def build_3dgrid(me, sp1, R1, sp2, R2, level=3):
from pyscf import dft
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_gauleg import leggauss_ab
assert sp1 >= 0
assert sp2 >= 0
if ((R1 - R2)**2).sum() < 1e-7:
mol = system_vars_c().init_xyzlike(
[[int(me.aos[0].sp2charge[sp1]), R1]])
else:
mol = system_vars_c().init_xyzlike(
[[int(me.aos[0].sp2charge[sp1]), R1],
[int(me.aos[1].sp2charge[sp2]), R2]])
atom2rcut = np.array([
me.aos[isp].sp_mu2rcut[sp].max() for isp, sp in enumerate([sp1, sp2])
])
grids = dft.gen_grid.Grids(mol)
grids.level = level # precision as implemented in pyscf
grids.radi_method = leggauss_ab
grids.build(atom2rcut=atom2rcut)
#grids.build()
return grids
def build_3dgrid3c(me, sp1, sp2, R1, R2, sp3, R3, level=3):
from pyscf import dft
from pyscf.nao.m_system_vars import system_vars_c
d12 = ((R1 - R2)**2).sum()
d13 = ((R1 - R3)**2).sum()
d23 = ((R2 - R3)**2).sum()
z1 = int(me.aos[0].sp2charge[sp1])
z2 = int(me.aos[0].sp2charge[sp2])
z3 = int(me.aos[1].sp2charge[sp3])
rc1 = me.aos[0].sp2rcut[sp1]
rc2 = me.aos[0].sp2rcut[sp2]
rc3 = me.aos[1].sp2rcut[sp3]
if d12 < 1e-7 and d23 < 1e-7:
mol = system_vars_c(atom=[[z1, R1]])
elif d12 < 1e-7 and d23 > 1e-7 and d13 > 1e-7:
mol = system_vars_c(atom=[[z1, R1], [z3, R3]])
elif d23 < 1e-7 and d12 > 1e-7 and d13 > 1e-7:
mol = system_vars_c(atom=[[z1, R1], [z2, R2]])
elif d13 < 1e-7 and d12 > 1e-7 and d23 > 1e-7:
mol = system_vars_c(atom=[[z1, R1], [z2, R2]])
else:
mol = system_vars_c(atom=[[z1, R1], [z2, R2], [z3, R3]])
atom2rcut = np.array([rc1, rc2, rc3])
grids = dft.gen_grid.Grids(mol)
grids.level = level # precision as implemented in pyscf
grids.radi_method = gauss_legendre
grids.build(atom2rcut=atom2rcut)
return grids
def build_3dgrid3c(me, sp1, sp2, R1, R2, sp3, R3, level=3):
from pyscf import dft
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_gauleg import gauss_legendre
d12 = ((R1-R2)**2).sum()
d13 = ((R1-R3)**2).sum()
d23 = ((R2-R3)**2).sum()
z1 = int(me.aos[0].sp2charge[sp1])
z2 = int(me.aos[0].sp2charge[sp2])
z3 = int(me.aos[1].sp2charge[sp3])
rc1 = me.aos[0].sp2rcut[sp1]
rc2 = me.aos[0].sp2rcut[sp2]
rc3 = me.aos[1].sp2rcut[sp3]
if d12<1e-7 and d23<1e-7 :
mol = system_vars_c(atom=[ [z1, R1] ])
elif d12<1e-7 and d23>1e-7 and d13>1e-7:
mol = system_vars_c(atom=[ [z1, R1], [z3, R3] ])
elif d23<1e-7 and d12>1e-7 and d13>1e-7:
mol = system_vars_c(atom=[ [z1, R1], [z2, R2] ])
elif d13<1e-7 and d12>1e-7 and d23>1e-7:
mol = system_vars_c(atom=[ [z1, R1], [z2, R2] ])
else :
mol = system_vars_c(atom=[ [z1, R1], [z2, R2], [z3, R3] ])
atom2rcut=np.array([rc1, rc2, rc3])
grids = dft.gen_grid.Grids(mol)
grids.level = level # precision as implemented in pyscf
grids.radi_method = gauss_legendre
grids.build(atom2rcut=atom2rcut)
return grids
def test_siesta2sv_df(self):
from pyscf import scf
from pyscf.nao.m_siesta_utils import get_siesta_command, get_pseudo
import subprocess
import os
siesta_fdf = """
xml.write .true.
