def test_water_pp_pb(self):
""" This is for initializing with SIESTA radial orbitals """
from numpy import einsum, array
import os
dname = os.path.dirname(os.path.abspath(__file__))
sv = mf(label='water', cd=dname)
sv.diag_check()
self.assertTrue(abs(sv.ucell).sum()>0)
pb = sv.pb
self.assertEqual(sv.norbs, 23)
self.assertEqual(len(pb.bp2info), 3)
vden = pb.get_ac_vertex_array()
ccden = pb.get_da2cc_den()
moms = pb.comp_moments()
oref = sv.overlap_coo().toarray()
over = einsum('lab,l->ab', vden, moms[0])
dcoo = sv.dipole_coo()
dref = array([dc.toarray() for dc in dcoo])
dipo = einsum('lab,lx->xab', vden, moms[1])
emean = (abs(oref-over).sum()/(oref.size))
emax = (abs(oref-over).max())
self.assertAlmostEqual(emean, 0.000102115844911, 4)
self.assertAlmostEqual(emax, 0.00182562129245, 4)
emean = (abs(dref-dipo).sum()/(dref.size))
emax = (abs(dref-dipo).max())
self.assertAlmostEqual(emean, 0.000618731257284, 4)
self.assertAlmostEqual(emax, 0.0140744946617, 4)
def test_dens_elec(self):
""" Compute density in coordinate space with scf, integrate and compare with number of electrons """
from timeit import default_timer as timer
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
dm = sv.make_rdm1()
#dm = sv.comp_dm()
#print(sv.get_occupations())
#print(dir(sv.ao_log) )
#print((sv.ao_log.psi_log[0][0]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[0][1]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[0][2]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[0][3]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[0][4]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#
#print((sv.ao_log.psi_log[1][0]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[1][1]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
#print((sv.ao_log.psi_log[1][2]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum())
grid = sv.build_3dgrid_pp(level=5)
#t1 = timer()
#dens1 = sv.dens_elec_vec(grid.coords, dm)
#t2 = timer(); print(t2-t1); t1 = timer()
t1 = timer()
dens = sv.dens_elec(grid.coords, dm)
#t2 = timer(); print(t2-t1); t1 = timer()
nelec = np.einsum("is,i", dens, grid.weights)[0]
#t2 = timer(); print(t2-t1, nelec, sv.hsx.nelec, dens.shape); t1 = timer()
self.assertAlmostEqual(nelec, sv.hsx.nelec, 2)
def test_aos_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=20, ny=20, nz=20) aos = sv.comp_aos_den(cc.get_coords()) self.assertEqual(aos.shape[0], cc.nx*cc.ny*cc.nz) self.assertEqual(aos.shape[1], sv.norbs)
def test_aos_libnao(self):
""" Computing of the atomic orbitals """
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
cc = Cube(sv, nx=20, ny=20, nz=20)
aos = sv.comp_aos_den(cc.get_coords())
self.assertEqual(aos.shape[0], cc.nx * cc.ny * cc.nz)
self.assertEqual(aos.shape[1], sv.norbs)
def test_sv_after_gpaw(self):
""" init ao_log_c with it radial orbitals from GPAW """
if calc is None: return
self.assertTrue(hasattr(calc, 'setups'))
sv = mf(gpaw=calc)
self.assertEqual(sv.ao_log.nr, 1024)
def test_sv_after_gpaw(self):
""" init ao_log_c with it radial orbitals from GPAW """
if calc is None: return
self.assertTrue(hasattr(calc, 'setups'))
sv = mf(gpaw=calc)
self.assertEqual(sv.ao_log.nr, 1024)
def test_exc(self): """ Compute exchange-correlation energy """ from timeit import default_timer as timer sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) dm = sv.make_rdm1() exc = sv.exc(dm, xc_code='1.0*LDA,1.0*PZ', level=4) #self.assertAlmostEqual(exc, -4.1422234271159333) ? redone water? self.assertAlmostEqual(exc, -4.1422239276270201)
def test_mo_cube_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=40, ny=40, nz=40) co2val = sv.comp_aos_den(cc.get_coords()) nocc_0t = int(sv.nelectron / 2) c2orb = np.dot(co2val, sv.wfsx.x[0,0,nocc_0t,:,0]).reshape((cc.nx, cc.ny, cc.nz)) cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_sv_after_gpaw(self):
""" init ao_log_c with it radial orbitals from GPAW """
if calc is None: return
self.assertTrue(hasattr(calc, 'setups'))
sv = mf(gpaw=calc)
self.assertEqual(sv.ao_log.nr, 1024)
over = sv.overlap_coo().toarray()
error = sv.hsx.check_overlaps(over)
self.assertLess(error, 1e-4)
def test_mo_cube_libnao(self):
""" Computing of the atomic orbitals """
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
cc = Cube(sv, nx=40, ny=40, nz=40)
co2val = sv.comp_aos_den(cc.get_coords())
nocc_0t = int(sv.nelectron / 2)
c2orb = np.dot(co2val, sv.wfsx.x[0, 0, nocc_0t, :, 0]).reshape(
(cc.nx, cc.ny, cc.nz))
cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_137_h2o_rks_nonin_pb(self):
""" This """
mol = gto.M(verbose=1,
atom='O 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',
basis='cc-pvdz')
gto_mf = dft.RKS(mol)
gto_mf.kernel()
nao_mf = mf(gto=mol, mf=gto_mf, gen_pb=False)
comega = np.arange(0.0, 2.0, 0.01) + 1j * 0.03
pnonin = -nao_mf.polariz_nonin_ave_matelem(comega).imag
