def test_grad(self):
coords = [(0.0, 0.1, 0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges).run()
hfg = itrf.mm_charge_grad(grad.RHF(mf), coords, charges).run()
self.assertAlmostEqual(numpy.linalg.norm(hfg.de), 26.978089280783195,
9)
mfs = mf.as_scanner()
e1 = mfs('''
H -0.00000000 -0.000 0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
e2 = mfs('''
H -0.00000000 -0.000 -0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
self.assertAlmostEqual((e1 - e2) / 0.002 * lib.param.BOHR,
hfg.de[0, 2], 5)
bak = pyscf.DEBUG
pyscf.DEBUG = 1
ref = hfg.get_hcore()
pyscf.DEBUG = 0
v = hfg.get_hcore()
self.assertAlmostEqual(abs(ref - v).max(), 0, 12)
pyscf.DEBUG = bak
def test_mp2_grad(self):
pt = mp.mp2.MP2(mf)
pt.kernel()
g1 = pt.nuc_grad_method().kernel(pt.t2,
mf_grad=grad.RHF(mf),
atmlst=[0, 1, 2])
self.assertAlmostEqual(lib.finger(g1), -0.035681131697586257, 6)
def test_finite_diff_x2c_rhf_grad(self):
mf = scf.RHF(mol).x2c()
mf.conv_tol = 1e-14
e0 = mf.kernel()
g = grad.RHF(mf).kernel()
self.assertAlmostEqual(lib.finger(g), 0.0056363502746766807, 6)
mf_scanner = mf.as_scanner()
pmol = mol.copy()
e1 = mf_scanner(
pmol.set_geom_(
'O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
e2 = mf_scanner(
pmol.set_geom_(
'O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
self.assertAlmostEqual(g[0, 2], (e1 - e2) / 2e-4 * lib.param.BOHR, 5)
#e1 = mf_scanner(pmol.set_geom_('O 0. 1e-5 0.; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
#e2 = mf_scanner(pmol.set_geom_('O 0. -1e-5 0.; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
#self.assertAlmostEqual(g[0,1], (e1-e2)/2e-5*lib.param.BOHR, 5)
e1 = mf_scanner(
pmol.set_geom_(
'O 0. 0. 0.; 1 0. -0.7571 0.587; 1 0. 0.757 0.587'))
e2 = mf_scanner(
pmol.set_geom_(
'O 0. 0. 0.; 1 0. -0.7569 0.587; 1 0. 0.757 0.587'))
self.assertAlmostEqual(g[1, 1], (e2 - e1) / 2e-4 * lib.param.BOHR, 5)
def test_nr_rhf(self):
rhf = scf.RHF(mol)
rhf.conv_tol = 1e-14
rhf.scf()
g = grad.RHF(rhf)
self.assertAlmostEqual(finger(g.grad_elec()), 7.9210392362911595, 6)
self.assertAlmostEqual(finger(g.kernel()), 0.367743084803, 6)
def test_ccsd_grad(self):
mycc = cc.ccsd.CCSD(mf)
mycc.max_memory = 1
mycc.conv_tol = 1e-10
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
g1 = ccsd_grad.kernel(mycc, t1, t2, l1, l2, mf_grad=grad.RHF(mf))
self.assertAlmostEqual(lib.finger(g1), -0.036999389889460096, 6)
mol = gto.M(
verbose = 5,
output = '/dev/null',
atom = 'H 0 0 0; H 0 0 1.706',
basis = '631g',
unit='Bohr')
mf0 = scf.RHF(mol).run(conv_tol=1e-14)
mycc0 = cc.ccsd.CCSD(mf0).run(conv_tol=1e-10)
mol.set_geom_('H 0 0 0; H 0 0 1.704', unit='Bohr')
mf1 = scf.RHF(mol).run(conv_tol=1e-14)
