def main():
li = Molecule('Li',
atomlist = [(3,(0,0,0))],
units='Angs',
multiplicity=2)
en,orbe,orbs = dft(li,ETemp=1e4)
return en
def main():
r = 0.7
h2 = Molecule('h2',
atomlist=[(1, (0, 0, r / 2.)), (1, (0, 0, -r / 2.))],
units='Angs')
en, orbe, orbs = dft(h2, ETemp=1e4)
return en
def main(**opts):
r = opts.get('r', 1.0)
lih = Molecule('lih',
atomlist=[(3, (0, 0, 0)), (1, (0, 0, r))],
units='Angs')
en, orbe, orbs = dft(lih, **opts)
return en
def main(**opts):
r = opts.get('r',0.70)
h2 = Molecule('h2',
atomlist = [(1,(0,0,r/2.)),
(1,(0,0,-r/2.))],
units='Angs')
en,orbe,orbs = dft(h2,**opts)
return en
def main():
r = 0.7
h2 = Molecule('h2',
atomlist = [(1,(0,0,r/2.)),
(1,(0,0,-r/2.))],
units='Angs')
en,orbe,orbs = dft(h2,ETemp=1e4)
return en
def main(**opts):
r = opts.get('r',1.0)
lih = Molecule('lih',
atomlist = [(3,(0,0,0)),
(1,(0,0,r))],
units='Angs')
en,orbe,orbs = dft(lih,**opts)
return en
def test_exx():
logging.basicConfig(filename='test_exx.log',
level=logging.INFO,
format="%(message)s",
filemode='w')
logging.info("Testing EXX functions")
logging.info(time.asctime())
h2o = Molecule('H2O',
atomlist = [(8,(0,0,0)), # the geo corresponds to the
(1,(0.959,0,0)),# one that Yang used
(1,(-.230,0.930,0))],
units = 'Angstrom')
h2 = Molecule('H2',
atomlist = [(1,(0.,0.,0.7)),(1,(0.,0.,-0.7))],
units = 'Bohr')
he = Molecule('He',atomlist = [(2,(0,0,0))])
ne = Molecule('Ne',atomlist = [(10,(0,0,0))])
ohm = Molecule('OH-',atomlist = [(8,(0.0,0.0,0.0)),
(1,(0.971,0.0,0.0))],
units = 'Angstrom',
charge = -1)
be = Molecule('Be',atomlist = [(4,(0.0,0.0,0.0))],
units = 'Angstrom')
lih = Molecule('LiH',
atomlist = [(1,(0,0,1.5)),(3,(0,0,-1.5))],
units = 'Bohr')
#for atoms in [h2,he,be,lih,ohm,ne,h2o]:
for atoms in [h2,lih]:
logging.info("--%s--" % atoms.name)
# Caution: the rydberg molecules (He, Ne) will need a
# much much larger basis set than the default returned
# by getbasis (which is 6-31G**)
bfs = getbasis(atoms)
S,h,Ints = getints(bfs,atoms)
enhf,orbehf,orbshf = rhf(atoms,integrals=(S,h,Ints))
logging.info("HF total energy = %f"% enhf)
enlda,orbelda,orbslda = dft(atoms,
integrals=(S,h,Ints),
bfs = bfs)
logging.info("LDA total energy = %f" % enlda)
energy,orbe_exx,orbs_exx = exx(atoms,orbslda,
integrals=(S,h,Ints),
bfs = bfs,
verbose=True,
opt_method="BFGS")
logging.info("EXX total energy = %f" % energy)
return
def test_grad(atoms,**opts):
basis = opts.get('basis',None)
verbose = opts.get('verbose',False)
bfs = getbasis(atoms,basis)
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
energy, orbe, orbs = dft(atoms,return_flag=1)
nclosed,nopen = atoms.get_closedopen()
D = mkdens_spinavg(orbs,nclosed,nopen)
# Now set up a minigrid on which to evaluate the density and gradients:
npts = opts.get('npts',1)
d = opts.get('d',1e-4)
# generate any number of random points, and compute
# analytical and numeric gradients:
print "Computing Grad Rho for Molecule %s" % atoms.name
maxerr = -1
for i in range(npts):
x,y,z = rand_xyz()
rho = get_rho(x,y,z,D,bfs)
rho_px = get_rho(x+d,y,z,D,bfs)
rho_mx = get_rho(x-d,y,z,D,bfs)
rho_py = get_rho(x,y+d,z,D,bfs)
rho_my = get_rho(x,y-d,z,D,bfs)
rho_pz = get_rho(x,y,z+d,D,bfs)
rho_mz = get_rho(x,y,z-d,D,bfs)
gx,gy,gz = get_grad_rho(x,y,z,D,bfs)
gx_num = (rho_px-rho_mx)/2/d
