#Find the O 2s labels
if (('2s' in x) and ('O' in x)):
O_2s_orbitals.append(i)
#Find the O 2p labels
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:
# ''' DF-MP2 natural orbitals for the allyl radical ''' from pyscf.gto import Mole from pyscf.scf import UHF from pyscf.tools import molden from pyscf.mp.dfump2_native import DFMP2 mol = Mole() mol.atom = ''' C -1.1528 -0.1151 -0.4645 C 0.2300 -0.1171 -0.3508 C 0.9378 0.2246 0.7924 H 0.4206 0.5272 1.7055 H 2.0270 0.2021 0.8159 H -1.6484 -0.3950 -1.3937 H -1.7866 0.1687 0.3784 H 0.8086 -0.4120 -1.2337 ''' mol.basis = 'def2-TZVP' mol.spin = 1 mol.build() mf = UHF(mol).run() # MP2 natural occupation numbers and natural orbitals natocc, natorb = DFMP2(mf).make_natorbs() # store the natural orbitals in a molden file molden.from_mo(mol, 'allyl_mp2nat.molden', natorb, occ=natocc)
#Various analyses
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
charge = 0
for name in ['4Phi', '4Delta', '2Delta', '4SigmaM']:
mol_spin = int(name[0]) - 1
for r in [1.963925]:
for method in ['B3LYP']:
for basis in ['vtz']:
for el in ['Cu']:
for charge in [0]:
chkfile = "../full_chk/" + el + basis + "_r" + str(
r) + "_c" + str(charge) + "_s" + str(
mol_spin) + "_" + method + "_" + name + ".chk"
mol = lib.chkfile.load_mol(chkfile)
if ("U" in method): m = UHF(mol)
else: m = ROHF(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
#Generate files for plotting orbitals in ../orbs
#print_qwalk_mol(mol,m,basename="../full_orbs/"+el+basis+"_r"+str(r)+"_c"+str(charge)+"_s"+str(mol_spin)+"_"+method+"_"+name)
for el in ['Cu']:
molname=el+'O'
mol=gto.Mole()
mol.ecp={}
mol.basis={}
for e in [el,'O']:
mol.ecp[e]=gto.basis.parse_ecp(df[e]['ecp'])
mol.basis[e]=gto.basis.parse(df[e][basis])
mol.charge=charge
mol.spin=S
mol.build(atom="%s 0. 0. 0.; O 0. 0. %g"%(el,r),verbose=4,symmetry=True)
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
if basis=='vdz':
#m=m.newton()
m.chkfile=el+basis+"_r"+str(r)+"_s"+str(S)+"_"+method+"_"+str(run)+"mirror.chk"
m.irrep_nelec = symm_dict[run]
m.max_cycle=100
#Gather IAOs
f = 'b3lyp_iao_b.pickle'
a = np.load(f)
print(a.shape)
for mol_spin in [1]:
for r in [1.963925]:
for method in ['B3LYP']:
for basis in ['vtz']:
for el in ['Cu']:
for charge in [0]:
chkfile = "../chkfiles/" + el + basis + "_r" + str(
r) + "_c" + str(charge) + "_s" + str(
mol_spin) + "_" + method + ".chk"
mol = lib.chkfile.load_mol(chkfile)
if ("U" in method): m = UHF(mol)
else: m = ROHF(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
#Highest 3 MOs transformed into IAO basis
s = m.get_ovlp()
act = np.zeros(s.shape[1])
act[10:14] = 1
H1 = np.diag(act * m.mo_energy)
e1 = reduce(np.dot, (a.T, s, m.mo_coeff, H1,
m.mo_coeff.T, s.T, a)) * 27.2114
e1 = (e1 + e1.T) / 2.
labels = [
"3s", "4s", "3px", "3py", "3pz", "3dxy", "3dyz",
"3dz2", "3dxz", "3dx2y2", "2s", "2px", "2py", "2pz"
def init_density(self,
in_dmat=None,
scf_obj=None,
env_method=None,
kpts=None):
"""
Initializes the periodic subsystem density
Parameters
----------
in_dmat : ndarray, optional
New subsystem density matrix (default is None).
scf_obj : pyscf:pbc:scf object, optional
The PySCF subsystem object (default is None).
env_method : str, optional
Subsystem environment energy method (default is None).
kpts : ndarray, optional
Kpoints to use in calculation (default is None).
Returns
-------
dmat : ndarray
The new / guessed density matrix
"""
import numpy as np
import pyscf
from pyscf.scf import RKS, RHF, ROKS, ROHF, UKS, UHF
if in_dmat is not None:
return in_dmat
if scf_obj is None: scf_obj = self.env_scf
if env_method is None: env_method = self.env_method
if kpts is None: kpts = self.kpts
nkpts = len(kpts)
nao = scf_obj.cell.nao_nr()
dmat = np.zeros((2, nkpts, nao, nao))
mol = scf_obj.cell.to_mol()
mol.verbose = 0
if self.unrestricted:
if env_method in ('hf', 'hartree-fock'):
mf = UHF(mol)
else:
mf = UKS(mol)
mf.xc = env_method
mf.kernel()
dtemp = mf.make_rdm1()
elif mol.spin != 0:
if env_method in ('hf', 'hartree-fock'):
mf = ROHF(mol)
else:
mf = ROKS(mol)
mf.xc = env_method
mf.kernel()
dtemp = mf.make_rdm1()
else:
if env_method in ('hf', 'hartree-fock'):
mf = RHF(mol)
else:
mf = RKS(mol)
mf.xc = env_method
mf.kernel()
dtemp = mf.make_rdm1() / 2.0
dtemp = [dtemp, dtemp]
for k in range(nkpts):
dmat[0, k] = dtemp[0]
dmat[1, k] = dtemp[0]
return dmat
#Find the O 2s labels
if (('2s' in x) and ('O' in x)):
O_2s_orbitals.append(i)
#Find the O 2p labels
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: