def test_flosic_opt(self):
# FLO-SIC SCF OPT
vsic_every = 1
flosic = flosic_optimize('flosic-scf',
molecule,
0,
0,
'LDA,PW',
get_dfo_basis(sysname),
None,
opt='FIRE',
maxstep=0.1,
fmax=0.1,
conv_tol=1e-6,
grid=7,
vsic_every=vsic_every,
verbose=4)
f = open('OPT_FRMORB.log', 'r')
e_calc = f.readlines()[-1].split()[-2]
f.close()
if e_calc.find('*'):
e_calc = e_calc.split('*')[0]
e_calc = float(e_calc) / Ha
e_ref = -40.697563
self.assertAlmostEqual(e_calc, e_ref, 4)
from ase.io import read
from ase_pyflosic_calculator import PYFLOSIC
from nrlmol_basis import get_dfo_basis
from ase.optimize import LBFGS, FIRE
# Set up a structure.
atoms = read('LiH.xyz')
# We want to use the NRLMOL DFO basis set.
basis = get_dfo_basis('LiH')
# Set up ase calculator.
calc = PYFLOSIC(atoms=atoms,
charge=0,
spin=0,
xc='LDA,PW',
basis=basis,
mode='dft')
# Asign the calculator to the ase.atoms object.
atoms.set_calculator(calc)
# Set up ase optimizer.
label = 'OPT_NUCLEI'
maxstep = 0.1
fmax = 0.0001
steps = 1000
# Perform the nuclei optimization.
dyn = FIRE(atoms,
logfile=label + '.log',
trajectory=label + '.traj',
force_consistent=True)
from flosic_os import xyz_to_nuclei_fod, ase2pyscf, flosic
from flosic_scf import FLOSIC
from nrlmol_basis import get_dfo_basis
from ase_pyflosic_optimizer import flosic_optimize
from ase.units import Ha
# Geometry
#f_xyz = '../examples/advanced_applications/CH4.xyz'
f_xyz = 'CH4.xyz'
sysname = 'CH4'
molecule = read(f_xyz)
geo, nuclei, fod1, fod2, included = xyz_to_nuclei_fod(molecule)
spin = 0
charge = 0
mol = gto.M(atom=ase2pyscf(nuclei),
basis=get_dfo_basis(sysname),
spin=spin,
charge=charge)
class KnownValues(unittest.TestCase):
def test_dft(self):
# DFT
mf = dft.UKS(mol)
mf.verbose = 4 # Amount of output. 4: full output.
mf.max_cycle = 300 # Number of SCF iterations.
mf.conv_tol = 1e-6 # Accuracy of the SCF cycle.
mf.grids.level = 7 # Level of the numerical grid. 3 is the standard value.
mf.xc = 'LDA,PW' # Exchange-correlation functional in the form: (exchange,correlation)
e_ref = -40.1187154486949
self.assertAlmostEqual(mf.kernel(), e_ref, 5)
from ase.io import read
from pyscf import gto,dft
from flosic_os import xyz_to_nuclei_fod,ase2pyscf
from flosic_scf import FLOSIC
from onstuff import ON
from nrlmol_basis import get_dfo_basis
# Loading the structure
ase_atoms = read('C.xyz')
pyscf_atoms,nuclei,fod1,fod2,included = xyz_to_nuclei_fod(ase_atoms)
# Computational details
b = get_dfo_basis('C') #'cc-pvqz'
spin = 2
charge = 0
mol = gto.M(atom=ase2pyscf(nuclei),
basis=b,
spin=spin,
charge=charge)
grid_level = 9
mol.verbose = 4
mol.max_memory = 2000
mol.build()
xc = 'LDA,PW'
# quick dft calculation
mdft = dft.UKS(mol)
mdft.xc = xc
mdft.kernel()