def generate_data():
mol = Molecule.from_file("eth.cml")
scf = SCF(mol, basis="sto3g")
scf.iterate()
shelf = open_shelf()
shelf["scf"] = scf
shelf.close()
def generate_data():
mol = Molecule.from_file("eth.cml")
scf = SCF(mol, basis="sto3g")
scf.iterate()
shelf = open_shelf()
shelf["scf"]=scf
shelf.close()
def test_fci():
""" test FCI calculation"""
from Molecule import Molecule
from PyQuante import SCF
nel = 2
mult = 1
m_s = 0
k=10
# h2 = Molecule('h2',[(1,(0,0,0)),(1,(1.4,0,0))], multiplicity = mult)
h2 = Molecule('h2',[(1,(0,0,0)),(1,(1.4,0,0))])
Solver = SCF(h2,method = "HF")
Solver.iterate()
print "orbital energies ",Solver.solver.orbe
print "HF energy = ",Solver.energy
# FCIInst = FCISolver(Solver.h, Solver.ERI, Solver.solver.orbs, nel, mult, m_s, k=k, sigma_eigs=None)
# eva, eve = FCIInst.iterate()
FCIInst = FCIExactSolver(Solver.h, Solver.ERI, h2.get_enuke(), Solver.solver.orbs, nel, mult, m_s)
eva,eve = FCIInst.diagonalize()
print "eva = ", eva
# print "eve = ",eve
print "correlation energy = ", eva[0] - Solver.energy
print "correlation energy should be (with 6-31g**) -0.03387 a.u."
def pyquante_hf(mol, x, eps, basis = "sto-3g"):
atoms = [None]*mol.num_atoms
for i in xrange(mol.num_atoms):
atoms[i] = (mol.atoms[i].charge,
(mol.atoms[i].rad[0],mol.atoms[i].rad[1],mol.atoms[i].rad[2]))
mol_pq = Molecule(mol.name, atoms, units='Bohr')
solver = SCF(mol_pq,method="HF",ConvCriteria=1e-7,MaxIter=40,basis=basis)
print 'SCF iteration - done'
solver.iterate()
norb=int(solver.solver.nclosed)
w=solver.basis_set.get()
cf=solver.solver.orbs[:,0:norb]
psi = [None]*norb
for i in xrange(norb):
psi[i] = gto2tuck(w,cf[:,i],x)
print psi[i].r
psi[i] = local(psi[i],1e-14)
psi[i] = tuck.round(psi[i],eps)
print psi[i].r
E = solver.solver.orbe[:norb]
return psi,E
def test_fci():
""" test FCI calculation"""
from Molecule import Molecule
from PyQuante import SCF
nel = 2
mult = 1
m_s = 0
k = 10
# h2 = Molecule('h2',[(1,(0,0,0)),(1,(1.4,0,0))], multiplicity = mult)
h2 = Molecule('h2', [(1, (0, 0, 0)), (1, (1.4, 0, 0))])
Solver = SCF(h2, method="HF")
Solver.iterate()
print "orbital energies ", Solver.solver.orbe
print "HF energy = ", Solver.energy
# FCIInst = FCISolver(Solver.h, Solver.ERI, Solver.solver.orbs, nel, mult, m_s, k=k, sigma_eigs=None)
# eva, eve = FCIInst.iterate()
FCIInst = FCIExactSolver(Solver.h, Solver.ERI, h2.get_enuke(),
Solver.solver.orbs, nel, mult, m_s)
eva, eve = FCIInst.diagonalize()
print "eva = ", eva
# print "eve = ",eve
print "correlation energy = ", eva[0] - Solver.energy
print "correlation energy should be (with 6-31g**) -0.03387 a.u."