PAO.EnergyShift 100 meV
%block ChemicalSpeciesLabel
1 11 Na
%endblock ChemicalSpeciesLabel
NumberOfAtoms 2
NumberOfSpecies 1
%block AtomicCoordinatesAndAtomicSpecies
0.77573521 0.00000000 0.00000000 1
-0.77573521 0.00000000 0.00000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MD.NumCGsteps 0
COOP.Write .true.
WriteDenchar .true.
"""
label = 'siesta'
fi = open(label + '.fdf', 'w')
print(siesta_fdf, file=fi)
fi.close()
for sp in ['Na']:
try:
os.remove(sp + '.psf')
except:
pass
try:
pppath = get_pseudo(sp)
except:
print('get_pseudo( ' + sp +
' ) is not working--> skip siesta run')
return
os.symlink(pppath, sp + '.psf')
errorcode = subprocess.call(get_siesta_command(label), shell=True)
if errorcode:
raise RuntimeError(
'siesta returned an error: {0}'.format(errorcode))
# run test system_vars
from pyscf.nao.m_system_vars import system_vars_c, diag_check, overlap_check
sv = system_vars_c().init_siesta_xml(label)
self.assertEqual(sv.norbs, 10)
self.assertTrue(sv.diag_check())
self.assertTrue(sv.overlap_check())
if self._nelectron is None:
return tot_electrons(self)
else:
return self._nelectron
#
# Example of reading pySCF orbitals.
#
if __name__=="__main__":
from pyscf import gto
from pyscf.nao.m_system_vars import system_vars_c
import matplotlib.pyplot as plt
""" Interpreting small Gaussian calculation """
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0; Be 1 0 0', basis='ccpvtz') # coordinates in Angstrom!
sv = system_vars_c(gto=mol, tol=1e-8, nr=512, rmin=1e-5)
print(sv.ao_log.sp2norbs)
print(sv.ao_log.sp2nmult)
print(sv.ao_log.sp2rcut)
print(sv.ao_log.sp_mu2rcut)
print(sv.ao_log.nr)
print(sv.ao_log.rr[0:4], sv.ao_log.rr[-1:-5:-1])
print(sv.ao_log.psi_log[0].shape, sv.ao_log.psi_log_rl[0].shape)
sp = 0
for mu,[ff,j] in enumerate(zip(sv.ao_log.psi_log[sp], sv.ao_log.sp_mu2j[sp])):
nc = abs(ff).max()
if j==0 : plt.plot(sv.ao_log.rr, ff/nc, '--', label=str(mu)+' j='+str(j))
if j>0 : plt.plot(sv.ao_log.rr, ff/nc, label=str(mu)+' j='+str(j))
return tot_electrons(self)
else:
return self._nelectron
#
# Example of reading pySCF orbitals.
#
if __name__ == "__main__":
from pyscf import gto
from pyscf.nao.m_system_vars import system_vars_c
import matplotlib.pyplot as plt
""" Interpreting small Gaussian calculation """
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0; Be 1 0 0',
basis='ccpvtz') # coordinates in Angstrom!
