def build(self):
t0 = (time.clock(), time.time())
lib.logger.TIMER_LEVEL = 3
cell = libpbc.chkfile.load_cell(self.chkfile)
cell.ecp = None
self.cell = cell
self.a = self.cell.lattice_vectors()
self.b = self.cell.reciprocal_vectors()
self.vol = self.cell.vol
self.nelectron = self.cell.nelectron
self.charge = self.cell.charge
self.spin = self.cell.spin
self.natm = self.cell.natm
self.kpts = lib.chkfile.load(self.chkfile, 'kcell/kpts')
self.nkpts = len(self.kpts)
self.ls = cell.get_lattice_Ls(dimension=3)
self.ls = self.ls[numpy.argsort(lib.norm(self.ls, axis=1))]
self.atm = numpy.asarray(cell._atm, dtype=numpy.int32, order='C')
self.bas = numpy.asarray(cell._bas, dtype=numpy.int32, order='C')
self.env = numpy.asarray(cell._env, dtype=numpy.double, order='C')
self.nbas = self.bas.shape[0]
self.ao_loc = cell.ao_loc_nr()
self.shls_slice = (0, self.nbas)
sh0, sh1 = self.shls_slice
self.nao = self.ao_loc[sh1] - self.ao_loc[sh0]
self.non0tab = numpy.empty((1,self.nbas), dtype=numpy.int8)
# non0tab stores the number of images to be summed in real space.
# Initializing it to 255 means all images are summed
self.non0tab[:] = 0xff
self.coords = numpy.asarray([(numpy.asarray(atom[1])).tolist() for atom in cell._atom])
self.charges = cell.atom_charges()
self.mo_coeff = lib.chkfile.load(self.chkfile, 'scf/mo_coeff')
self.mo_occ = lib.chkfile.load(self.chkfile, 'scf/mo_occ')
nprims, nmo = self.mo_coeff[0].shape
self.nprims = nprims
self.nmo = nmo
self.cart = cell.cart
if (not self.leb):
self.npang = self.npphi*self.nptheta
self.rcut = _estimate_rcut(self)
kpts = numpy.reshape(self.kpts, (-1,3))
kpts_lst = numpy.reshape(kpts, (-1,3))
self.explk = numpy.exp(1j * numpy.asarray(numpy.dot(self.ls, kpts_lst.T), order='C'))
if (self.ntrial%2 == 0): self.ntrial += 1
geofac = numpy.power(((self.rmaxsurf-0.1)/self.rprimer),(1.0/(self.ntrial-1.0)))
self.rpru = numpy.zeros((self.ntrial))
for i in range(self.ntrial):
self.rpru[i] = self.rprimer*numpy.power(geofac,(i+1)-1)
self.rsurf = numpy.zeros((self.npang,self.ntrial), order='C')
self.nlimsurf = numpy.zeros((self.npang), dtype=numpy.int32)
if self.verbose >= logger.WARN:
self.check_sanity()
if self.verbose > logger.NOTE:
self.dump_input()
if (self.iqudt == 'legendre'):
self.iqudt = 1
if (self.leb):
self.grids = grid.lebgrid(self.npang)
else:
self.grids = grid.anggrid(self.iqudt,self.nptheta,self.npphi)
self.xyzrho = numpy.zeros((self.natm,3))
t = time.time()
logger.info(self,'Time finding nucleus %.3f (sec)' % (time.time()-t))
if (self.backend == 'rkck'):
backend = 1
elif (self.backend == 'rkdp'):
backend = 2
else:
raise NotImplementedError('Only rkck or rkdp ODE solver yet available')
ct_ = numpy.asarray(self.grids[:,0], order='C')
st_ = numpy.asarray(self.grids[:,1], order='C')
cp_ = numpy.asarray(self.grids[:,2], order='C')
sp_ = numpy.asarray(self.grids[:,3], order='C')
mo_coeff = numpy.zeros((self.nkpts,self.nprims,self.nmo), dtype=numpy.complex128)
mo_occ = numpy.zeros((self.nkpts,self.nmo))
for k in range(self.nkpts):
mo_coeff[k,:,:] = self.mo_coeff[k][:,:]
mo_occ[k,:] = self.mo_occ[k][:]
t = time.time()
feval = 'surf_driver'
drv = getattr(libaim, feval)
with lib.with_omp_threads(self.nthreads):
drv(ctypes.c_int(self.inuc),
self.xyzrho.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.npang),
ct_.ctypes.data_as(ctypes.c_void_p),
st_.ctypes.data_as(ctypes.c_void_p),
cp_.ctypes.data_as(ctypes.c_void_p),
