def test_vrtx_cc_apairs(self):
""" This is to test a batch generation vertices for bilocal atomic pairs. """
from pyscf.nao import system_vars_c, prod_basis_c
from numpy import allclose
import os
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
pbb = prod_basis_c().init_prod_basis_pp_batch(sv)
pba = prod_basis_c().init_prod_basis_pp(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_coo().tocsr() -
pba.get_da2cc_coo().tocsr()).sum(), 1e-9)
self.assertLess(
abs(pbb.get_dp_vertex_coo().tocsr() -
pba.get_dp_vertex_coo().tocsr()).sum(), 1e-10)
def test_water_pp_pb(self):
""" This is for initializing with SIESTA radial orbitals """
from pyscf.nao import system_vars_c, prod_basis_c
from numpy import einsum, array
import os
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
self.assertTrue(abs(sv.ucell).sum() > 0)
pb = prod_basis_c().init_prod_basis_pp(sv)
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 do_overlap_check_of_pb(self, **kvargs): from pyscf.nao import prod_basis_c, vertex_loop_c self.pb = prod_basis_c(self.sv, **kvargs) self.vl = vertex_loop_c(self.pb, **kvargs) self.mom0,self.mom1 = self.pb.prod_log.comp_moments() ad2cc = self.pb.get_ad2cc_den() pab2v = self.pb.get_vertex_array()
def test_tddft_iter_lda(self):
""" Compute polarization with LDA TDDFT """
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
from pyscf.nao.m_comp_dm import comp_dm
from timeit import default_timer as timer
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
pb = prod_basis_c().init_prod_basis_pp(sv, jcutoff=7)
td = tddft_iter_c(pb.sv,
pb,
tddft_iter_broadening=1e-2,
xc_code='LDA,PZ',
level=0)
omegas = np.linspace(0.0, 2.0, 150) + 1j * td.eps
pxx = -td.comp_polariz_xx(omegas).imag
data = np.array([omegas.real * 27.2114, pxx])
np.savetxt('water.tddft_iter_lda.omega.inter.pxx.txt',
data.T,
fmt=['%f', '%f'])
data_ref = np.loadtxt(dname +
'/water.tddft_iter_lda.omega.inter.pxx.txt-ref')
#print(' td.rf0_ncalls ', td.rf0_ncalls)
#print(' td.matvec_ncalls ', td.matvec_ncalls)
self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05))
def run_tddft_iter(calculator, label, freq):
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
if label == "siesta":
sv = system_vars_c().init_siesta_xml()
elif label == "gpaw":
sv = system_vars_c().init_gpaw(calculator)
else:
raise ValueError("Only siesta or gpaw calculator for the moment!")
pb = prod_basis_c().init_prod_basis_pp(sv)
td = tddft_iter_c(pb.sv, pb, tddft_iter_broadening=1e-2)
omegas = np.linspace(freq[0], freq[freq.shape[0] - 1],
freq.shape[0]) + 1j * td.eps
pxx_nonin = np.zeros(omegas.shape[0], dtype=float)
pxx_inter = np.zeros(omegas.shape[0], dtype=float)
vext = np.transpose(td.moms1)
for iomega, omega in enumerate(omegas):
pxx_nonin[iomega] = -np.dot(td.apply_rf0(vext[0, :], omega),
vext[0, :]).imag
pxx_inter = -td.comp_polariz_xx(omegas).imag
return pxx_nonin, pxx_inter
def test_bse_iter_rpa(self):
""" Compute polarization with LDA TDDFT """
from timeit import default_timer as timer
from pyscf.nao import system_vars_c, prod_basis_c, bse_iter_c
from timeit import default_timer as timer
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
pb = prod_basis_c().init_prod_basis_pp(sv)
bse = bse_iter_c(pb.sv, pb, iter_broadening=1e-2)
omegas = np.linspace(0.0, 2.0, 500) + 1j * bse.eps
dab = [d.toarray() for d in sv.dipole_coo()]
pxx = np.zeros(len(omegas))
for iw, omega in enumerate(omegas):
for ixyz in range(1):
vab = bse.apply_l0(dab[ixyz], omega)
pxx[iw] = pxx[iw] - (vab.imag * dab[ixyz]).sum()
data = np.array([omegas.real * 27.2114, pxx])
#np.savetxt('water.bse_iter.omega.nonin.pxx.txt', data.T, fmt=['%f','%f'])
data_ref = np.loadtxt(dname +
'/water.bse_iter_rpa.omega.nonin.pxx.txt-ref')
#print(' bse.l0_ncalls ', bse.l0_ncalls)
self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05))
def test_fxc(self):
""" Compute TDDFT interaction kernel """
from timeit import default_timer as timer
from pyscf.nao import system_vars_c, prod_basis_c
from pyscf.nao.m_comp_dm import comp_dm
