def init_gto(self, **kw):
"""Interpret previous pySCF calculation"""
from pyscf.lib import logger
gto = kw['gto']
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self.cart = False
self._nelectron = gto.nelectron
self._built = True
self.max_memory = 20000
self.spin = gto.spin
#print(__name__, 'dir(gto)', dir(gto), gto.nelec)
self.nspin = 1 if gto.spin == 0 else 2 # this can be wrong and has to be redetermined at in the mean-field class (mf)
self.label = kw['label'] if 'label' in kw else 'pyscf'
self.mol = gto # Only some data must be copied, not the whole object. Otherwise, an eventual deepcopy(...) may fail.
self.natm = self.natoms = gto.natm
a2s = [gto.atom_symbol(ia) for ia in range(gto.natm)]
self.sp2symbol = sorted(list(set(a2s)))
self.nspecies = len(self.sp2symbol)
self.atom2sp = np.empty((gto.natm), dtype=np.int64)
for ia, sym in enumerate(a2s):
self.atom2sp[ia] = self.sp2symbol.index(sym)
self.sp2charge = [-999] * self.nspecies
for ia, sp in enumerate(self.atom2sp):
self.sp2charge[sp] = gto.atom_charge(ia)
self.ao_log = ao_log_c().init_ao_log_gto_suggest_mesh(nao=self, **kw)
self.atom2coord = np.zeros((self.natm, 3))
for ia, coord in enumerate(gto.atom_coords()):
self.atom2coord[ia, :] = coord # must be in Bohr already?
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom +
1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.norbs = self.norbs_sc = self.atom2s[-1]
self.ucell = 30.0 * np.eye(3)
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
self._atom = gto._atom
self.basis = gto.basis
### implement when needed self.init_libnao()
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas + 1), dtype=np.int64)
for sp, mu_s in zip(self.atom2sp, self.atom2mu_s):
for mu, j in enumerate(self.ao_log.sp_mu2j[sp]):
self.mu2orb_s[mu_s + mu +
1] = self.mu2orb_s[mu_s + mu] + 2 * j + 1
self.sp_mu2j = self.ao_log.sp_mu2j
self.nkpoints = 1
return self
def init_pyscf_gto(self, gto, label='pyscf', verbose=0, **kw):
"""Interpret previous pySCF calculation"""
from pyscf.lib import logger
self.verbose = verbose
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self.cart = False
self._nelectron = gto.nelectron
self._built = True
self.max_memory = 20000
self.label = label
self.mol = gto # Only some data must be copied, not the whole object. Otherwise, an eventual deepcopy(...) may fail.
self.natm = self.natoms = gto.natm
a2s = [gto.atom_symbol(ia) for ia in range(gto.natm)]
self.sp2symbol = sorted(list(set(a2s)))
self.nspecies = len(self.sp2symbol)
self.atom2sp = np.empty((gto.natm), dtype=np.int64)
for ia, sym in enumerate(a2s):
self.atom2sp[ia] = self.sp2symbol.index(sym)
self.sp2charge = [-999] * self.nspecies
for ia, sp in enumerate(self.atom2sp):
self.sp2charge[sp] = gto.atom_charge(ia)
self.ao_log = ao_log_c().init_ao_log_gto_suggest_mesh(gto=gto,
nao=self,
**kw)
self.atom2coord = np.zeros((self.natm, 3))
for ia, coord in enumerate(gto.atom_coords()):
self.atom2coord[ia, :] = coord # must be in Bohr already?