mycc1= cc.ccsd.CCSD(mf1).run(conv_tol=1e-10)
mol.set_geom_('H 0 0 0; H 0 0 1.705', unit='Bohr')
mycc2 = cc.ccsd.CCSD(scf.RHF(mol))
g_scanner = mycc2.nuc_grad_method().as_scanner().as_scanner()
g1 = g_scanner(mol)[1]
self.assertTrue(g_scanner.converged)
self.assertAlmostEqual(g1[0,2], (mycc1.e_tot-mycc0.e_tot)*500, 6)
def test_frozen(self):
myci = ci.cisd.CISD(mf)
myci.frozen = [0, 1, 10, 11, 12]
myci.max_memory = 1
myci.kernel()
g1 = cisd_grad.kernel(myci, myci.ci, mf_grad=grad.RHF(mf))
self.assertAlmostEqual(lib.finger(g1), 0.10224149952700579, 6)
def test_frozen(self):
pt = mp.mp2.MP2(mf)
pt.frozen = [0, 1, 10, 11, 12]
pt.max_memory = 1
pt.kernel()
g1 = mp2_grad.kernel(pt, pt.t2, mf_grad=grad.RHF(mf))
self.assertAlmostEqual(lib.finger(g1), 0.12457973399092415, 6)
def test_cisd_grad(self):
myci = ci.cisd.CISD(mf)
myci.conv_tol = 1e-10
myci.kernel()
g1 = myci.nuc_grad_method().kernel(myci.ci,
mf_grad=grad.RHF(mf),
atmlst=[0, 1, 2])
self.assertAlmostEqual(lib.finger(g1), -0.032562347119070523, 6)
def hf_grad(self):
if self._hf_grad is not NotImplemented:
return self._hf_grad
if self.hf_eng.mo_coeff is None:
self.hf_eng.kernel()
hf_grad = grad.RHF(self.hf_eng)
self._hf_grad = hf_grad
return self._hf_grad
def grad(self, crd):
crd =crd / ANGSTROM
atom=" "
for i in range(len(self.atoms)):
atom+=self.atoms[i]+'\t'+str(crd[i, 0])+'\t'+str(crd[i, 1])+'\t'+str(crd[i, 2])+'\n'
print atom
mol = gto.M(atom=atom,basis=self.basis)
rhf= scf.RHF(mol)
energy = rhf.kernel()
return energy* EH, grad.RHF(rhf).kernel()* (EH / BOHR)
def test_rhf_scanner(self):
mol1 = mol.copy()
mol1.set_geom_('''
H 0. 0. 0.9
F 0. 0.1 0.''')
mf_scanner = grad.RHF(scf.RHF(mol).set(conv_tol=1e-14)).as_scanner()
e, de = mf_scanner(mol)
self.assertAlmostEqual(finger(de), 0.367743084803, 6)
e, de = mf_scanner(mol1)
self.assertAlmostEqual(finger(de), 0.041822093538, 6)
def calc_gradients_elec(mole, one_dm: np.ndarray, mf, coeffs, occs, energies):
"""Calculate electronic part of nuclear gradients.
Parameters
----------
mole
A PySCF mole object.
one_dm
One-particle density matrix understood by IOdata
projected and formatted in a PySCF-compatible way
(single 2d array or list for a,b 2d arrays)
mf
A PySCF mean field object. Its only use is method specification.
coeffs
AO coefficient matrix understood by IOdata
projected and formatted in a PySCF-compatible way
(single 2d array or list for a,b 2d arrays)
occs
Occupation numbers formatted in a PySCF-compatible way
(single 1d array or list for a,b 1d arrays)
energies
MO energies formatted in a PySCF-compatible way
(single 1d array or list for a,b 1d arrays)
Returns
-------
grad_elec
Nuclear gradients in a.u. per cartesian coordinate per atom.