sp_.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.ntrial),
self.rpru.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(self.epsiscp),
ctypes.c_double(self.epsroot),
ctypes.c_double(self.rmaxsurf),
ctypes.c_int(backend),
ctypes.c_double(self.epsilon),
ctypes.c_double(self.step),
ctypes.c_int(self.mstep),
ctypes.c_int(self.natm),
self.coords.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.cart),
ctypes.c_int(self.nmo),
ctypes.c_int(self.nprims),
self.atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.nbas),
self.bas.ctypes.data_as(ctypes.c_void_p),
self.env.ctypes.data_as(ctypes.c_void_p),
self.ao_loc.ctypes.data_as(ctypes.c_void_p),
mo_coeff.ctypes.data_as(ctypes.c_void_p),
mo_occ.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(self.occdrop),
#
self.a.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(self.ls)),
self.ls.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.nkpts),
self.explk.ctypes.data_as(ctypes.c_void_p),
self.rcut.ctypes.data_as(ctypes.c_void_p),
self.non0tab.ctypes.data_as(ctypes.c_void_p),
#
self.nlimsurf.ctypes.data_as(ctypes.c_void_p),
self.rsurf.ctypes.data_as(ctypes.c_void_p))
for i in range(self.nkpts):
print k,self.mo_occ[k][:]
logger.info(self,'Time finding surface %.3f (sec)' % (time.time()-t))
r = numpy.array([0.00000, 0.00000, 0.00000])
r = numpy.reshape(r, (-1,3))
ao = dft.numint.eval_ao_kpts(self.cell, r, kpts=self.kpts, deriv=1)
print rhograd(self,[0,0,0])
logger.info(self,'Surface of atom %d saved',self.inuc)
logger.timer(self,'BaderSurf build', *t0)
return self
def build(self):
t0 = (time.clock(), time.time())
lib.logger.TIMER_LEVEL = 3
mol = lib.chkfile.load_mol(self.chkfile)
self.nelectron = mol.nelectron
self.charge = mol.charge
self.spin = mol.spin
self.natm = mol.natm
self.atm = numpy.asarray(mol._atm, dtype=numpy.int32, order='C')
self.bas = numpy.asarray(mol._bas, dtype=numpy.int32, order='C')
self.nbas = self.bas.shape[0]
self.env = numpy.asarray(mol._env, dtype=numpy.double, order='C')
self.ao_loc = mol.ao_loc_nr()
self.shls_slice = (0, self.nbas)
sh0, sh1 = self.shls_slice
self.nao = self.ao_loc[sh1] - self.ao_loc[sh0]
self.non0tab = numpy.ones((1, self.nbas), dtype=numpy.int8)
self.coords = numpy.asarray([(numpy.asarray(atom[1])).tolist()
for atom in mol._atom])
self.charges = mol.atom_charges()
#if (self.cas):
# self.mo_coeff = lib.chkfile.load(self.chkfile, 'mcscf/mo_coeff')
#else:
# self.mo_coeff = lib.chkfile.load(self.chkfile, 'scf/mo_coeff')
self.mo_coeff = lib.chkfile.load(self.chkfile, 'scf/mo_coeff')
self.mo_occ = lib.chkfile.load(self.chkfile, 'scf/mo_occ')
nprims, nmo = self.mo_coeff.shape
self.nprims = nprims
self.nmo = nmo
self.cart = mol.cart
if (not self.leb):
self.npang = self.npphi * self.nptheta
if (self.corr):
self.rdm1 = lib.chkfile.load(self.chkfile, 'rdm/rdm1')
nmo = self.rdm1.shape[0]
natocc, natorb = numpy.linalg.eigh(self.rdm1)
if (self.cas):
self.mo_coeff = lib.chkfile.load(self.chkfile,
'mcscf/mo_coeff')
natorb = numpy.dot(self.mo_coeff, natorb)
self.mo_coeff = natorb
self.mo_occ = natocc
nocc = self.mo_occ[abs(self.mo_occ) > self.occdrop]
nocc = len(nocc)
self.nocc = nocc
if (self.ntrial % 2 == 0): self.ntrial += 1
geofac = numpy.power(((self.rmaxsurf - 0.1) / self.rprimer),
(1.0 / (self.ntrial - 1.0)))
self.rpru = numpy.zeros((self.ntrial))
for i in range(self.ntrial):
self.rpru[i] = self.rprimer * numpy.power(geofac, (i + 1) - 1)