sv = system_vars_c(gto=mol, tol=1e-8, nr=512, rmin=1e-5)
print(sv.ao_log.sp2norbs)
print(sv.ao_log.sp2nmult)
print(sv.ao_log.sp2rcut)
print(sv.ao_log.sp_mu2rcut)
print(sv.ao_log.nr)
print(sv.ao_log.rr[0:4], sv.ao_log.rr[-1:-5:-1])
print(sv.ao_log.psi_log[0].shape, sv.ao_log.psi_log_rl[0].shape)
sp = 0
for mu, [ff,
j] in enumerate(zip(sv.ao_log.psi_log[sp],
sv.ao_log.sp_mu2j[sp])):
nc = abs(ff).max()
if j == 0:
for mu1,l1,s1,f1 in self.ao1.sp2info[sp1]:
f1f2_mom = self.ao1.psi_log_mom[sp2][mu2,:] * self.ao1.psi_log_mom[sp1][mu1,:]
l2S.fill(0.0)
for l3 in range( abs(l1-l2), l1+l2+1):
l2S[l3] = (f1f2_mom[:]*bessel_pp[l3,:]).sum() + f1f2_mom[0]*bessel_pp[l3,0]/dkappa
cS.fill(0.0)
for m1 in range(-l1,l1+1):
for m2 in range(-l2,l2+1):
gc,m3 = self.get_gaunt(l1,-m1,l2,m2), m2-m1
for l3ind,l3 in enumerate(range(abs(l1-l2),l1+l2+1)):
if abs(m3) > l3 : continue
cS[m1+_j,m2+_j] = cS[m1+_j,m2+_j] + l2S[l3]*ylm[ l3*(l3+1)+m3] *\
gc[l3ind] * (-1.0)**((3*l1+l2+l3)//2+m2)
self.c2r_( l1,l2, self.jmx,cS,rS,cmat)
oo2co[s1:f1,s2:f2] = rS[-l1+_j:l1+_j+1,-l2+_j:l2+_j+1]
#sys.exit()
oo2co = oo2co * (4*np.pi)**2 * self.interp_pp.dg_jt
return oo2co
if __name__ == '__main__':
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_prod_log import prod_log_c
from pyscf.nao.m_ao_matelem import ao_matelem_c
sv = system_vars_c("siesta")
ra = np.array([0.0, 0.1, 0.2])
rb = np.array([0.0, 0.1, 0.0])
coulo = ao_matelem_c(sv.ao_log).coulomb_am(me, 0, ra, 0, rb)
#
# See above
#
def ao_eval_libnao(ao, ra, isp, coords):
res = np.zeros((ao.sp2norbs[isp],coords.shape[0]), dtype='float64')
ao_eval_libnao_(ao, ra, isp, coords, res)
return res
if __name__ == '__main__':
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_ao_eval import ao_eval
from pyscf.nao.m_ao_eval_libnao import ao_eval_libnao
sv = system_vars_c()
ra = np.array([0.3, -0.5, 0.77], dtype='float64')
#coords = np.array([[0.07716887, 2.82933578, 3.73214881]])
coords = np.random.rand(35580,3)*5.0
print('ao_val2 (reference)')
ao_val1 = ao_eval(sv.ao_log, ra, 0, coords)
print('ao_val2_libnao')
ao_val2 = ao_eval_libnao(sv.ao_log, ra, 0, coords)
print(np.allclose(ao_val1,ao_val2))
for iorb,[oo1,oo2] in enumerate(zip(ao_val1,ao_val2)):
print(iorb, abs(oo1-oo2).argmax(), abs(oo1-oo2).max(), coords[abs(oo1-oo2).argmax(),:])
#
# See above
#
def ao_eval_libnao(ao, ra, isp, coords):
res = np.zeros((ao.sp2norbs[isp], coords.shape[0]), dtype='float64')