(Due to electrons)
"""
mo_energy = energies
mo_coeff = coeffs
mo_occ = occs
if len(one_dm) == 2:
try:
grad_elec = grad.UKS(mf).grad_elec(mo_energy=mo_energy,
mo_coeff=mo_coeff,
mo_occ=mo_occ)
except:
grad_elec = grad.UHF(mf).grad_elec(mo_energy=mo_energy,
mo_coeff=mo_coeff,
mo_occ=mo_occ)
else:
try:
grad_elec = grad.RKS(mf).grad_elec(mo_energy=mo_energy,
mo_coeff=mo_coeff,
mo_occ=mo_occ)
except:
grad_elec = grad.RHF(mf).grad_elec(mo_energy=mo_energy,
mo_coeff=mo_coeff,
mo_occ=mo_occ)
return grad_elec
def initialization_pyscf(self):
self.scf_eng = scf.RHF(self.mol)
self.scf_eng.conv_tol = 1e-11
self.scf_eng.conv_tol_grad = 1e-9
self.scf_eng.max_cycle = 100
if self.init_scf:
self.eng = self.scf_eng.kernel()
if not self.scf_eng.converged:
warnings.warn("SCF not converged!")
self.scf_grad = grad.RHF(self.scf_eng)
self.scf_hess = hessian.RHF(self.scf_eng)
return
def test_finite_diff_rhf_grad(self):
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
e0 = mf.kernel()
g = grad.RHF(mf).kernel(atmlst=range(mol.natm))
self.assertAlmostEqual(lib.finger(g), 0.0055115512502467556, 6)
mf_scanner = mf.as_scanner()
pmol = mol.copy()
e1 = mf_scanner(
pmol.set_geom_(
'O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
e2 = mf_scanner(
pmol.set_geom_(
'O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))
self.assertAlmostEqual(g[0, 2], (e1 - e2) / 2e-4 * lib.param.BOHR, 5)
def initialization_pyscf(self):
if (self.scf_eng.mo_coeff is NotImplemented or self.scf_eng.mo_coeff is None) and self.init_scf:
self.scf_eng.kernel()
if not self.scf_eng.converged:
warnings.warn("SCF not converged!")
if isinstance(self.scf_eng, dft.rks.RKS):
self.xc = self.scf_eng.xc
self.grids = self.scf_eng.grids
self.xc_type = dft.libxc.xc_type(self.xc)
self.cx = dft.numint.NumInt().hybrid_coeff(self.xc)
self.scf_grad = grad.rks.Gradients(self.scf_eng)
self.scf_hess = hessian.rks.Hessian(self.scf_eng)
else:
self.scf_grad = grad.RHF(self.scf_eng)
self.scf_hess = hessian.RHF(self.scf_eng)
return
def get_forces(self, atoms=None):
if self.method == 'HF':
mf = scf.RHF(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0)).run()
gradient = grad.RHF(mf).kernel()
forces = gradient * convert_forces
self.results['forces'] = forces
return forces
elif self.method == "DFT":
mf = dft.RKS(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0)).run()
mf.xc = self.xc
#gradient = grad.rks(mf).kernel()
gradient = mf.nuc_grad_method().kernel()
forces = gradient * convert_forces
self.results['forces'] = forces
return forces
elif self.method == "MP2":
mf = scf.RHF(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0)).run()
mp2 = mp.MP2(mf).run()
gradient = mp2.nuc_grad_method().kernel()
forces = gradient * convert_forces
self.results['forces'] = forces
return forces
def calculate(self,
atoms=None,
properties=['energy', 'forces'],
system_changes=[
'positions', 'numbers', 'cell', 'pbc', 'charges',
'magmoms'
]):
