def test_dens_elec(self):
""" Compute density in coordinate space with system_vars_c, integrate and compare with number of electrons """
from pyscf.nao import system_vars_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__)))
dm = comp_dm(sv.wfsx.x, sv.get_occupations())
#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_exc(self):
""" Compute exchange-correlation energy """
from timeit import default_timer as timer
from pyscf.nao import system_vars_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__)))
dm = comp_dm(sv.wfsx.x, sv.get_occupations())
exc = sv.exc(dm, xc_code='1.0*LDA,1.0*PZ', level=4)
self.assertAlmostEqual(exc, -4.14222392763)
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_dft_sv(self):
""" Try to run DFT with system_vars_c """
from pyscf.nao import system_vars_c
from pyscf.nao.m_comp_dm import comp_dm
from pyscf.nao.m_fermi_dirac import fermi_dirac_occupations
sv = system_vars_c().init_siesta_xml(label='water',
cd=os.path.dirname(
os.path.abspath(__file__)))
ksn2fd = fermi_dirac_occupations(sv.hsx.telec, sv.wfsx.ksn2e,
sv.fermi_energy)
ksn2f = (3 - sv.nspin) * ksn2fd
dm = comp_dm(sv.wfsx.x, ksn2f)
vxc = sv.vxc_lil(dm, 'LDA,PZ')
def comp_dm(self):
""" Computes the density matrix """
from pyscf.nao.m_comp_dm import comp_dm
return comp_dm(self.wfsx.x, self.get_occupations())
def comp_dm(self): """ Computes the density matrix """ from pyscf.nao.m_comp_dm import comp_dm return comp_dm(self.wfsx.x, self.get_occupations())
def __init__(self,
sv,
pb,
tddft_iter_tol=1e-2,
tddft_iter_broadening=0.00367493,
nfermi_tol=1e-5,
telec=None,
nelec=None,
fermi_energy=None,
xc_code='LDA,PZ',
GPU=False,
precision="single",
**kvargs):
""" Iterative TDDFT a la PK, DF, OC JCTC """
from pyscf.nao.m_fermi_dirac import fermi_dirac_occupations
from pyscf.nao.m_comp_dm import comp_dm
import sys
assert tddft_iter_tol > 1e-6
assert type(tddft_iter_broadening) == float
assert sv.wfsx.x.shape[-1] == 1 # i.e. real eigenvectors we accept here
if precision == "single":
self.dtype = np.float32
self.dtypeComplex = np.complex64
elif precision == "double":
self.dtype = np.float64
self.dtypeComplex = np.complex128
else:
raise ValueError("precision can be only single or double")
self.rf0_ncalls = 0
self.l0_ncalls = 0
self.matvec_ncalls = 0
self.tddft_iter_tol = tddft_iter_tol
self.eps = tddft_iter_broadening
self.sv, self.pb, self.norbs, self.nspin = sv, pb, sv.norbs, sv.nspin
self.v_dab = pb.get_dp_vertex_coo(dtype=self.dtype).tocsr()
self.cc_da = pb.get_da2cc_coo(dtype=self.dtype).tocsr()
self.moms0, self.moms1 = pb.comp_moments(dtype=self.dtype)
self.nprod = self.moms0.size
self.kernel, self.kernel_dim = pb.comp_coulomb_pack(dtype=self.dtype)
if xc_code.upper() != 'RPA':
dm = comp_dm(sv.wfsx.x, sv.get_occupations())
pb.comp_fxc_pack(dm,
xc_code,
kernel=self.kernel,
dtype=self.dtype,
**kvargs)
self.telec = sv.hsx.telec if telec is None else telec
self.nelec = sv.hsx.nelec if nelec is None else nelec
self.fermi_energy = sv.fermi_energy if fermi_energy is None else fermi_energy
self.x = np.require(sv.wfsx.x, dtype=self.dtype, requirements='CW')
self.ksn2e = np.require(sv.wfsx.ksn2e,
dtype=self.dtype,
requirements='CW')
ksn2fd = fermi_dirac_occupations(self.telec, self.ksn2e,
self.fermi_energy)
self.ksn2f = (3 - self.nspin) * ksn2fd
self.nfermi = np.argmax(ksn2fd[0, 0, :] < nfermi_tol)
self.vstart = np.argmax(1.0 - ksn2fd[0, 0, :] > nfermi_tol)
self.xocc = self.x[0, 0, 0:self.nfermi, :,
0] # does python creates a copy at this point ?
