def new_gs(parms):
print(parms)
e4s, e3d, epi, ez, tpi, tds, tdz, tsz = parms
#dx, dy, dz2, dd, px, py, pz, 4s
H = np.diag([e3d, e3d, e3d, e3d, e3d, epi, epi, ez, e4s])
H[[0, 1, 5, 6], [5, 6, 0, 1]] = tpi
H[[2, 7], [7, 2]] = tdz
H[[7, 8], [8, 7]] = tsz
H[[2, 8], [8, 2]] = tds
w, vr = np.linalg.eigh(H)
from pyscf import lib, gto, scf, mcscf, fci, lo, ci, cc
from pyscf.scf import ROHF, UHF, ROKS
from pyscf2qwalk import print_qwalk_mol
chkfile = "../../pyscf/chk/Cuvtz_r1.725_s1_B3LYP_1.chk"
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
m.mo_coeff[:, 5:14] = np.dot(m.mo_coeff[:, 5:14], vr)
print_qwalk_mol(mol, m, basename="new_gs/new_gs")
zz = 0
ns = []
nd = []
npi = []
nz = []
tpi = []
tsz = []
tdz = []
tds = []
for chkfile in chkfiles:
mol = lib.chkfile.load_mol(chkfile)
m = UKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
print_qwalk_mol(mol, m, basename=chkfile)
print(chkfile, "---------------")
print(m.mo_occ[0])
print(m.mo_occ[1])
'''
#Build RDM on IAO basis
s=m.get_ovlp()
mo_occ=m.mo_occ
M=m.mo_coeff[0][:,mo_occ[0]>0]
M=reduce(np.dot,(a.T,s,M))
dm_u=np.dot(M,M.T)
M=m.mo_coeff[1][:,mo_occ[1]>0]
M=reduce(np.dot,(a.T,s,M))
dm_d=np.dot(M,M.T)
'''
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'))
#Generate files for plotting orbitals in ../orbs
print_qwalk_mol(mol,
m,
basename="../orbs/" + el + basis +
"_r" + str(r) + "_c" + str(charge) +
"_s" + str(mol_spin) + "_" + method)
if (m.mo_energy.shape[0] == 2):
plt.plot(m.mo_energy[0], '*', label=method)
plt.plot(m.mo_energy[1], '*')
else:
plt.plot(m.mo_energy * 27.2114, 'o', label=method)
#Generate s(#)_eigenvalue_comp.pdf
plt.title("Spin=" + str(mol_spin) + " eigenvalue comparison")
plt.legend(loc='best')
plt.show()
if(i[0]==0): cu_basis.append(i)
elif(len(cu_basis)==2):
if(i[0]==1): cu_basis.append(i)
elif(len(cu_basis)==3):
if(i[0]==2): cu_basis.append(i)
else:
pass
'''
o_basis = mol.basis["O"]
'''
o_basis=[]
for i in (mol.basis["O"]):
if(len(o_basis)==0):
if(i[0]==0): o_basis.append(i)
elif(len(o_basis)==1):
if(i[0]==1): o_basis.append(i)
else:
pass
'''
minbasis = {'Cu': cu_basis, 'O': o_basis}
#Build IAOs
s = m.get_ovlp()
a = lo.iao.iao(mol, mo_coeff, minao=minbasis)
a = lo.vec_lowdin(a, s)
a.dump('b3lyp_iao_b_overshoot.pickle')
#Write orbs
m.mo_coeff[0][:, :a.shape[1]] = a
print_qwalk_mol(mol, m, 'scf', basename='b3lyp_iao_b_overshoot')
#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 from pyscf.mcscf import newton_casscf from pyscf2qwalk import print_qwalk_mol chkfile = "Cuvtz_r1.725_s1_UB3LYP_12.chk" mol = lib.chkfile.load_mol(chkfile) m = ROHF(mol) m.__dict__.update(lib.chkfile.load(chkfile, 'scf')) print(sum(m.mo_occ[0]), sum(m.mo_occ[1])) print_qwalk_mol(mol, m, method='scf', basename='Cuvtz_r1.725_s1_UB3LYP_12')
if (mo_coeff is None):
mo_coeff = [None, None]
mo_coeff[0] = m.mo_coeff[0][:, occ]
mo_coeff[1] = m.mo_coeff[1][:, occ]
else:
mo_coeff[0] = np.concatenate((mo_coeff[0], m.mo_coeff[0][:, occ]),
axis=1)
mo_coeff[1] = np.concatenate((mo_coeff[1], m.mo_coeff[1][:, occ]),
axis=1)