from timeit import default_timer as timer
sv = system_vars_c().init_siesta_xml(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
pb = prod_basis_c().init_prod_basis_pp(sv)
dm = comp_dm(sv.wfsx.x, sv.get_occupations())
fxc = pb.comp_fxc_lil(dm, xc_code='1.0*LDA,1.0*PZ', level=4)
def test_ls_contributing(self):
""" To test the list of contributing centers """
from pyscf.nao import system_vars_c, prod_basis_c
sv = system_vars_c().init_pyscf_gto(mol)
pb = prod_basis_c()
pb.sv = sv
pb.sv.ao_log.sp2rcut[0] = 10.0
pb.prod_log = sv.ao_log
pb.prod_log.sp2rcut[0] = 10.0
pb.ac_rcut = max(sv.ao_log.sp2rcut)
pb.ac_npc_max = 10
lsc = pb.ls_contributing(0, 1)
self.assertEqual(len(lsc), 10)
lsref = [0, 1, 13, 7, 5, 43, 42, 39, 38, 10]
for i, ref in enumerate(lsref):
self.assertEqual(lsc[i], ref)
def test_bse_rpa(self):
""" Compute polarization with RPA via 2-point non-local potentials (BSE solver) """
from timeit import default_timer as timer
from pyscf.nao import system_vars_c, prod_basis_c, bse_iter_c
from timeit import default_timer as timer
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
pb = prod_basis_c().init_prod_basis_pp(sv)
bse = bse_iter_c(pb.sv, pb, iter_broadening=1e-2)
omegas = np.linspace(0.0, 2.0, 150) + 1j * bse.eps
pxx = np.zeros(len(omegas))
for iw, omega in enumerate(omegas):
for ixyz in range(1):
vab = bse.apply_l(bse.dab[ixyz], omega)
pxx[iw] = pxx[iw] - (vab.imag * bse.dab[ixyz]).sum()
data = np.array([omegas.real * 27.2114, pxx])
#np.savetxt('water.bse_iter_rpa.omega.inter.pxx.txt', data.T, fmt=['%f','%f'])
data_ref = np.loadtxt(dname +
'/water.bse_iter_rpa.omega.inter.pxx.txt-ref')
""" Our standard minimal check """
dipcoo = self.sv.dipole_coo(**kw)
mom0,mom1 = self.comp_moments()
vpab = self.get_ac_vertex_array()
xyz2err = []
for i,dref in enumerate(dipcoo):
dref = dref.toarray()
dprd = np.einsum('p,pab->ab', mom1[:,i],vpab)
xyz2err.append([abs(dprd-dref).sum()/dref.size, np.amax(abs(dref-dprd))])
return xyz2err
#
#
#
if __name__=='__main__':
from pyscf.nao import prod_basis_c, nao
from pyscf.nao.m_overlap_coo import overlap_coo
from pyscf import gto
import numpy as np
mol = gto.M(atom='O 0 0 0; H 0 0 0.5; H 0 0.5 0', basis='ccpvdz') # coordinates in Angstrom!
sv = nao(gto=mol)
print(sv.atom2s)
s_ref = overlap_coo(sv).todense()
pb = prod_basis_c()
pb.init_prod_basis_pp_batch(sv)
mom0,mom1=pb.comp_moments()
pab2v = pb.get_ac_vertex_array()
s_chk = einsum('pab,p->ab', pab2v,mom0)
print(abs(s_chk-s_ref).sum()/s_chk.size, abs(s_chk-s_ref).max())
# 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 numpy as np
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
sv = system_vars_c().init_siesta_xml(label='siesta', cd='.', force_gamma=True)
pb = prod_basis_c().init_prod_basis_pp(sv)
td = tddft_iter_c(pb.sv, pb)
omegas = np.linspace(0.0,0.25,150)+1j*td.eps
pxx = -td.comp_polariz_xx(omegas).imag
data = np.array([omegas.real*27.2114, pxx])
print(' td.rf0_ncalls ', td.rf0_ncalls)
print(' td.matvec_ncalls ', td.matvec_ncalls)
np.savetxt('tddft_iter.omega.inter.pxx.txt', data.T, fmt=['%f','%f'])
# 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, numpy as np
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
import h5py
dname = os.path.dirname(os.path.abspath(__file__))
sv = system_vars_c().init_siesta_xml(label='water', cd=dname)
pb = prod_basis_c().init_prod_basis_pp(sv, jcutoff=7)
td = tddft_iter_c(pb.sv, pb, tddft_iter_broadening=1e-2, xc_code='RPA')
np.savetxt("kernel.txt", td.kernel)
np.save("kernel.npy", td.kernel)
hdf = h5py.File("kernel.hdf5", "w")
hdf.create_dataset("kernel_pack", data=td.kernel)
hdf.close()
class KnowValues(unittest.TestCase):
def test_non_inter_polariz(self):
""" This is non-interacting polarizability TDDFT with SIESTA starting point """
omegas = np.linspace(0.0, 2.0, 500) + 1j * td.eps
pxx = td.comp_nonin(omegas).imag
from __future__ import print_function, division
import numpy as np
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