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom +
1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.norbs = self.norbs_sc = self.atom2s[-1]
self.spin = gto.spin if hasattr(gto, 'spin') else 0
self.nspin = self.spin + 1
self.ucell = 20.0 * np.eye(3)
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
self._atom = gto._atom
self.basis = gto.basis
self.init_libnao()
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas + 1), dtype=np.int64)
for sp, mu_s in zip(self.atom2sp, self.atom2mu_s):
for mu, j in enumerate(self.ao_log.sp_mu2j[sp]):
self.mu2orb_s[mu_s + mu +
1] = self.mu2orb_s[mu_s + mu] + 2 * j + 1
self.state = 'should be useful for something'
return self
def ao_log_hartree_lap_libnao(ao):
"""
Computes radial parts of Hartree potentials generated by the radial orbitals using Laplace transform (r_>, r_<)
Uses a call to Fortran version of the calculation.
Args:
self: class instance of ao_log_c
Result:
ao_pot with respective radial parts
"""
from ctypes import POINTER, c_double, c_int64
from pyscf.nao.m_ao_log import ao_log_c
from pyscf.nao.m_libnao import libnao
libnao.ao_hartree_lap.argtypes = (
POINTER(c_double), # rr(nr)
POINTER(c_int64), # nmult
POINTER(c_double), # mu2ff(nr,nmult)
POINTER(c_int64), # nr
POINTER(c_int64), # mu2j
POINTER(c_double)) # mu2vh(nr,nmult)
ao_pot = ao_log_c(ao_log=ao)
rr = np.require(ao.rr, dtype=c_double, requirements='C')
for sp in range(ao.nspecies):
mu2j = np.require(ao.sp_mu2j[sp], dtype=c_int64, requirements='C')
ff_rad = np.require(ao.psi_log[sp], dtype=c_double, requirements='C')
ff_pot = np.require(ao_pot.psi_log[sp],
dtype=c_double,
requirements='CW')
libnao.ao_hartree_lap(rr.ctypes.data_as(POINTER(c_double)),
c_int64(ao.sp2nmult[sp]),
ff_rad.ctypes.data_as(POINTER(c_double)),
c_int64(ao.nr),
mu2j.ctypes.data_as(POINTER(c_int64)),
ff_pot.ctypes.data_as(POINTER(c_double)))
ao_pot.psi_log[sp] = ff_pot
for mu, am in enumerate(ao.sp_mu2j[sp]):
ao_pot.psi_log_rl[sp][mu, :] = ao_pot.psi_log[sp][mu, :] / (ao.rr**
am)
for sp in range(ao.nspecies):
ao_pot.sp_mu2rcut[sp].fill(ao.rr[-1])
ao_pot.sp2rcut.fill(ao.rr[-1])
return ao_pot
def init_gto(self, **kw):
"""Interpret previous pySCF calculation"""
from pyscf.lib import logger
gto = kw['gto']
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self.cart = False
self._nelectron = gto.nelectron
self._built = True
self.max_memory = 20000
self.spin = gto.spin
#print(__name__, 'dir(gto)', dir(gto), gto.nelec)
self.nspin = 1 if gto.spin==0 else 2 # this can be wrong and has to be redetermined at in the mean-field class (mf)
self.label = kw['label'] if 'label' in kw else 'pyscf'
self.mol=gto # Only some data must be copied, not the whole object. Otherwise, an eventual deepcopy(...) may fail.
self.natm=self.natoms = gto.natm
a2s = [gto.atom_symbol(ia) for ia in range(gto.natm) ]
self.sp2symbol = sorted(list(set(a2s)))
self.nspecies = len(self.sp2symbol)
self.atom2sp = np.empty((gto.natm), dtype=np.int64)
for ia,sym in enumerate(a2s): self.atom2sp[ia] = self.sp2symbol.index(sym)
self.sp2charge = [-999]*self.nspecies
for ia,sp in enumerate(self.atom2sp): self.sp2charge[sp]=gto.atom_charge(ia)
self.ao_log = ao_log_c().init_ao_log_gto_suggest_mesh(nao=self, **kw)
self.atom2coord = np.zeros((self.natm, 3))
for ia,coord in enumerate(gto.atom_coords()): self.atom2coord[ia,:]=coord # must be in Bohr already?