#Write to file
m.mo_coeff = mo_coeff
print(m.mo_coeff[0].shape)
print(m.mo_coeff[1].shape)
print_qwalk_mol(mol, m, basename="all_s1")
'''
chkfiles = ['../ub3lyp_full/Cuvtz_r1.725_s3_UB3LYP_'+str(i)+'.chk' for i in range(6)]
chkfiles += ['Cuvtz_r1.725_s3_UB3LYP_13.chk']
occ=np.arange(14)
mo_coeff=None
for chkfile in chkfiles:
mol=lib.chkfile.load_mol(chkfile)
m=ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
if(mo_coeff is None):
mo_coeff=[None,None]
mo_coeff[0]=m.mo_coeff[0][:,occ]
mo_coeff[1]=m.mo_coeff[1][:,occ]
s = m.get_ovlp()
mo_occ = m.mo_coeff[:, :h**o + 1]
a = lo.iao.iao(mol, mo_occ, minao=minao)
a = lo.vec_lowdin(a, s)
mo_occ = reduce(np.dot, (a.T, s, mo_occ))
dm_old = np.identity(h**o + 1)
dm_u = np.dot(mo_occ, np.dot(dm_old, mo_occ.T))
dm_old[h**o, h**o] = 0
dm_d = np.dot(mo_occ, np.dot(dm_old, mo_occ.T))
#Save to qwalk orb files
for i in range(a.shape[1]):
m.mo_coeff[:, i] = a[:, i]
print_qwalk_mol(mol,
m,
basename="../qwalk/" + el + basis + str(charge) + "_" +
method + "iao")
#Print traces and plot occ numbers
print(np.trace(dm_d) + np.trace(dm_u))
'''
plt.subplot(211)
if(basis=='vdz'):
plt.plot(np.diag(dm_u),'ko')
else:
plt.plot(np.diag(dm_u),'ks')
plt.subplot(212)
if(basis=='vtz'):
plt.plot(np.diag(dm_d),'ro')
else:
plt.plot(np.diag(dm_d),'rs')
m.__dict__.update(lib.chkfile.load('rohf/Cuvtz_r1.725_s1_ROHF_0.chk', 'scf'))
for i in (mol.basis["Cu"]):
if (len(cu_basis) < 2):
if (i[0] == 0): cu_basis.append(i)
elif (len(cu_basis) == 2):
if (i[0] == 1): cu_basis.append(i)
elif (len(cu_basis) == 3):
if (i[0] == 2): cu_basis.append(i)
else:
pass
o_basis = []
for i in (mol.basis["O"]):
if (len(o_basis) == 0):
if (i[0] == 0): o_basis.append(i)
elif (len(o_basis) == 1):
if (i[0] == 1): o_basis.append(i)
else:
pass
minbasis = {'Cu': cu_basis, 'O': o_basis}
#Build IAOs
s = m.get_ovlp()
a = lo.iao.iao(mol, mo_coeff, minao=minbasis)
a = lo.vec_lowdin(a, s)
a.dump('b3lyp_iao_b.pickle')
#Plot IAOs
m.mo_coeff[:, :a.shape[1]] = a
print_qwalk_mol(mol, m, method='scf', basename='qwalk/b3lyp_iao_b')
#build minimum basis b3lyp_iao_b.pickle (cu: 2s, 1p, 1d; o: 1s, 1p)
cu_basis = []
for i in (mol.basis["Cu"]):
if (len(cu_basis) < 2):
if (i[0] == 0): cu_basis.append(i)
elif (len(cu_basis) == 2):
if (i[0] == 1): cu_basis.append(i)
elif (len(cu_basis) == 3):
if (i[0] == 2): cu_basis.append(i)
else:
pass
o_basis = []
for i in (mol.basis["O"]):
if (len(o_basis) == 0):
if (i[0] == 0): o_basis.append(i)
elif (len(o_basis) == 1):
if (i[0] == 1): o_basis.append(i)
else:
pass
minbasis = {'Cu': cu_basis, 'O': o_basis}
#Build IAOs
s = m.get_ovlp()
a = lo.iao.iao(mol, mo_coeff, minao=minbasis)
a = lo.vec_lowdin(a, s)
a.dump('b3lyp_iao_b.pickle')
#Write orbs
m.mo_coeff[0][:, :a.shape[1]] = a
print_qwalk_mol(mol, m, 'scf', basename='b3lyp_iao_b')
for chkfile in chkfiles:
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
print(chkfile)
print(m.mo_occ[0])
print(m.mo_occ[1])
occ0 = m.mo_occ[0][:14]
occ1 = m.mo_occ[1][:14]
occ0 = np.argsort(-occ0)
occ1 = np.argsort(-occ1)