sv = system_vars_c().init_siesta_xml(label='siesta', cd='.', force_gamma=True)
pb = prod_basis_c().init_prod_basis_pp(sv)
td = tddft_iter_c(pb.sv, pb)
omegas = np.linspace(0.0, 0.25, 150) + 1j * td.eps
pxx = -td.comp_polariz_xx(omegas).imag
data = np.array([omegas.real * 27.2114, pxx])
print(' td.rf0_ncalls ', td.rf0_ncalls)
print(' td.matvec_ncalls ', td.matvec_ncalls)
np.savetxt('tddft_iter.omega.inter.pxx.txt', data.T, fmt=['%f', '%f'])
# 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 timeit import default_timer as timer
import os
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
from numpy import allclose
t1 = timer()
sv = system_vars_c().init_siesta_xml(label='siesta', cd='.', force_gamma=True)
t2 = timer(); print(t2-t1); t1 = timer()
pbb = prod_basis_c().init_prod_basis_pp_batch(sv)
t2 = timer(); print(t2-t1); t1 = timer()
pba = prod_basis_c().init_prod_basis_pp(sv)
t2 = timer(); print(t2-t1); t1 = timer()
for a,b in zip(pba.bp2info,pbb.bp2info):
for a1,a2 in zip(a.atoms,b.atoms): assert a1==a2
for a1,a2 in zip(a.cc2a, b.cc2a): assert a1==a2
assert allclose(a.vrtx, b.vrtx)
assert allclose(a.cc, b.cc)
print(abs(pbb.get_da2cc_coo().tocsr()-pba.get_da2cc_coo().tocsr()).sum(), \
abs(pbb.get_dp_vertex_coo().tocsr()-pba.get_dp_vertex_coo().tocsr()).sum())
# 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 system_vars_c, prod_basis_c
import unittest, numpy as np
sv = system_vars_c().init_siesta_xml(label='water',
cd=dirname(abspath(__file__)))
pb = prod_basis_c().init_prod_basis_pp_batch(sv)
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. """
self.assertEqual(len(vab_arr_ref.shape), 3)
self.vdata = np.zeros(self.i2inf[-1][0])
for i in range(niter):
s, f, c, tr = self.i2inf[i][0], self.i2inf[
i + 1][0], self.i2inf[i][3], self.i2inf[i][10]
if tr == 0:
self.vdata[s:f] = self.c2d[c]["vertex"].reshape(f - s)
elif tr == 1:
self.vdata[s:f] = einsum('pab->pba',
self.c2d[c]["vertex"]).reshape(f - s)
else:
raise RuntimeError('!tr?')
#
#
#
if __name__ == '__main__':
from pyscf.nao import system_vars_c, prod_basis_c, vertex_loop_c
from pyscf import gto
import numpy as np
from timeit import default_timer as timer
import matplotlib.pyplot as plt
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0',
basis='ccpvdz') # coordinates in Angstrom!
sv = system_vars_c(gto=mol)
pb = prod_basis_c(sv)
vl = vertex_loop_c(pb)
print(dir(vl))
print(vl.vdata.sum())
for i, dref in enumerate(dipcoo):
dref = dref.toarray()
dprd = np.einsum('p,pab->ab', mom1[:, i], vpab)
xyz2err.append([
abs(dprd - dref).sum() / dref.size,
np.amax(abs(dref - dprd))
])
return xyz2err
#
#
#
if __name__ == '__main__':
from pyscf.nao import prod_basis_c, nao
from pyscf.nao.m_overlap_coo import overlap_coo
from pyscf import gto
import numpy as np
mol = gto.M(atom='O 0 0 0; H 0 0 0.5; H 0 0.5 0',
basis='ccpvdz') # coordinates in Angstrom!
sv = nao(gto=mol)
print(sv.atom2s)
s_ref = overlap_coo(sv).todense()
pb = prod_basis_c()
pb.init_prod_basis_pp_batch(sv)
mom0, mom1 = pb.comp_moments()
pab2v = pb.get_ac_vertex_array()
s_chk = einsum('pab,p->ab', pab2v, mom0)
print(abs(s_chk - s_ref).sum() / s_chk.size, abs(s_chk - s_ref).max())
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import print_function, division
from timeit import default_timer as timer
import os
from pyscf.nao import system_vars_c, prod_basis_c, tddft_iter_c
from numpy import allclose
t1 = timer()
sv = system_vars_c().init_siesta_xml(label='siesta', cd='.', force_gamma=True)
t2 = timer()
print('system_vars_c().init_siesta_xml ', t2 - t1)
t1 = timer()
pbb = prod_basis_c().init_prod_basis_pp_batch(sv)
t2 = timer()
print('prod_basis_c().init_prod_basis_pp_batch(sv) ', t2 - t1)
t1 = timer()
pba = prod_basis_c().init_prod_basis_pp(sv)
t2 = timer()
print('prod_basis_c().init_prod_basis_pp(sv) ', t2 - t1)
t1 = timer()
for a, b in zip(pba.bp2info, pbb.bp2info):
for a1, a2 in zip(a.atoms, b.atoms):
assert a1 == a2
for a1, a2 in zip(a.cc2a, b.cc2a):
assert a1 == a2
assert allclose(a.vrtx, b.vrtx)
