#! /usr/bin/env python3 # Note import path which is different to molecule code #from pyscf.pbc import gto, scf, df, dft from pyscf import gto, scf, df, dft import numpy cell = gto.M( atom ='''O 0.0 0.0 0.0''', basis ='cc-pcvdz', unit ='A', spin=2, verbose = 5, cart=False, ) mf = scf.UHF(cell) mf.kernel() title='O-UHF-Triplet' from PyscfToQmcpack import savetoqmcpack savetoqmcpack(cell,mf,title)
urlretrieve("{0}/{1}/{2}/{3}".format(pplib,atom,pptype,basfile),
filename=basfile)
urlretrieve("{0}/{1}/{2}/{3}".format(pplib,atom,pptype,ecpfile),
filename=ecpfile)
urlretrieve("{0}/{1}/{2}/{3}".format(pplib,atom,pptype,xmlfile),
filename=xmlfile)
#Initialize molecule object
mol = gto.Mole()
mol.atom = "{0} 0.0 0.0 0.0".format(atom)
with open(os.path.join(cwd,basfile)) as f:
bas = f.read()
mol.basis = {atom: gto.basis.parse(bas)}
with open(os.path.join(cwd,ecpfile)) as f:
ecp = f.read()
mol.ecp = {atom: gto.basis.parse_ecp(ecp)}
mol.spin = 2
mol.charge = 0
mol.build()
#run HF and PBE
hf = scf.ROHF(mol)
hf.kernel()
pbe = dft.ROKS(mol)
pbe.xc = 'pbe'
pbe.kernel()
savetoqmcpack(mol,hf,title='{}.hf'.format(atom))
savetoqmcpack(mol,pbe,title='{}.pbe'.format(atom))
ecp2 = f.read()
mol.basis = {atom1: gto.basis.parse(bas1), atom2: gto.basis.parse(bas2)}
mol.ecp = {atom1: gto.basis.parse_ecp(ecp1), atom2: gto.basis.parse_ecp(ecp2)}
mol.build()
#~~~Run HF on molecule~~~~
mf = scf.RKS(mol)
mf.xc = 'hf'
#mf.irrep_nelec = {
#'Ag' : (4,2), # s
#'B3u': (1,1), # x 1
#'B1u': (1,1), # z 0
#'B2u': (1,1), # y -1
#'B2g': (1,1), # xz 1
#'B3g': (1,0), # yz -1
#'B1g': (1,0), # xy -2
#'Au' : (0,0) # xyz
#}
mf.verbose = 4
mf.max_cycle = 100
#dm=mf.init_guess_by_chkfile('../../scf_guess/guess/scf.chkfile')
mf.chkfile = 'scf.chkfile'
#en=mf.kernel(dm)
en = mf.kernel()
### generated conversion text ###
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(mol, mf, 'scf')
### end generated conversion text ###
sp_twist = [0.07761248, 0.07761248, -0.07761248]
kmesh = [2, 1, 1]
kpts = array([[0.07761248, 0.07761248, -0.07761248],
[0.54328733, 0.54328733, -0.54328733]])
mydf = df.GDF(cell, kpts)
mydf.auxbasis = 'weigend'
mydf._cderi_to_save = 'df_ints.h5'
mydf.build()
mf = scf.KROHF(cell, kpts).density_fit()
mf.exxdiv = 'ewald'
mf.max_cycle = 200
mf.with_df = mydf
mf.chkfile = 'diamond-scf.chk'
mf.with_df._cderi = 'df_ints.h5'
e_scf = mf.kernel()
ener = open('e_scf', 'w')
ener.write('%s\n' % (e_scf))
print('e_scf', e_scf)
ener.close()
title = "C_diamond-twist"
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(cell, mf, title=title, kmesh=kmesh, kpts=kpts, sp_twist=sp_twist)
from MolPyscfToQPkpts import pyscf2QP
pyscf2QP(cell, mf, kpts=kpts, int_threshold=1E-15)
cell.unit = 'B'
cell.drop_exponent = 0.1
cell.ke_cutoff = 120
cell.verbose = 5
cell.build()
supcell = super_cell(cell, nmp)
mydf = df.FFTDF(supcell)
mydf.auxbasis = 'weigend'
kpts = []
mf = dft.RKS(supcell)
mf.xc = 'lda'
mf.exxdiv = 'ewald'
mf.with_df = mydf
e_scf = mf.kernel()
assert mf.converged
ener = open('e_scf', 'w')
ener.write('%s\n' % (e_scf))
title = "C_Diamond"
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(supcell, mf, title=title, kpts=kpts)
cell.atom = '''
C 0.00000000 0.00000000 0.00000000
C 1.686580575 1.686580575 1.686580575
'''
cell.basis = 'bfd-vtz'
cell.ecp = 'bfd'
cell.unit = 'B'
cell.drop_exponent = 0.1
cell.verbose = 5
cell.build()
kpts = cell.make_kpts(kmesh)
kpts -= kpts[0]
supcell = cell
mydf = df.GDF(supcell, kpts)
mydf.auxbasis = 'weigend'
mf = scf.KRHF(supcell, kpts).density_fit()
mf.exxdiv = 'ewald'
mf.with_df = mydf
e_scf = mf.kernel()
title = "C_Diamond-211"
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(supcell, mf, title=title, kpts=kpts, kmesh=kmesh)
cell.verbose = 5
cell.charge = 0
cell.spin = 0
cell.build()
kpts = array([
[0.0, 0.0, 0.0],
[0.4656748546088228, 0.4656748546088228, -0.4656748546088228]])
### end generated system text ###
#print cell.make_kpts([2,1,1])
#exit()
gdf = df.GDF(cell,kpts)
gdf.auxbasis = 'weigend'
gdf.build()
mf = scf.KRKS(cell,kpts).density_fit()
mf.xc ='b3lyp'
mf.tol = 1e-10
mf.exxdiv = 'ewald'
mf.with_df = gdf
mf.kernel()
### generated conversion text ###
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(cell,mf,'scf',kpts)
### end generated conversion text ###
2 13.65512 85.86406
'''),
'H':
gto.basis.parse_ecp('''
H nelec 0
H ul
1 21.24359508259891 1.00000000000000
3 21.24359508259891 21.24359508259891
2 21.77696655044365 -10.85192405303825
H S
2 1.000000000000000 0.00000000000000
''')
}
mol.spin = 0 #Value of S where the spin multiplicity is 2S+1
mol.build()
#Hartree Fock
#mf = scf.ROHF(mol)
#DFT
mf = dft.ROKS(mol)
mf.xc = 'b3lyp'
e_scf = mf.kernel()
#Section for QMCPACK
title = "H2O_DFT_NCSU"
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(mol, mf, title=title)
#! /usr/bin/env python3 from pyscf import gto from pyscf import scf, dft, df mol = gto.Mole() mol.verbose = 5 mol.atom = ''' C 0.97091888623401 -0.07609978449644 -0.06440023695551 N -0.17562187186916 -0.07610010775030 -0.06439988152408 H 2.03800298563516 -0.07610010775326 -0.06439988152041 ''' mol.unit = 'A' mol.basis = 'cc-pvtz' #mol.cart=True mol.build() mf = dft.RKS(mol).density_fit() mf.xc = 'B3LYP' mf.chkfile = 'CHN.chk' e_scf = mf.kernel() title = "CHN" kpts = [] from PyscfToQmcpack import savetoqmcpack savetoqmcpack(mol, mf, title=title, kpts=kpts)