print(occ0)
print(occ1)
if (mo_coeff is None):
mo_coeff = [None, None]
mo_coeff[0] = m.mo_coeff[0][:, occ0]
mo_coeff[1] = m.mo_coeff[1][:, occ1]
else:
mo_coeff[0] = np.concatenate((mo_coeff[0], m.mo_coeff[0][:, occ0]),
axis=1)
mo_coeff[1] = np.concatenate((mo_coeff[1], m.mo_coeff[1][:, occ1]),
axis=1)
#Write to file
m.mo_coeff = mo_coeff
print(m.mo_coeff[0].shape)
print(m.mo_coeff[1].shape)
print_qwalk_mol(mol, m, basename="all_3extra")
#sigma orbitals
n = 3
vs = np.concatenate(
(vecs_list[0, :, :], vecs_list[3, :, :], vecs_list[6, :, :]), axis=1)
v_opt = optmo(vs, vs[3], ovlp, symm=True, n=n)
print(v_opt.fun)
N = int(vs.shape[1] / 3)
v_opt_list.append(v_opt.x[:N])
v_opt_list.append(v_opt.x[N:2 * N])
v_opt_list.append(v_opt.x[2 * N:])
v_opt_list = np.array(v_opt_list).T
print(v_opt_list.shape)
#check overlaps
for i in range(v_opt_list.shape[1]):
for j in range(i + 1, v_opt_list.shape[1]):
s = reduce(np.dot, (v_opt_list[:, i], ovlp, v_opt_list[:, j]))
print(i, j, s)
#Write to qwalk plot
from pyscf2qwalk import print_qwalk_mol
mol = lib.chkfile.load_mol(flist[0])
m = ROHF(mol)
m.__dict__.update(lib.chkfile.load(flist[0], 'scf'))
m.mo_coeff[:, act_orbs[0]] = v_opt_list
print_qwalk_mol(mol, m, basename='./plots/qw')
#Write to pickle
v_opt_list.dump('b3lyp_mo_symm.pickle')
#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
#S=[1,1,3,3,1,3]
S = [1, 3, 1, 3]
r = 1.725
method = 'B3LYP'
basis = 'vtz'
el = 'Cu'
for run in range(len(S)):
chkfile = "../chk/" + el + basis + "_r" + str(r) + "_s" + str(
S[run]) + "_" + method + "_" + str(run) + "mirror.chk"
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
print_qwalk_mol(mol, m, basename="../orbs/gs" + str(run) + "mirror")
S = 1
r = 1.725
method = 'UB3LYP'
basis = 'vtz'
el = 'Cu'
occ = np.arange(14)
mo_coeff = None
for run in range(11):
chkfile = el + basis + "_r" + str(r) + "_s" + str(
S) + "_" + method + "_" + str(run) + ".chk"
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
if (mo_coeff is None):
mo_coeff = [None, None]
mo_coeff[0] = m.mo_coeff[0][:, occ]
mo_coeff[1] = m.mo_coeff[1][:, occ]
else:
mo_coeff[0] = np.concatenate((mo_coeff[0], m.mo_coeff[0][:, occ]),
axis=1)
mo_coeff[1] = np.concatenate((mo_coeff[1], m.mo_coeff[1][:, occ]),
axis=1)
#Write to file
m.mo_coeff = mo_coeff
print(m.mo_coeff[0].shape)
print(m.mo_coeff[1].shape)
print_qwalk_mol(mol, m, basename="all_1do")
S = 3
r = 1.725
method = 'UB3LYP'
basis = 'vtz'
el = 'Cu'
occ = np.arange(14)
mo_coeff = None
for run in range(6):
chkfile = el + basis + "_r" + str(r) + "_s" + str(
S) + "_" + method + "_" + str(run) + ".chk"
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
if (mo_coeff is None):
mo_coeff = [None, None]
mo_coeff[0] = m.mo_coeff[0][:, occ]
mo_coeff[1] = m.mo_coeff[1][:, occ]
else:
mo_coeff[0] = np.concatenate((mo_coeff[0], m.mo_coeff[0][:, occ]),
axis=1)
mo_coeff[1] = np.concatenate((mo_coeff[1], m.mo_coeff[1][:, occ]),
axis=1)
#Write to file
m.mo_coeff = mo_coeff
print(m.mo_coeff[0].shape)
print(m.mo_coeff[1].shape)