ao_eval_libnao_(ao, ra, isp, coords, res)
return res
if __name__ == '__main__':
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_ao_eval import ao_eval
from pyscf.nao.m_ao_eval_libnao import ao_eval_libnao
sv = system_vars_c()
ra = np.array([0.3, -0.5, 0.77], dtype='float64')
#coords = np.array([[0.07716887, 2.82933578, 3.73214881]])
coords = np.random.rand(35580, 3) * 5.0
print('ao_val2 (reference)')
ao_val1 = ao_eval(sv.ao_log, ra, 0, coords)
print('ao_val2_libnao')
ao_val2 = ao_eval_libnao(sv.ao_log, ra, 0, coords)
print(np.allclose(ao_val1, ao_val2))
for iorb, [oo1, oo2] in enumerate(zip(ao_val1, ao_val2)):
print(iorb,
abs(oo1 - oo2).argmax(),
abs(oo1 - oo2).max(), coords[abs(oo1 - oo2).argmax(), :])
l2S.fill(0.0)
for l3 in range(abs(l1 - l2), l1 + l2 + 1):
l2S[l3] = (f1f2_mom[:] * bessel_pp[l3, :]).sum(
) + f1f2_mom[0] * bessel_pp[l3, 0] / dkappa
cS.fill(0.0)
for m1 in range(-l1, l1 + 1):
for m2 in range(-l2, l2 + 1):
gc, m3 = self.get_gaunt(l1, -m1, l2, m2), m2 - m1
for l3ind, l3 in enumerate(
range(abs(l1 - l2), l1 + l2 + 1)):
if abs(m3) > l3: continue
cS[m1+_j,m2+_j] = cS[m1+_j,m2+_j] + l2S[l3]*ylm[ l3*(l3+1)+m3] *\
gc[l3ind] * (-1.0)**((3*l1+l2+l3)//2+m2)
self.c2r_(l1, l2, self.jmx, cS, rS, cmat)
oo2co[s1:f1, s2:f2] = rS[-l1 + _j:l1 + _j + 1,
-l2 + _j:l2 + _j + 1]
#sys.exit()
oo2co = oo2co * (4 * np.pi)**2 * self.interp_pp.dg_jt
return oo2co
if __name__ == '__main__':
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_ao_matelem import ao_matelem_c
sv = system_vars_c("siesta")
ra = np.array([0.0, 0.1, 0.2])
rb = np.array([0.0, 0.1, 0.0])
coulo = ao_matelem_c(sv.ao_log).coulomb_am(me, 0, ra, 0, rb)
grids = build_3dgrid3c(me, sp1, sp2, R1, R2, sp3, R3, **kvargs)
ao1 = grids.weights * ao_eval(me.aos[0], R1, sp1, grids.coords)
ao2 = ao_eval(me.aos[0], R2, sp2, grids.coords)
aoao = np.einsum('ar,br->abr', ao1, ao2)
pbf = ao_eval(me.aos[1], R3, sp3, grids.coords)
abp2eri = np.einsum('abr,pr->abp', aoao, pbf)
return abp2eri
if __name__ == "__main__":
from pyscf.nao.m_system_vars import system_vars_c, ao_matelem_c, prod_log_c
from pyscf.nao.m_eri3c import eri3c
sv = system_vars_c(label='siesta')
R0 = sv.atom2coord[0, :]
prod_log = prod_log_c(sv.ao_log)
me_prod = ao_matelem_c(prod_log)
vc = me_prod.coulomb_am(0, R0, 0, R0)
eri_am = np.einsum('pab,pq->abq', prod_log.sp2vertex[0], vc)
print(eri_am.shape)