gy_num = (rho_py-rho_my)/2/d
gz_num = (rho_pz-rho_mz)/2/d
dx,dy,dz = gx-gx_num,gy-gy_num,gz-gz_num
error = sqrt(dx*dx+dy*dy+dz*dz)
maxerr = max(error,maxerr)
print " Point %10.6f %10.6f %10.6f %10.6f" % (x,y,z,error)
print " Numerical %10.6f %10.6f %10.6f" % (gx_num,gy_num,gz_num)
print " Analytic %10.6f %10.6f %10.6f" % (gx,gy,gz)
print "The maximum error in the gradient calculation is ",maxerr
return
def dissoc(**opts):
rmin = opts.get('rmin', 0.65)
rmax = opts.get('rmax', 1.01)
step = opts.get('step', 0.05)
doplot = opts.get('doplot', False)
rs = arange(rmin, rmax, step)
E = []
for r in rs:
lih = Molecule('lih',
atomlist=[(3, (0, 0, 0)), (1, (0, 0, r))],
units='Angs')
en, orbe, orbs = dft(lih, **opts)
print "%.3f %.5f" % (r, en)
E.append(en)
if doplot:
from pylab import plot
plot(rs, E, 'bo-')
return
def main(**opts):
functional = opts.get('functional', 'BLYP')
h = Molecule('H', atomlist=[(1, (0, 0, 0))], multiplicity=2)
he = Molecule('He', atomlist=[(2, (0, 0, 0))])
li = Molecule('Li', atomlist=[(3, (0, 0, 0))], multiplicity=2)
be = Molecule('Be', atomlist=[(4, (0, 0, 0))])
b = Molecule('B', atomlist=[(5, (0, 0, 0))], multiplicity=2)
c = Molecule('C', atomlist=[(6, (0, 0, 0))], multiplicity=3)
n = Molecule('N', atomlist=[(7, (0, 0, 0))], multiplicity=4)
o = Molecule('O', atomlist=[(8, (0, 0, 0))], multiplicity=3)
f = Molecule('F', atomlist=[(9, (0, 0, 0))], multiplicity=2)
ne = Molecule('Ne', atomlist=[(10, (0, 0, 0))])
#for atoms in [h,he,li,be,b,c,n,o,f,ne]:
# Just do singlets now, since higher multiplicities are off
# b/c of Average Open Shell issues
print "Running Pople atom tests using %s functional" % functional
for atoms in [he, be, ne]:
en, orbe, orbs = dft(atoms, functional=functional)
print atoms.name, en
return
def dissoc(**opts):
rmin = opts.get('rmin',0.65)
rmax = opts.get('rmax',1.01)
step = opts.get('step',0.05)
doplot = opts.get('doplot',False)
rs = arange(rmin,rmax,step)
E = []
for r in rs:
lih = Molecule('lih',
atomlist = [(3,(0,0,0)),
(1,(0,0,r))],
units='Angs')
en,orbe,orbs = dft(lih,**opts)
print "%.3f %.5f" % (r,en)
E.append(en)
if doplot:
from pylab import plot
plot(rs,E,'bo-')
return
def main():
he = Molecule('He',atomlist=[(2,(0,0,0))])
be = Molecule('Be',atomlist=[(4,(0,0,0))])
ne = Molecule('Ne',atomlist=[(10,(0,0,0))])
h2 = Molecule('H2',atomlist = [(1,(0,0,0.70)),
(1,(0,0,-0.70))])
#mols = [he,h2,be]
mols = [he,h2,be,ne]
#mols = [ne]
for mol in mols:
#for functional in ['SVWN','BLYP','PBE']:
#for functional in ['S0','PBE']:
for functional in ['PBE']:
en,orbe,orbs = dft(mol,functional = functional)
if (mol.name,functional) in results:
worked = is_close(en,results[mol.name,functional])
else:
worked = None
print mol.name,functional,en,worked
return
def main():
he = Molecule('He',atomlist=[(2,(0,0,0))])
ne = Molecule('Ne',atomlist=[(10,(0,0,0))])
he3 = Molecule('He3',atomlist=[(2,(0,0,0))],multiplicity=3)
# S0 functional
en,orbe,orbs = dft(he,functional='S0',basis=basis_data)
print "He S0 sb %10.5f is %10.5f" % (-2.7229973821,en)
en,orbe,orbs = dft(ne,functional='S0',basis=basis_data)
print "Ne S0 sb %10.5f is %10.5f" % (-127.4597878033,en)
en,orbe,orbs = dft(he3,functional='S0',basis=basis_data)
print "He3 S0 sb %10.5f is %10.5f" % (-1.7819689849,en)
