basis = 'vqz'
element = 'Mn'
mol = gto.Mole()
mol.ecp = {}
mol.basis = {}
for el in [element, 'O']:
mol.ecp[el] = gto.basis.parse_ecp(df[el]['ecp'])
mol.basis[el] = gto.basis.parse(df[el][basis])
mol.charge = 0
mol.spin = spins[element + 'O']
mol.build(atom="%s 0. 0. 0.; O 0. 0. %g" % (element, re[element + 'O']),
verbose=4)
m = ROHF(mol)
m.level_shift = 1000.0
dm = m.from_chk("../../../../HF/monoxides/" + element + basis + "0.chk")
hf = m.kernel(dm)
m.analyze()
from pyscf.shciscf import shci
mc = shci.SHCISCF(m, 9, 4 + cas[element])
#mc.fcisolver.conv_tol = 1e-14
mc.fcisolver.mpiprefix = "mpirun -np 28"
mc.fcisolver.num_thrds = 12
mc.verbose = 4
cas = mc.kernel()[0]
from pyscf.icmpspt import icmpspt
pt=icmpspt.icmpspt(mc,rdmM=500, PTM=1000,\
el = 'Mn'
charge = 0
mol = gto.Mole()
mol.ecp = {}
mol.basis = {}
mol.ecp[el] = gto.basis.parse_ecp(df[el]['ecp'])
mol.basis[el] = gto.basis.parse(df[el][basis])
mol.charge = charge
if el == 'Cr' or el == 'Cu':
mol.spin = spins[el] - charge
else:
mol.spin = spins[el] + charge
mol.build(atom="%s 0. 0. 0." % el, verbose=4)
m = ROHF(mol)
m.level_shift = 1000.0
dm = m.from_chk("../../../../HF/atoms/" + el + basis + str(charge) + ".chk")
hf = m.kernel(dm)
m.analyze()
from pyscf.shciscf import shci
mc = shci.SHCISCF(m, 6, cas[el] - charge)
#mc.fcisolver.conv_tol = 1e-14
mc.fcisolver.mpiprefix = "srun -n20"
mc.fcisolver.num_thrds = 12
mc.verbose = 4
cas = mc.kernel()[0]
from pyscf.icmpspt import icmpspt
pt=icmpspt.icmpspt(mc,rdmM=500, PTM=1000,\
if (('2p' in x) and ('O' in x)):
O_2p_orbitals.append(i)
#There should be 5 3d TM orbitals. Let's check this!
assert len(TM_3d_orbitals) == 5
##############################################################################################
if ("U" in method):
if ("HF" in method):
m = UHF(mol)
else:
m = UKS(mol)
m.xc = method[1:]
else:
if (method == "ROHF"):
m = ROHF(mol)
else:
m = ROKS(mol)
m.xc = method
##############################################################################################
dm = np.zeros(m.init_guess_by_minao().shape)
#The 3s is always doubly-occupied for the TM atom
for s in TM_3s_orbitals:
for spin in [0, 1]:
dm[spin, s, s] = 1
#The 4s is always at least singly-occupied for the TM atom
for s in TM_4s_orbitals:
dm[0, s, s] = 1
datacsv[nm] = []
basis = 'vqz'
el = 'O'
charge = 0
mol = gto.Mole()
mol.ecp = {}
mol.basis = {}
mol.ecp[el] = gto.basis.parse_ecp(df[el]['ecp'])
mol.basis[el] = gto.basis.parse(df[el][basis])
mol.charge = charge
mol.spin = 2
mol.build(atom="%s 0. 0. 0." % el, verbose=4)
m = ROHF(mol)
m.level_shift = 1000.0
#dm=m.from_chk("../../../../HF/atoms/"+el+basis+str(charge)+".chk")
hf = m.kernel() #dm)
m.analyze()
from pyscf.shciscf import shci
mc = shci.SHCISCF(m, 3, 4)
#mc.fcisolver.conv_tol = 1e-14
mc.fcisolver.mpiprefix = "srun -n20"
mc.fcisolver.num_thrds = 12
mc.verbose = 4
cas = mc.kernel()[0]
from pyscf.icmpspt import icmpspt
import json
from pyscf import lib, gto, scf, mcscf, fci, lo, ci, cc
from pyscf.scf import ROHF, UHF, ROKS
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pyscf2qwalk import print_qwalk_mol
from functools import reduce
#Gather optimized MOs
f = 'b3lyp_mo_symm.pickle'
a = np.load(f)
flist = [
'../chkfiles/Cuvtz_r1.963925_c0_s-1_B3LYP.chk',
'../chkfiles/Cuvtz_r1.963925_c0_s1_B3LYP.chk',
'../full_chk/Cuvtz_r1.963925_c0_s1_B3LYP_2Y.chk',
'../chkfiles/Cuvtz_r1.963925_c0_s3_B3LYP.chk'
]
for chkfile in flist:
mol = lib.chkfile.load_mol(chkfile)
m = ROHF(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
#Build MO RDMs
s = m.get_ovlp()
rho1 = np.diag(m.mo_occ)
M = reduce(np.dot, (a.T, s, m.mo_coeff))
dm = reduce(np.dot, (M, rho1, M.T))
print(dm.shape, np.trace(dm))