print(eri_am.sum(), eri_am.max(), np.argmax(eri_am), eri_am.min(),
np.argmin(eri_am))
vhpf = prod_log.hartree_pot()
me = ao_matelem_c(sv.ao_log, vhpf)
eri_ni = eri3c(me, 0, 0, R0, R0, 0, R0, level=4)
print(eri_ni.shape)
#
def ao_log_hartree(ao, ao_log_hartree_method='lap'):
if ao_log_hartree_method.upper() == 'LAP':
return ao_log_hartree_lap_libnao(ao)
if ao_log_hartree_method.upper() == 'SBT': return ao_log_hartree_sbt(ao)
raise RuntimeError('!method')
#
#
#
if __name__ == '__main__':
from pyscf.nao.m_system_vars import system_vars_c
import matplotlib.pyplot as plt
sv = system_vars_c('siesta')
ao_h_lap = ao_log_hartree(sv.ao_log, ao_log_hartree_method='lap')
ao_h_sbt = ao_log_hartree(sv.ao_log, ao_log_hartree_method='sbt')
sp = 0
for mu, [ff_lap, ff_sbt, j] in enumerate(
zip(ao_h_lap.psi_log[sp], ao_h_sbt.psi_log[sp],
ao_h_sbt.sp_mu2j[sp])):
nc = abs(ff_lap).max()
if j == 0:
plt.plot(ao_h_lap.rr,
ff_lap / nc,
'--',
label=str(mu) + ' j=' + str(j))
plt.plot(ao_h_lap.rr,
for ib,[at,l,ngto,nctr,a,b,c,d] in enumerate(_bas): atom2bas_s[at] = min(atom2bas_s[at],ib)
return atom2bas_s
if __name__ == '__main__':
"""
Compute only bilocal part of the four-orbitals, two-center Coulomb integrals
"""
from pyscf import gto
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_conv_yzx2xyz import conv_yzx2xyz_c
tol = 1e-5
mol = gto.M(atom='O 0 0 0; H 0 -0.1 1; H 0 0.1 -1', basis='ccpvdz')
sv = system_vars_c(gto=mol)
na = sv.natm
for ia1,n1 in zip(range(na), sv.atom2s[1:]-sv.atom2s[0:na]):
for ia2,n2 in zip(range(ia1+1,sv.natm+1), sv.atom2s[ia1+2:]-sv.atom2s[ia1+1:na]):
mol2 = gto.Mole_pure(atom=[mol._atom[ia1], mol._atom[ia2]], basis=mol.basis).build()
bs = get_atom2bas_s(mol2._bas)
ss = (bs[0],bs[1], bs[1],bs[2], bs[0],bs[1], bs[1],bs[2])
eri = mol2.intor('cint2e_sph', shls_slice=ss).reshape([n1,n2,n1,n2])
eri = conv_yzx2xyz_c(mol2).conv_yzx2xyz_4d(eri, 'pyscf2nao', ss).reshape([n1*n2,n1*n2])
ee,xx = np.linalg.eigh(eri)
nlinindep = list(ee>tol).count(True)
print(' ia1, ia2, n1, n2: ', ia1, ia2, n1, n2, eri.shape, n1*n2, nlinindep, n1*n2/nlinindep)
AtomicCoordinatesFormat Ang
NumberOfAtoms 3
NumberOfSpecies 2
%block AtomicCoordinatesAndAtomicSpecies
0.00000000 -0.00164806 0.00000000 1 1 O
0.77573521 0.59332141 0.00000000 2 2 H
-0.77573521 0.59332141 0.00000000 2 3 H
%endblock AtomicCoordinatesAndAtomicSpecies
MD.NumCGsteps 0
MaxSCFIterations 100
COOP.Write .true.
WriteDenchar .true.