self.xvrt = self.x[0, 0, self.vstart:, :,
0] # does python creates a copy at this point ?
self.tddft_iter_gpu = tddft_iter_gpu_c(GPU, self.v_dab, self.ksn2f,
self.ksn2e, self.norbs,
self.nfermi, self.vstart)
def __init__(self,
sv,
pb,
tddft_iter_tol=1e-2,
tddft_iter_broadening=0.00367493,
nfermi_tol=1e-5,
telec=None,
nelec=None,
fermi_energy=None,
xc_code='LDA,PZ',
GPU=False,
precision="single",
load_kernel=False,
**kvargs):
""" Iterative TDDFT a la PK, DF, OC JCTC """
from pyscf.nao.m_fermi_dirac import fermi_dirac_occupations
from pyscf.nao.m_comp_dm import comp_dm
assert tddft_iter_tol > 1e-6
assert type(tddft_iter_broadening) == float
assert sv.wfsx.x.shape[-1] == 1 # i.e. real eigenvectors we accept here
if precision == "single":
self.dtype = np.float32
self.dtypeComplex = np.complex64
self.gemm = blas.sgemm
if scipy_ver > 0:
self.spmv = blas.sspmv
else:
self.spmv = spmv_wrapper
elif precision == "double":
self.dtype = np.float64
self.dtypeComplex = np.complex128
self.gemm = blas.dgemm
if scipy_ver > 0:
self.spmv = blas.dspmv
else:
self.spmv = spmv_wrapper
else:
raise ValueError("precision can be only single or double")
self.rf0_ncalls = 0
self.l0_ncalls = 0
self.matvec_ncalls = 0
self.tddft_iter_tol = tddft_iter_tol
self.eps = tddft_iter_broadening
self.sv, self.pb, self.norbs, self.nspin = sv, pb, sv.norbs, sv.nspin
self.v_dab = pb.get_dp_vertex_sparse(dtype=self.dtype,
sparseformat=coo_matrix).tocsr()
self.cc_da = pb.get_da2cc_sparse(dtype=self.dtype,
sparseformat=coo_matrix).tocsr()
self.moms0, self.moms1 = pb.comp_moments(dtype=self.dtype)
self.nprod = self.moms0.size
if load_kernel:
self.load_kernel(**kvargs)
else:
self.kernel, self.kernel_dim = pb.comp_coulomb_pack(
dtype=self.dtype) # Lower Triangular Part of the kernel
assert self.nprod == self.kernel_dim, "%r %r " % (self.nprod,
self.kernel_dim)
if xc_code.upper() != 'RPA':
dm = comp_dm(sv.wfsx.x, sv.get_occupations())
pb.comp_fxc_pack(dm,
xc_code,
kernel=self.kernel,
dtype=self.dtype,
**kvargs)
self.telec = sv.hsx.telec if telec is None else telec
self.nelec = sv.hsx.nelec if nelec is None else nelec
self.fermi_energy = sv.fermi_energy if fermi_energy is None else fermi_energy
# probably unnecessary, require probably does a copy
# problematic for the dtype, must there should be another option
#self.x = np.require(sv.wfsx.x, dtype=self.dtype, requirements='CW')
self.ksn2e = np.require(sv.wfsx.ksn2e,
dtype=self.dtype,
requirements='CW')
ksn2fd = fermi_dirac_occupations(self.telec, self.ksn2e,
self.fermi_energy)
self.ksn2f = (3 - self.nspin) * ksn2fd
self.nfermi = np.argmax(ksn2fd[0, 0, :] < nfermi_tol)
self.vstart = np.argmax(1.0 - ksn2fd[0, 0, :] > nfermi_tol)
self.xocc = sv.wfsx.x[0, 0, 0:self.nfermi, :,
0] # does python creates a copy at this point ?
self.xvrt = sv.wfsx.x[0, 0, self.vstart:, :,
0] # does python creates a copy at this point ?
self.tddft_iter_gpu = tddft_iter_gpu_c(GPU, self.v_dab, self.ksn2f,
self.ksn2e, self.norbs,
self.nfermi, self.vstart)