self.rsurf = numpy.zeros((self.npang, self.ntrial), order='C')
self.nlimsurf = numpy.zeros((self.npang), dtype=numpy.int32)
if self.verbose >= logger.WARN:
self.check_sanity()
if self.verbose > logger.NOTE:
self.dump_input()
if (self.iqudt == 'legendre'):
self.iqudt = 1
if (self.leb):
self.grids = grid.lebgrid(self.npang)
else:
self.grids = grid.anggrid(self.iqudt, self.nptheta, self.npphi)
self.xyzrho = numpy.zeros((self.natm, 3))
t = time.time()
for i in range(self.natm):
self.xyzrho[i], gradmod = gradrho(self, self.coords[i], self.step)
if (gradmod > 1e-4):
if (self.charges[i] > 2.0):
logger.info(self, 'Good rho position %.6f %.6f %.6f',
*self.xyzrho[i])
else:
raise RuntimeError('Failed finding nucleus:',
*self.xyzrho[i])
else:
logger.info(self, 'Check rho position %.6f %.6f %.6f',
*self.xyzrho[i])
logger.info(self, 'Setting xyzrho for atom to imput coords')
self.xyzrho[i] = self.coords[i]
self.xnuc = numpy.asarray(self.xyzrho[self.inuc])
logger.info(self,
'Time finding nucleus %.3f (sec)' % (time.time() - t))
if (self.backend == 'rkck'):
backend = 1
elif (self.backend == 'rkdp'):
backend = 2
else:
raise NotImplementedError(
'Only rkck or rkdp ODE solver yet available')
ct_ = numpy.asarray(self.grids[:, 0], order='C')
st_ = numpy.asarray(self.grids[:, 1], order='C')
cp_ = numpy.asarray(self.grids[:, 2], order='C')
sp_ = numpy.asarray(self.grids[:, 3], order='C')
t = time.time()
feval = 'surf_driver'
drv = getattr(libaim, feval)
with lib.with_omp_threads(self.nthreads):
drv(ctypes.c_int(self.inuc),
self.xyzrho.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.npang), ct_.ctypes.data_as(ctypes.c_void_p),
st_.ctypes.data_as(ctypes.c_void_p),
cp_.ctypes.data_as(ctypes.c_void_p),
sp_.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(self.ntrial),
self.rpru.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(self.epsiscp), ctypes.c_double(self.epsroot),
ctypes.c_double(self.rmaxsurf), ctypes.c_int(backend),
ctypes.c_double(self.epsilon), ctypes.c_double(self.step),
ctypes.c_int(self.mstep), ctypes.c_int(self.natm),
self.coords.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.cart), ctypes.c_int(self.nmo),
ctypes.c_int(self.nprims),
self.atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.nbas),
self.bas.ctypes.data_as(ctypes.c_void_p),
self.env.ctypes.data_as(ctypes.c_void_p),
self.ao_loc.ctypes.data_as(ctypes.c_void_p),
self.mo_coeff.ctypes.data_as(ctypes.c_void_p),
self.mo_occ.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(self.occdrop),
self.nlimsurf.ctypes.data_as(ctypes.c_void_p),
self.rsurf.ctypes.data_as(ctypes.c_void_p))
logger.info(self,
'Time finding surface %.3f (sec)' % (time.time() - t))
self.rmin = 1000.0
self.rmax = 0.0
for i in range(self.npang):
nsurf = int(self.nlimsurf[i])
self.rmin = numpy.minimum(self.rmin, self.rsurf[i, 0])
self.rmax = numpy.maximum(self.rmax, self.rsurf[i, nsurf - 1])
logger.info(self, 'Rmin for surface %.6f', self.rmin)
logger.info(self, 'Rmax for surface %.6f', self.rmax)
logger.info(self, 'Write HDF5 surface file')
atom_dic = {
'inuc': self.inuc,
'xnuc': self.xnuc,
'xyzrho': self.xyzrho,
'coords': self.grids,
'npang': self.npang,
'ntrial': self.ntrial,
'rmin': self.rmin,
'rmax': self.rmax,
'nlimsurf': self.nlimsurf,
'rsurf': self.rsurf
}
lib.chkfile.save(self.surfile, 'atom' + str(self.inuc), atom_dic)
logger.info(self, 'Surface of atom %d saved', self.inuc)
logger.timer(self, 'BaderSurf build', *t0)
return self