"""
label = 'siesta'
print(siesta_fdf, file=open(label+'.fdf', 'w'))
for sp in ['O', 'H']: os.symlink(get_pseudo(sp), sp+'.psf')
errorcode = subprocess.call(get_siesta_command(label), shell=True)
if errorcode: raise RuntimeError('siesta returned an error: {0}'.format(errorcode))
# run test system_vars
from pyscf.nao.m_system_vars import system_vars_c, diag_check, overlap_check
sv = system_vars_c().init_siesta_xml(label = label)
assert sv.norbs == 23
assert diag_check(sv)
assert overlap_check(sv)
grids = build_3dgrid3c(me, sp1,sp2,R1,R2, sp3,R3, **kvargs)
ao1 = grids.weights * ao_eval(me.aos[0], R1, sp1, grids.coords)
ao2 = ao_eval(me.aos[0], R2, sp2, grids.coords)
aoao = np.einsum('ar,br->abr', ao1, ao2)
pbf = ao_eval(me.aos[1], R3, sp3, grids.coords)
abp2eri = np.einsum('abr,pr->abp',aoao,pbf)
return abp2eri
if __name__=="__main__":
from pyscf.nao.m_system_vars import system_vars_c, ao_matelem_c, prod_log_c
from pyscf.nao.m_eri3c import eri3c
sv = system_vars_c(label='siesta')
R0 = sv.atom2coord[0,:]
prod_log = prod_log_c(sv.ao_log)
me_prod = ao_matelem_c(prod_log)
vc = me_prod.coulomb_am(0, R0, 0, R0)
eri_am = np.einsum('pab,pq->abq', prod_log.sp2vertex[0], vc)
print( eri_am.shape )
print( eri_am.sum(), eri_am.max(), np.argmax(eri_am), eri_am.min(), np.argmin(eri_am))
vhpf = prod_log.hartree_pot()
me = ao_matelem_c(sv.ao_log, vhpf)
eri_ni = eri3c(me, 0, 0, R0, R0, 0, R0, level=4)
print( eri_ni.shape )
print( eri_ni.sum(), eri_ni.max(), np.argmax(eri_ni), eri_ni.min(), np.argmin(eri_ni))
1 11 Na
%endblock ChemicalSpeciesLabel
NumberOfAtoms 2
NumberOfSpecies 1
%block AtomicCoordinatesAndAtomicSpecies
0.77573521 0.00000000 0.00000000 1
-0.77573521 0.00000000 0.00000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MD.NumCGsteps 0
COOP.Write .true.
WriteDenchar .true.
"""
label = 'siesta'
print(siesta_fdf, file=open(label+'.fdf', 'w'))
for sp in ['Na']: os.symlink(get_pseudo(sp), sp+'.psf')
errorcode = subprocess.call(get_siesta_command(label), shell=True)
if errorcode: raise RuntimeError('siesta returned an error: {0}'.format(errorcode))
# run test system_vars
from pyscf.nao.m_system_vars import system_vars_c, diag_check, overlap_check
sv = system_vars_c().init_siesta_xml(label = label)
assert sv.norbs == 10
assert diag_check(sv)
assert overlap_check(sv)
for ib,[at,l,ngto,nctr,a,b,c,d] in enumerate(_bas): atom2bas_s[at] = min(atom2bas_s[at],ib)
return atom2bas_s
if __name__ == '__main__':
"""
Compute only bilocal part of the four-orbitals, two-center Coulomb integrals
"""
from pyscf import gto
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_conv_yzx2xyz import conv_yzx2xyz_c
tol = 1e-5
mol = gto.M(atom='O 0 0 0; H 0 -0.1 1; H 0 0.1 -1', basis='ccpvdz')
sv = system_vars_c(gto=mol)
na = sv.natm
for ia1,n1 in zip(range(na), sv.atom2s[1:]-sv.atom2s[0:na]):
for ia2,n2 in zip(range(ia1+1,sv.natm+1), sv.atom2s[ia1+2:]-sv.atom2s[ia1+1:na]):
mol2 = gto.Mole_pure(atom=[mol._atom[ia1], mol._atom[ia2]], basis=mol.basis).build()
bs = get_atom2bas_s(mol2._bas)
ss = (bs[0],bs[1], bs[1],bs[2], bs[0],bs[1], bs[1],bs[2])
eri = mol2.intor('cint2e_sph', shls_slice=ss).reshape([n1,n2,n1,n2])
eri = conv_yzx2xyz_c(mol2).conv_yzx2xyz_4d(eri, 'pyscf2nao', ss).reshape([n1*n2,n1*n2])
ee,xx = np.linalg.eigh(eri)
nlinindep = list(ee>tol).count(True)
print(' ia1, ia2, n1, n2: ', ia1, ia2, n1, n2, eri.shape, n1*n2, nlinindep, n1*n2/nlinindep)