data = np.array([comega.real * HARTREE2EV, pnonin])
np.savetxt('test_137_h2o_rks_nonin_pb.txt', data.T, fmt=['%f', '%f'])
data_ref = np.loadtxt('test_137_h2o_rks_nonin_pb.txt-ref').T
self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
def test_dens_elec(self):
""" Compute density in coordinate space with scf, integrate and compare with number of electrons """
from timeit import default_timer as timer
gto_mf = scf_gto.RKS(mol)
gto_mf.kernel()
sv = mf(mf=gto_mf, gto=mol)
dm = sv.make_rdm1()
grid = sv.build_3dgrid_pp(level=5)
dens = sv.dens_elec(grid.coords, dm)
nelec = np.einsum("is,i", dens, grid.weights)[0]
self.assertAlmostEqual(nelec, sv.nelectron, 6)
def test_siesta2sv_df(self):
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 import mf
sv = mf(label=label)
self.assertEqual(sv.norbs, 10)
self.assertTrue(sv.diag_check())
self.assertTrue(sv.overlap_check())
def test_vrtx_cc_apairs(self):
""" This is to test a batch generation vertices for bilocal atomic pairs. """
from numpy import allclose
dname = os.path.dirname(os.path.abspath(__file__))
sv = mf(label='water', cd=dname)
pbb = sv.pb
pba = prod_basis(sv)
for a,b in zip(pba.bp2info,pbb.bp2info):
for a1,a2 in zip(a.atoms,b.atoms): self.assertEqual(a1,a2)
for a1,a2 in zip(a.cc2a, b.cc2a): self.assertEqual(a1,a2)
self.assertTrue(allclose(a.vrtx, b.vrtx))
self.assertTrue(allclose(a.cc, b.cc))
self.assertLess(abs(pbb.get_da2cc_sparse().tocsr()-pba.get_da2cc_sparse().tocsr()).sum(), 1e-9)
self.assertLess(abs(pbb.get_dp_vertex_sparse().tocsr()-pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)
def test_siesta2sv_df(self):
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 import mf
sv = mf(label=label)
self.assertEqual(sv.norbs, 10)
self.assertTrue( sv.diag_check() )
self.assertTrue( sv.overlap_check())
def test_vrtx_cc_apairs(self):
""" This is to test a batch generation vertices for bilocal atomic pairs. """
from numpy import allclose
dname = os.path.dirname(os.path.abspath(__file__))
sv = mf(label='water', cd=dname)
pbb = sv.pb
pba = prod_basis(sv)
for a, b in zip(pba.bp2info, pbb.bp2info):
for a1, a2 in zip(a.atoms, b.atoms):
self.assertEqual(a1, a2)
for a1, a2 in zip(a.cc2a, b.cc2a):
self.assertEqual(a1, a2)
self.assertTrue(allclose(a.vrtx, b.vrtx))
self.assertTrue(allclose(a.cc, b.cc))
self.assertLess(
abs(pbb.get_da2cc_sparse().tocsr() -
pba.get_da2cc_sparse().tocsr()).sum(), 1e-9)
self.assertLess(
abs(pbb.get_dp_vertex_sparse().tocsr() -
pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)
def test_read_siesta_bulk_spin(self):
""" Test reading of bulk, spin-resolved SIESTA calculation """
chdir = os.path.dirname(os.path.abspath(__file__)) + '/ice'
sv = mf(label='siesta', cd=chdir)
sv.diag_check()
def test_fireball(self):
""" Test computation of matrix elements of overlap after fireball """
sv = mf(fireball="fireball.out", gen_pb=False)
s_ref = sv.hsx.s4_csr.toarray()
s = sv.overlap_coo().toarray()
def test_dft_sv(self):
""" Try to compute the xc potential """
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
vxc = sv.vxc_lil()
def test_sf_gw_res_corr(self): """ This is choice of wmin and wmax in GW """ mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587''', basis = 'cc-pvdz',) gto_mf = scf.RHF(mol) gto_mf.kernel() s = mf(mf=gto_mf, gto=mol)
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao import mf
dname = os.path.dirname(os.path.abspath(__file__))
dft = mf(label='water', cd=dname)
class KnowValues(unittest.TestCase):
def test_dos(self):
""" This is DoS with the KS eigenvalues """
omegas = np.linspace(-1.0,1.0,500)+1j*0.01
dos = dft.dos(omegas)
data = np.array([27.2114*omegas.real, dos])
np.savetxt('water.dos.txt', data.T, fmt=['%f','%f'])
data_ref = np.loadtxt(dname+'/water.dos.txt-ref')
self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05))
def test_pdos(self):
""" This is PDoS with SIESTA starting point """
omegas = np.linspace(-1.0,1.0,500)+1j*0.01
pdos = dft.pdos(omegas)
data = np.array([27.2114*omegas.real, pdos[0], pdos[1], pdos[2]])
np.savetxt('water.pdos.txt', data.T)
data_ref = np.loadtxt(dname+'/water.pdos.txt-ref')
self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05))
if __name__ == "__main__": unittest.main()
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import print_function, division
import os,unittest
from pyscf.nao import mf
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
class KnowValues(unittest.TestCase):
def test_init_sv_libnao(self):
""" Init system variables on libnao's site """
sv.init_libnao()
if __name__ == "__main__": unittest.main()
def test_read_siesta_bulk_spin(self): """ Test reading of bulk, spin-resolved SIESTA calculation """ chdir = os.path.dirname(os.path.abspath(__file__))+'/ice' sv = mf(label='siesta', cd=chdir) sv.diag_check()