# SVWN functional
en,orbe,orbs = dft(he,functional='SVWN',basis=basis_data)
print "He SVWN sb %10.5f is %10.5f" % (-2.834247,en)
en,orbe,orbs = dft(ne,functional='SVWN',basis=basis_data)
print "Ne SVWN sb %10.5f is %10.5f" % (-127.203239,en)
en,orbe,orbs = dft(he3,functional='SVWN',basis=basis_data)
print "He3 SVWN sb %10.5f is %10.5f" % (-1.833287,en)
# XPBE functional
return
def main():
he = Molecule('He', atomlist=[(2, (0, 0, 0))])
ne = Molecule('Ne', atomlist=[(10, (0, 0, 0))])
he3 = Molecule('He3', atomlist=[(2, (0, 0, 0))], multiplicity=3)
# S0 functional
en, orbe, orbs = dft(he, functional='S0', basis=basis_data)
print "He S0 sb %10.5f is %10.5f" % (-2.7229973821, en)
en, orbe, orbs = dft(ne, functional='S0', basis=basis_data)
print "Ne S0 sb %10.5f is %10.5f" % (-127.4597878033, en)
en, orbe, orbs = dft(he3, functional='S0', basis=basis_data)
print "He3 S0 sb %10.5f is %10.5f" % (-1.7819689849, en)
# SVWN functional
en, orbe, orbs = dft(he, functional='SVWN', basis=basis_data)
print "He SVWN sb %10.5f is %10.5f" % (-2.834247, en)
en, orbe, orbs = dft(ne, functional='SVWN', basis=basis_data)
print "Ne SVWN sb %10.5f is %10.5f" % (-127.203239, en)
en, orbe, orbs = dft(he3, functional='SVWN', basis=basis_data)
print "He3 SVWN sb %10.5f is %10.5f" % (-1.833287, en)
# XPBE functional
return
#!/usr/bin/env python
from PyQuante import Molecule
from PyQuante.dft import dft
coord = [(1, (0.0998334, 0.995004, -0.6)), (1, (0.911616, 0.411044, 1.6)),
(1, (0.811782, -0.58396, -0.6)), (1, (-0.0998334, -0.995004, 1.6)),
(1, (-0.911616, -0.411044, -0.6)), (1, (-0.811782, 0.583961, 1.6)),
(6, (0, 0, 0)), (6, (0, 0, 1))]
ethane = Molecule('ethane', coord, units="Angstrom")
en, orbe, orbs = dft(ethane, functional="LDA", basis="sto-3g")
def main():
atomlist = Molecule('Li',atomlist = [(3,(0,0,0))],multiplicity=2)
en,orbe,orbs = dft(atomlist,verbose=True)
return en
def H2O_Molecule(tst, info, auX, auZ):
H2O = Molecule('H2O', [('O', (0.0, 0.0, 0.0)), ('H', (auX, 0.0, auZ)),
('H', (-auX, 0.0, auZ))],
units='Bohr')
# Get a better energy estimate
if dft:
print "# info=%s A.U.=(%g,%g) " % (info, auX, auZ)
edft, orbe2, orbs2 = dft(H2O, functional='SVWN')
bfs = getbasis(H2O, basis_data=basis_data)
#S is overlap of 2 basis funcs
#h is (kinetic+nucl) 1 body term
#ints is 2 body terms
S, h, ints = getints(bfs, H2O)
#enhf is the Hartee-Fock energy
#orbe is the orbital energies
#orbs is the orbital overlaps
enhf, orbe, orbs = rhf(H2O, integrals=(S, h, ints))
enuke = Molecule.get_enuke(H2O)
# print "orbe=%d" % len(orbe)
temp = matrixmultiply(h, orbs)
hmol = matrixmultiply(transpose(orbs), temp)
MOInts = TransformInts(ints, orbs)
if single:
print "h = \n", h
print "S = \n", S
print "ints = \n", ints
print "orbe = \n", orbe
print "orbs = \n", orbs
print ""
print "Index 0: 1 or 2 in the paper, Index 1: 3 or 4 in the paper (for pqrs)"
print ""
print "hmol = \n", hmol
print "MOInts:"
print "I,J,K,L = PQRS order: Cre1,Cre2,Ann1,Ann2"
if 1:
print "tst=%d info=%s nuc=%.9f Ehf=%.9f" % (tst, info, enuke, enhf),
cntOrbs = 0
maxOrb = 0
npts = len(hmol[:])
for i in xrange(npts):
for j in range(i, npts):
if abs(hmol[i, j]) > 1.0e-7:
print "%d,%d=%.9f" % (i, j, hmol[i, j]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
nbf, nmo = orbs.shape
mos = range(nmo)