def calculate(self, verbose=False):
from PyQuante import SCF, Molecule
if verbose:
logging.basicConfig(level=logging.DEBUG)
pyquante_atoms = []
for a in self._atoms:
pyquante_atoms.append( (a.number, a.position) )
m = Molecule('molecule', pyquante_atoms)
lda = SCF(m, method="DFT")
lda.iterate()
result = {
"total_energy": lda.energy,
"orbital_energies": lda.solver.orbe,
}
return result
def new_grid_tester():
from PyQuante.TestMolecules import he,h2
from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.Ints import getbasis
from PyQuante import SCF
mol = h2
gr = MolecularGrid(mol,do_grad_dens=True)
gr2 = MG2(mol,do_grad_dens=True)
print "test_length: ",test_length(gr,gr2)
print "test_distance: ",test_distance(gr,gr2)
bfs = getbasis(mol)
gr.set_bf_amps(bfs)
gr2.add_basis(bfs)
print "test_bfgrid: ",test_bfgrid(gr,gr2)
# This is a little weird, but now use the hf density matrix to
# test whether the densities are the same
hf = SCF(mol)
hf.iterate()
gr.setdens(hf.dmat)
gr2.set_density(hf.dmat)
print "test_density: ",test_density(gr,gr2)
print "test_gamma: ",test_gamma(gr,gr2)
def new_grid_tester():
from PyQuante.TestMolecules import he,h2
from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.Ints import getbasis
from PyQuante import SCF
mol = h2
gr = MolecularGrid(mol,do_grad_dens=True)
gr2 = MG2(mol,do_grad_dens=True)
print "test_length: ",test_length(gr,gr2)
print "test_distance: ",test_distance(gr,gr2)
bfs = getbasis(mol)
gr.set_bf_amps(bfs)
gr2.add_basis(bfs)
print "test_bfgrid: ",test_bfgrid(gr,gr2)
# This is a little weird, but now use the hf density matrix to
# test whether the densities are the same
hf = SCF(mol)
hf.iterate()
gr.setdens(hf.dmat)
gr2.set_density(hf.dmat)
print "test_density: ",test_density(gr,gr2)
print "test_gamma: ",test_gamma(gr,gr2)
def Edot(method='ROHF'):
O = Molecule('O', atomlist=[('O', (0, 0, 0))], multiplicity=3)
job = SCF(O, method=method, basis='6-31G**')
job.iterate()
return job.energy
from PyQuante.Molecule import Molecule
from PyQuante import SCF
#Intializing the molecules
H2 = Molecule('H2', [(1, (0, 0, 0)), (1, (1.4, 0, 0))])
OHmin = Molecule('OHmin', [(8, (0., 0., -0.08687037)),
(1, (0., 0., 0.86464814))],
units='Angstrom',
charge=-1)
#HF method example
#Different basis can be used, sto-3g
#H2solver = SCF(H2, method="HF")
H2solver = SCF(H2, method="HF")
H2solver.iterate()
print "HF energy = ", H2solver.energy
#DFT method example
lda = SCF(H2, method="DFT")
lda.iterate()
blyp = SCF(H2, method="DFT", functional="BLYP")
blyp.iterate()
print "DFT results: LDA = ", lda.energy, " BLYP = ", blyp.energy
#Open shell Hartree Fock
# method='UHF' or method='ROHF'
from PyQuante import Molecule, SCF
# Define the atom
he = Molecule('he',atomlist=[(2,(0,0,0))],charge=0,multiplicity=1)
# Run HF
solver = SCF(he,method="HF",basis="dzvp")
solver.iterate()
# Show result
print solver
print "HF Energy = ",solver.energy
print "---With fractional charge---"
he = Molecule('he',atomlist=[(2.04,(0,0,0))],charge=0,multiplicity=1)
# Run HF
solver = SCF(he,method="HF",basis="dzvp")
solver.iterate()
# Show result
print solver
print "HF Energy = ",solver.energy
from numpy import *
def const_init(vec, label):
log = "const double %s[%d] = {" % (label, vec.size)
for i, v in enumerate(vec[:-1]):
log += "%15.8f," % v
if not i % 5: log += "\n"
log += "%15.8f};\n" % vec[-1]
print log
h2o = Molecule('H2O', [(8, (-3.08471, 1.12313, 0.00396)),
(1, (-2.11791, 0.90877, 0.01763)),
(1, (-3.12325, 2.07922, -0.24921))],
units='Angstrom')
solver = SCF(h2o, basis='sto3g', method="HF", etol=1e-15)
solver.iterate()
print "Energy: %14.12f" % solver.energy
D = (solver.dmat * 2.0).ravel()
S = solver.S.ravel()
F = solver.F.ravel()
H = solver.h.ravel()
const_init(D, "ref_D")
const_init(S, "ref_S")
const_init(F, "ref_F")
const_init(H, "ref_H")
from PyQuante.Molecule import Molecule