s = np.sqrt(ss + 0.25) - 0.5
return ss, s * 2 + 1
#
# Example of reading pySCF mean-field calculation.
#
if __name__ == "__main__":
from pyscf import gto, scf as scf_gto
from pyscf.nao import nao, mf
""" 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='ccpvdz') # coordinates in Angstrom!
dft = scf_gto.RKS(mol)
dft.kernel()
sv = mf(mf=dft, gto=dft.mol, rcut_tol=1e-9, nr=512, rmin=1e-6)
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)
print(dir(sv.pb))
print(sv.pb.norbs)
print(sv.pb.npdp)
print(sv.pb.c2s[-1])
def test_fireball(self): """ Test computation of matrix elements of overlap after fireball """ sv = mf(fireball="fireball.out", gen_pb=False) s_ref = sv.hsx.s4_csr.toarray() s = sv.overlap_coo().toarray() print(abs(s-s_ref).sum())
ax.grid(True, which='both')
ax.axhline(y=0, color='k')
ax.axvline(x=0, color='k')
plt.ylim(-3.0,3.0)
plt.show()
#
# Example of reading pySCF mean-field calculation.
#
if __name__=="__main__":
from pyscf import gto, scf as scf_gto
from pyscf.nao import nao, mf
""" 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='ccpvdz') # coordinates in Angstrom!
dft = scf_gto.RKS(mol)
dft.kernel()
sv = mf(mf=dft, gto=dft.mol, rcut_tol=1e-9, nr=512, rmin=1e-6)
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)
print(dir(sv.pb))
print(sv.pb.norbs)
print(sv.pb.npdp)
print(sv.pb.c2s[-1])
from __future__ import print_function, division
import os, unittest, numpy as np
from pyscf.nao import mf
dname = os.path.dirname(os.path.abspath(__file__))
dft = mf(label='water', cd=dname)
class KnowValues(unittest.TestCase):
def test_dos(self):
""" This is DoS with the KS eigenvalues """
omegas = np.linspace(-1.0, 1.0, 500) + 1j * 0.01
dos = dft.dos(omegas)
data = np.array([27.2114 * omegas.real, dos])
np.savetxt('water.dos.txt', data.T, fmt=['%f', '%f'])
data_ref = np.loadtxt(dname + '/water.dos.txt-ref')
self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05))
def test_pdos(self):
""" This is PDoS with SIESTA starting point """
omegas = np.linspace(-1.0, 1.0, 500) + 1j * 0.01
pdos = dft.pdos(omegas)
data = np.array([27.2114 * omegas.real, pdos[0], pdos[1], pdos[2]])
np.savetxt('water.pdos.txt', data.T)
data_ref = np.loadtxt(dname + '/water.pdos.txt-ref')
self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05))
if __name__ == "__main__":
unittest.main()
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import print_function, division
from os.path import abspath, dirname
from pyscf.nao import mf
import unittest, numpy as np
sv = mf(label='water', cd=dirname(abspath(__file__)))
pb = sv.pb
vab_arr_ref = pb.get_dp_vertex_array()
class KnowValues(unittest.TestCase):
def test_pb_doubly_sparse(self):
""" This is to test generation of a doubly sparse format. """
self.assertEqual(len(vab_arr_ref.shape), 3)
self.assertEqual(vab_arr_ref.shape, (pb.npdp,pb.norbs,pb.norbs))
vab_ds = pb.get_dp_vertex_doubly_sparse(axis=2)
vab_arr = vab_ds.toarray()
self.assertLess(abs(vab_arr-vab_arr_ref).sum()/vab_arr.size, 1e-15)
def test_pb_sparse(self):
""" This is to test generation of a doubly sparse format. """