for i in mos:
for j in xrange(i + 1):
ij = i * (i + 1) / 2 + j
for k in mos:
for l in xrange(k + 1):
kl = k * (k + 1) / 2 + l
if ij >= kl:
ijkl = ijkl2intindex(i, j, k, l)
if abs(MOInts[ijkl]) > 1.0e-7:
print "%d,%d,%d,%d=%.9f" % (l, i, j, k,
MOInts[ijkl]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
print ""
return (maxOrb, cntOrbs)
gradient_diatomic(sol, smoothing=0.005)
# In[33]:
from PyQuante.Molecule import Molecule
from PyQuante.dft import dft
h2 = Molecule('h2',[(1,(0,0,0)),(1,(1.4,0,0))])
# In[35]:
en,orbe,orbs = dft(h2,functional='LDA')
# In[ ]:
# In[8]:
gradient_diatomic(sol, smoothing=0.2)
# In[14]:
#!/usr/bin/env python
from PyQuante import Molecule
from PyQuante.dft import dft
lih = Molecule('LiH', [(1, (0, 0, -1.210905)), (3, (0, 0, 0.403635))],
units="Bohr")
en, orbe, orbs = dft(lih, functional="LDA", basis="sto-3g")
def main():
atomlist = Molecule("H", atomlist=[(1, (0, 0, 0))], multiplicity=2)
en, orbe, orbs = dft(atomlist)
return en
def main():
atomlist = Molecule('H', atomlist=[(1, (0, 0, 0))], multiplicity=2)
en, orbe, orbs = dft(atomlist)
return en
"""
Calculates the Boron atom using DFT.
"""
from PyQuante import SCF, Molecule, dft, Atom
B = Molecule('Boron',[(5, (0,0,0))])
B.multiplicity = 2
E, eigs, orbitals = dft.dft(B)
print "total energy:", E
print "KS energies:", eigs
def H2O_Molecule(tst,info,auX,auZ):
H2O = Molecule('H2O',
[('O', ( 0.0, 0.0, 0.0)),
('H', ( auX, 0.0, auZ)),
('H', (-auX, 0.0, auZ))],
units='Bohr')
# Get a better energy estimate
if dft:
print "# info=%s A.U.=(%g,%g) " % (info,auX,auZ)
edft,orbe2,orbs2 = dft(H2O,functional='SVWN')
bfs= getbasis(H2O,basis_data=basis_data)
#S is overlap of 2 basis funcs
#h is (kinetic+nucl) 1 body term
#ints is 2 body terms
S,h,ints=getints(bfs,H2O)
#enhf is the Hartee-Fock energy
#orbe is the orbital energies
#orbs is the orbital overlaps
enhf,orbe,orbs=rhf(H2O,integrals=(S,h,ints))
enuke = Molecule.get_enuke(H2O)
# print "orbe=%d" % len(orbe)
temp = matrixmultiply(h,orbs)
hmol = matrixmultiply(transpose(orbs),temp)
MOInts = TransformInts(ints,orbs)
if single:
print "h = \n",h
print "S = \n",S
print "ints = \n",ints
print "orbe = \n",orbe
print "orbs = \n",orbs
print ""
print "Index 0: 1 or 2 in the paper, Index 1: 3 or 4 in the paper (for pqrs)"
print ""
print "hmol = \n",hmol
print "MOInts:"
print "I,J,K,L = PQRS order: Cre1,Cre2,Ann1,Ann2"
if 1:
print "tst=%d info=%s nuc=%.9f Ehf=%.9f" % (tst,info,enuke,enhf),
cntOrbs = 0
maxOrb = 0
npts = len(hmol[:])
for i in xrange(npts):
for j in range(i,npts):
if abs(hmol[i,j]) > 1.0e-7:
print "%d,%d=%.9f" % (i,j,hmol[i,j]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
nbf,nmo = orbs.shape
mos = range(nmo)
for i in mos:
for j in xrange(i+1):
ij = i*(i+1)/2+j
for k in mos:
for l in xrange(k+1):
kl = k*(k+1)/2+l
if ij >= kl:
ijkl = ijkl2intindex(i,j,k,l)
if abs(MOInts[ijkl]) > 1.0e-7:
print "%d,%d,%d,%d=%.9f" % (l,i,j,k,MOInts[ijkl]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
print ""
return (maxOrb,cntOrbs)
__author__ = 'yutongpang'
from PyQuante.Molecule import Molecule
h2 = Molecule('H2',
[(1, (0.00000000, 0.00000000, 0.36628549)),
(1, (0.00000000, 0.00000000, -0.36628549))],
units='Angstrom')
from PyQuante.dft import dft
en,orbe,orbs = dft(h2)
print "HF Energy = ",orbs