from PyQuante import SCF
#Intializing the molecules
H2 = Molecule('H2', [ (1, (0,0,0)), (1,(1.4,0,0)) ] )
OHmin = Molecule( 'OHmin', [ (8, (0., 0., -0.08687037)) , (1, (0., 0., 0.86464814)) ], units='Angstrom', charge=-1 )
#HF method example
#Different basis can be used, sto-3g
#H2solver = SCF(H2, method="HF")
H2solver = SCF(H2, method="HF")
H2solver.iterate()
print "HF energy = ", H2solver.energy
#DFT method example
lda = SCF(H2,method="DFT")
lda.iterate()
blyp = SCF(H2,method="DFT",functional="BLYP")
blyp.iterate()
print "DFT results: LDA = ", lda.energy, " BLYP = ", blyp.energy
#Open shell Hartree Fock
# method='UHF' or method='ROHF'
def Edot(method='ROHF'):
O = Molecule('O',atomlist=[('O',(0,0,0))],multiplicity=3)
job = SCF(O,method=method,basis='6-31G**')
job.iterate()
return job.energy
def testH(self):
solv = SCF(h, method='DFT')
solv.iterate()
self.assertAlmostEqual(solv.energy, -7.431364, 4)
import logging
from numpy import array
from PyQuante import SCF, Molecule
atoms = [(14, array([0, 0, 0])), (14, array([ 2.3419588, 0. , 0. ])), (14, array([ 3.21218834, 2.05887837, 0. ])), (14, array([ 1.23984519, 3.29297073, -0.42228815])), (14, array([-0.05485092, 1.72185148, -1.63972761])), (14, array([ 1.15882181, 0.99278059, -3.55206339])), (14, array([ 3.39816913, 0.26950033, -3.1977073 ])), (14, array([ 4.55928267, 1.90791736, -1.93502226])), (14, array([ 3.39316637, -1.42643782, -1.53138653])), (1, array([-0.6106289 , 0.43621736, 1.28608097])), (1, array([-0.5834327 , -1.31182802, -0.39633738])), (1, array([-1.43155677, 2.12871605, -2.08077878])), (1, array([ 1.53825752, 4.55183661, -1.16374012])), (1, array([ 0.53075288, 3.66105357, 0.83588437])), (1, array([ 5.94172312, 1.43875952, -1.62950356])), (1, array([ 4.67251821, 3.2307785 , -2.61584443])), (1, array([ 3.97839267, -0.14357093, -4.51963896])), (1, array([ 2.59722827, -2.64784197, -1.83682433])), (1, array([ 4.77261873, -1.8301562 , -1.14139106])), (1, array([ 0.40165221, -0.13112135, -4.18238283])), (1, array([ 1.17882996, 2.10638397, -4.5476595 ]))]
logging.basicConfig(level=logging.DEBUG)
m = Molecule('molecule', atoms)
lda = SCF(m, method="DFT")
lda.iterate()
from PyQuante import Molecule, SCF
# Define the atom
he = Molecule('he', atomlist=[(2, (0, 0, 0))], charge=0, multiplicity=1)
# Run HF
solver = SCF(he, method="HF", basis="dzvp")
solver.iterate()
# Show result
print solver
print "HF Energy = ", solver.energy
print "---With fractional charge---"
he = Molecule('he', atomlist=[(2.04, (0, 0, 0))], charge=0, multiplicity=1)
# Run HF
solver = SCF(he, method="HF", basis="dzvp")
solver.iterate()
# Show result
print solver
print "HF Energy = ", solver.energy
def energy(R=1.217, method='UHF'):
O2 = Molecule('O2',atomlist=[('O',(0,0,0)),('O',(R,0,0))],\
units='Angstrom',multiplicity=3)
O2abinitio = SCF(O2, method=method, basis='6-31G**')
O2abinitio.iterate()
return O2abinitio.energy
"""
Calculates the H2 molecule using UHF.
And plots the charge density along the x-axis.
"""
from PyQuante import SCF, Molecule
from PyQuante.NumWrap import arange
from pylab import plot, savefig
# Do the lda calculation:
h2 = Molecule('h2', [(1, (-0.7, 0, 0)), (1, (0.7, 0, 0))])
hf = SCF(h2, method="UHF", basis="6-31G**")
hf.iterate()
# print some info:
print "UHF Results: energy =", hf.energy
print "orbital energies:", hf.solvera.orbe
# Get the items we'll need to compute the density with
orbs = hf.solvera.orbs
bfs = hf.basis_set.get()
nclosed,nopen = h2.get_closedopen()
nbf = len(bfs)
x,y,z = 0, 0, 0
xs = arange(-1.0, 1.1, 0.1)
ds = []
for x in xs:
amp_xyz = 0
for i in range(nclosed):
def energy(R=1.217,method='UHF'):
O2 = Molecule('O2',atomlist=[('O',(0,0,0)),('O',(R,0,0))],\
units='Angstrom',multiplicity=3)
O2abinitio = SCF(O2,method=method,basis='6-31G**')
O2abinitio.iterate()
return O2abinitio.energy