Calculator.calculate(self, atoms)
calc_molcell = self.molcell.copy()
calc_molcell.atom = ase_atoms_to_pyscf(atoms)
# calc_molcell.a = atoms.cell
calc_molcell.build(None, None)
self.mf = self.mf_class(calc_molcell)
for key in self.mf_dict:
self.mf.__dict__[key] = self.mf_dict[key]
self.results['energy'] = self.mf.scf(verbose=0)
self.results['forces'] = -1 * grad.RHF(self.mf).kernel(
) # convert forces to gradient (*-1) !!!!! for the NEB run
self.results['mf'] = self.mf
-486.638981725713393)
print('-----------------------------------')
mol = gto.M(verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis='631g')
mf = scf.RHF(mol)
ehf = mf.scf()
mycc = ccsd.CCSD(mf)
mycc.conv_tol = 1e-10
mycc.conv_tol_normt = 1e-10
ecc, t1, t2 = mycc.kernel()
l1, l2 = mycc.solve_lambda()
g1 = kernel(mycc, t1, t2, l1, l2, mf_grad=grad.RHF(mf))
print('gcc')
print(g1)
#[[ 0 0 1.00950925e-02]
# [ 0 2.28063426e-02 -5.04754623e-03]
# [ 0 -2.28063426e-02 -5.04754623e-03]]
lib.parameters.BOHR = 1
r = 1.76 #.748
mol = gto.M(verbose=0, atom='''H 0 0 0; H 0 0 %f''' % r, basis='631g')
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
ehf0 = mf.scf()
ghf = grad.RHF(mf).grad()
mycc = ccsd.CCSD(mf)
mycc.conv_tol = 1e-10
def test_energy_nuc(self):
rhf = scf.RHF(h2o)
g = grad.RHF(rhf)
self.assertAlmostEqual(finger(g.grad_nuc()), 10.086972893020102, 9)
def test_nr_rhf(self):
rhf = scf.RHF(h2o)
rhf.conv_tol = 1e-14
rhf.kernel()
g = grad.RHF(rhf)
self.assertAlmostEqual(finger(g.grad_elec()), 10.126405944938071, 6)
if __name__ == '__main__':
from pyscf import gto
from pyscf import scf
from pyscf.cc import ccsd
from pyscf import grad
mol = gto.M(verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis='631g')
mf = scf.RHF(mol).run()
mycc = ccsd.CCSD(mf)
ecc, t1, t2 = mycc.kernel()
l1, l2 = mycc.solve_lambda()
g1 = kernel(mycc, t1, t2, l1, l2)
ghf = grad.RHF(mf).grad()
print('gcc')
print(ghf + g1)
print(lib.finger(g1) - -0.042511000925747583)
#[[ 0 0 1.00950969e-02]
# [ 0 2.28063353e-02 -5.04754844e-03]
# [ 0 -2.28063353e-02 -5.04754844e-03]]
print('-----------------------------------')
mol = gto.M(verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis='631g')
mf = scf.RHF(mol).run()
mycc = ccsd.CCSD(mf)
mycc.frozen = [0, 1, 10, 11, 12]
def test_energy_nuc(self):
rhf = scf.RHF(mol)
rhf.scf()
g = grad.RHF(rhf)
self.assertAlmostEqual(finger(g.grad_nuc()), 8.2887823210941249, 9)
def test_grad(self):
coords = [(0.0,0.1,0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges).run()
hfg = itrf.mm_charge_grad(grad.RHF(mf), coords, charges).run()
self.assertAlmostEqual(numpy.linalg.norm(hfg.de), 30.316453059873059, 9)
fakemol._built = True
return fakemol
if __name__ == '__main__':
from pyscf import scf, cc, grad
mol = gto.Mole()
mol.atom = ''' O 0.00000000 0.00000000 -0.11081188
H -0.00000000 -0.84695236 0.59109389
H -0.00000000 0.89830571 0.52404783 '''
mol.basis = 'cc-pvdz'
mol.build()
coords = [(0.5, 0.6, 0.8)]
