def test_load_kernel(self):
data_ref_nonin = np.loadtxt(dname +
'/water.tddft_iter.omega.pxx.txt-ref')[:,
1]
data_ref_inter = np.loadtxt(
dname + '/water.tddft_iter.omega.inter.pxx.txt-ref')[:, 1]
for form in ["txt", "npy", "hdf5"]:
td = tddft_iter_c(pb.sv,
pb,
tddft_iter_broadening=1e-2,
xc_code='RPA',
load_kernel=True,
kernel_fname="kernel." + form,
kernel_format=form,
kernel_path_hdf5="kernel_pack")
# check nonin
omegas = np.linspace(0.0, 2.0, 500) + 1j * td.eps
pxx = td.comp_nonin(omegas).imag
self.assertTrue(
np.allclose(data_ref_nonin, pxx, rtol=1.0, atol=1e-05))
# check inter
omegas = np.linspace(0.0, 2.0, 150) + 1j * td.eps
pxx = -td.comp_polariz_xx(omegas).imag
self.assertTrue(
np.allclose(data_ref_inter, pxx, 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_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 test_tddft_iter(self):
""" This is iterative TDDFT with SIESTA starting point """
td = tddft_iter_c(pb.sv, pb)
self.assertTrue(hasattr(td, 'x'))
self.assertTrue(
td.ksn2f.sum() ==
8.0) # water: O -- 6 electrons in the valence + H2 -- 2 electrons
self.assertEqual(td.xocc.shape[0], 4)
self.assertEqual(td.xvrt.shape[0], 19)
dn0 = td.apply_rf0(td.moms1[:, 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
#pxx = np.zeros_like(omegas)
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'])
# 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'])