print_qwalk_mol(mol, m, basename="all_hispin")
if (dm_u.shape[0] > 12):
print('Active trace: ', sum(np.diag(dm_u)[act]),
sum(np.diag(dm_d)[act])) #Active Trace
print(np.diag(dm_u)[act] + np.diag(dm_d)[act])
print(labels)
#Check e matrix
s = m.get_ovlp()
H1 = np.diag(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"
]
#Eigenvalue comparison
w, __ = np.linalg.eigh(e1)
plt.plot(sorted(m.mo_energy[:len(w)] * 27.2114), 'go', label='MO')
plt.plot(w, 'b*', label='IAO')
plt.xlabel('Eigenvalue')
plt.ylabel('Energy (eV)')
plt.show()
plt.close()
#Plot iaos
for i in range(a.shape[1]):
m.mo_coeff[:, i] = a[:, i]
print_qwalk_mol(mol, m, basename="../full_orbs/b3lyp_iao_b_full")
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
S = [1, 1, 3, 3, 1, 3]
r = 1.725
method = 'B3LYP'
basis = 'vtz'
el = 'Cu'
occ = np.arange(14)
mo_coeff = None
for run in range(len(S)):
chkfile = "../chk/" + el + basis + "_r" + str(r) + "_s" + str(
S[run]) + "_" + method + "_" + str(run) + ".chk"
mol = lib.chkfile.load_mol(chkfile)
m = ROKS(mol)
m.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
if (mo_coeff is None): mo_coeff = m.mo_coeff[:, occ]
else: mo_coeff = np.concatenate((mo_coeff, m.mo_coeff[:, occ]), axis=1)
#Write to file
m.mo_coeff = mo_coeff
print_qwalk_mol(mol, m, basename="../orbs/all")
from pyscf2qwalk import print_qwalk_mol
el='Cu'
r=1.725
method='UB3LYP'
<<<<<<< HEAD
S=1
for run in range(10,11):
=======
S=3
for run in range(6):
>>>>>>> ba5cb5d2c420434d93aeb8fb854b6ac770efe311
chkfile=el+'vtz'+"_r"+str(r)+"_s"+str(S)+"_"+method+"_"+str(run)+".chk"
mol=lib.chkfile.load_mol(chkfile)
m=ROHF(mol)
m.__dict__.update(lib.chkfile.load(chkfile,'scf'))
print(sum(m.mo_occ[0]),sum(m.mo_occ[1]))
<<<<<<< HEAD
print_qwalk_mol(mol,m,method='scf',basename='qwalk_vtz/gs_do'+str(run))
=======
print_qwalk_mol(mol,m,method='scf',basename='qwalk_vtz/gs3_'+str(run))
>>>>>>> ba5cb5d2c420434d93aeb8fb854b6ac770efe311
exit(0)
#df=pd.DataFrame.from_csv('cuo_u.csv')
#df=df[df['basis']=='vtz']
#df['E']-=min(df['E'])
#df['E']*=27.2114
#print(df)
#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 from pyscf.mcscf import newton_casscf from pyscf2qwalk import print_qwalk_mol chkfile = "test_mom.chk" mol = lib.chkfile.load_mol(chkfile) m = ROHF(mol) m.__dict__.update(lib.chkfile.load(chkfile, 'scf')) print(sum(m.mo_occ[0]), sum(m.mo_occ[1])) print_qwalk_mol(mol, m, method='scf', basename='orbs/test_mom')
#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 from pyscf.mcscf import newton_casscf from pyscf2qwalk import print_qwalk_mol ''' el='Cu' r=1.725 method='UB3LYP' S=1 for run in range(14,15): chkfile=el+'vtz'+"_r"+str(r)+"_s"+str(S)+"_"+method+"_"+str(run)+".chk" mol=lib.chkfile.load_mol(chkfile) m=ROHF(mol) m.__dict__.update(lib.chkfile.load(chkfile,'scf')) print_qwalk_mol(mol,m,method='scf',basename='qwalk_vtz/gs'+str(run)) ''' chkfile = "3d8_vtz.chk" mol = lib.chkfile.load_mol(chkfile) m = ROHF(mol) m.__dict__.update(lib.chkfile.load(chkfile, 'scf')) print_qwalk_mol(mol, m, method='scf', basename='qwalk_vtz/3d8_vtz')