#coords = [(0.0,0.0,0.0)]
charges = [-0.5]
mf = mm_charge(scf.RHF(mol), coords, charges)
print(mf.kernel()) # -76.3206550372
mycc = cc.ccsd.CCSD(mf)
mycc.conv_tol = 1e-10
mycc.conv_tol_normt = 1e-10
ecc, t1, t2 = mycc.kernel() # ecc = -0.228939687075
l1, l2 = mycc.solve_lambda()[1:]
hfg = mm_charge_grad(grad.RHF(mf), coords, charges)
g1 = grad.ccsd.kernel(mycc, t1, t2, l1, l2, mf_grad=hfg)
print(g1 + hfg.grad_nuc(mol))
# [[-0.50179182 -0.61489747 -0.96396085]
# [-0.077348 -0.23457358 0.02839861]
# [-0.44182244 0.14559838 -0.22348068]]
[1, (0., 0.757, -0.587)]],
basis='631g')
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
ehf = mf.scf()
mycc = ccsd.CCSD(mf)
mycc.conv_tol = 1e-10
mycc.conv_tol_normt = 1e-10
ecc, t1, t2 = mycc.kernel()
eris = mycc.ao2mo()
e3ref = ccsd_t.kernel(mycc, eris, t1, t2)
print ehf + ecc + e3ref
eris = mycc.ao2mo(mf.mo_coeff)
conv, l1, l2 = ccsd_t_lambda.kernel(mycc, eris, t1, t2)
g1 = kernel(mycc, t1, t2, l1, l2, eris=eris, mf_grad=grad.RHF(mf))
print(g1 + grad.grad_nuc(mol))
#O 0.0000000000 0.0000000000 -0.0112045345
#H 0.0000000000 0.0234464201 0.0056022672
#H 0.0000000000 -0.0234464201 0.0056022672
mol = gto.M(verbose=0,
atom='''
H -1.90779510 0.92319522 0.08700656
H -1.08388168 -1.61405643 -0.07315086
H 2.02822318 -0.61402169 0.09396693
H 0.96345360 1.30488291 -0.10782263
''',
unit='bohr',
basis='631g')
mf = scf.RHF(mol)
def model_cisd(q, params, full_id):
"""
"""
Id = Cpp2Py(full_id)
indx = Id[-1]
r = q.col(indx)
x1 = r.get(0)
y1 = r.get(1)
z1 = r.get(2)
x2 = r.get(3)
y2 = r.get(4)
z2 = r.get(5)
r = (1.0 / 1.889725989) * r # convert to Angst
mol = gto.M(atom=[['H', (x1, y1, z1)], ['H', (x2, y2, z2)]], basis="631g")
mf = scf.RHF(mol)
mf.verbose = -1
res_mf = mf.kernel()
print "HF energy = ", res_mf
# force = mf.nuc_grad_method().kernel()
# force = mf.grad()
force = grad.RHF(mf).kernel()
print force
"""
myci = ci.cisd.CISD(mf)
myci.verbose = -1
myci.nstates = 1
res_ci = myci.kernel()
print "CISD correlation energy = ", res_ci[0]
print "CISD vectors = ", res_ci[1]
force = myci.nuc_grad_method().kernel(state=0)
print force
"""
obj = tmp()
obj.ham_dia = CMATRIX(1, 1)
obj.ovlp_dia = CMATRIX(1, 1)
d1ham_dia = CMATRIXList()
dc1_dia = CMATRIXList()
for i in xrange(6):
d1ham_dia.append(CMATRIX(1, 1))
dc1_dia.append(CMATRIX(1, 1))
obj.ham_dia.set(0, 0, (res_mf) * (1.0 + 0.0j))
# obj.ham_dia.set(0,0, (res_mf + res_ci[0])*(1.0+0.0j) )
obj.ovlp_dia.set(0, 0, 1.0 + 0.0j)
# d Hdia / dR_0
d1ham_dia[0].set(0, 0, (force[0][0]) * (1.0 + 0.0j))
d1ham_dia[1].set(0, 0, (force[0][1]) * (1.0 + 0.0j))
d1ham_dia[2].set(0, 0, (force[0][2]) * (1.0 + 0.0j))
d1ham_dia[3].set(0, 0, (force[1][0]) * (1.0 + 0.0j))
d1ham_dia[4].set(0, 0, (force[1][1]) * (1.0 + 0.0j))
d1ham_dia[5].set(0, 0, (force[1][2]) * (1.0 + 0.0j))
for i in xrange(6):
# <dia| d/dR_0| dia >
dc1_dia[i].set(0, 0, 0.0 + 0.0j)
obj.d1ham_dia = d1ham_dia
obj.dc1_dia = dc1_dia
return obj
