])
print('\n\n\n\n')
# GVB-BCCC
print('calculate GVB-BCCC energy')
# from bccc.ta1.ta import ta
# print('From ta1')
from bccc.iter import iter
# corr_bccc,t = ta(t, mh, self.p, nt, nc)
corr_bccc, t = iter(t, r, self.h, self.g, self.p, nt, nc, thd, ncyc,
xE)
print(F'corr(GVB-BCCC{nt}) = {corr_bccc}')
E_bccc = E_gvb + corr_bccc
print(F'E(GVB-BCCC{nt}) = {E_bccc}')
print('t(final) =')
for u, tu in t.items():
if abs(tu) > 1.0e-6: print(F'u,tu = {u},{tu}')
#print('t symmetry =')
#ul = list(t.keys()); ul_,nu_ = [],len(t)
#for i,u in enumerate(ul):
# if u not in ul_:
# tu=t[u]
# print(F'{u}: {tu}')
# ul_.append(u)
# tu_=abs(tu)
# for v in ul[i+1:]:
# if v not in ul_:
# tv=t[v]
# if abs(tu_-abs(tv))<1.0e-7:
# print(F'{v}: {tv}')
# ul_.append(v)
# print()
print('\n\n\n\n')