self.atom2s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp): self.atom2s[atom+1]=self.atom2s[atom]+self.ao_log.sp2norbs[sp]
self.norbs = self.norbs_sc = self.atom2s[-1]
self.ucell = 30.0*np.eye(3)
self.atom2mu_s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp): self.atom2mu_s[atom+1]=self.atom2mu_s[atom]+self.ao_log.sp2nmult[sp]
self._atom = gto._atom
self.basis = gto.basis
### implement when needed self.init_libnao()
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas+1), dtype=np.int64)
for sp,mu_s in zip(self.atom2sp,self.atom2mu_s):
for mu,j in enumerate(self.ao_log.sp_mu2j[sp]): self.mu2orb_s[mu_s+mu+1] = self.mu2orb_s[mu_s+mu] + 2*j+1
self.sp_mu2j = self.ao_log.sp_mu2j
self.nkpoints = 1
return self
def init_pyscf_gto(self, gto, label='pyscf', verbose=0, **kw):
"""Interpret previous pySCF calculation"""
from pyscf.lib import logger
self.verbose = verbose
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self.cart = False
self._nelectron = gto.nelectron
self._built = True
self.max_memory = 20000
self.label = label
self.mol=gto # Only some data must be copied, not the whole object. Otherwise, an eventual deepcopy(...) may fail.
self.natm=self.natoms = gto.natm
a2s = [gto.atom_symbol(ia) for ia in range(gto.natm) ]
self.sp2symbol = sorted(list(set(a2s)))
self.nspecies = len(self.sp2symbol)
self.atom2sp = np.empty((gto.natm), dtype=np.int64)
for ia,sym in enumerate(a2s): self.atom2sp[ia] = self.sp2symbol.index(sym)
self.sp2charge = [-999]*self.nspecies
for ia,sp in enumerate(self.atom2sp): self.sp2charge[sp]=gto.atom_charge(ia)
self.ao_log = ao_log_c().init_ao_log_gto_suggest_mesh(gto=gto, nao=self, **kw)
self.atom2coord = np.zeros((self.natm, 3))
for ia,coord in enumerate(gto.atom_coords()): self.atom2coord[ia,:]=coord # must be in Bohr already?
self.atom2s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp): self.atom2s[atom+1]=self.atom2s[atom]+self.ao_log.sp2norbs[sp]
self.norbs = self.norbs_sc = self.atom2s[-1]
self.spin = gto.spin if hasattr(gto, 'spin') else 0
self.nspin = self.spin + 1
self.ucell = 20.0*np.eye(3)
self.atom2mu_s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp): self.atom2mu_s[atom+1]=self.atom2mu_s[atom]+self.ao_log.sp2nmult[sp]
self._atom = gto._atom
self.basis = gto.basis
self.init_libnao()
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas+1), dtype=np.int64)
for sp,mu_s in zip(self.atom2sp,self.atom2mu_s):
for mu,j in enumerate(self.ao_log.sp_mu2j[sp]): self.mu2orb_s[mu_s+mu+1] = self.mu2orb_s[mu_s+mu] + 2*j+1
self.state = 'should be useful for something'
return self
def init_pyscf_gto(self, gto, label='pyscf', **kvargs):
"""Interpret previous pySCF calculation"""
from pyscf.lib import logger
self.verbose = logger.NOTE # To be similar to Mole object...
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self.label = label
self.mol = gto # Only some data must be copied, not the whole object. Otherwise, an eventual deepcopy(...) may fail.
self.natm = self.natoms = gto.natm
a2s = [gto.atom_symbol(ia) for ia in range(gto.natm)]
self.sp2symbol = sorted(list(set(a2s)))
self.nspecies = len(self.sp2symbol)
self.atom2sp = np.empty((gto.natm), dtype='int64')
for ia, sym in enumerate(a2s):
self.atom2sp[ia] = self.sp2symbol.index(sym)
self.sp2charge = [-999] * self.nspecies
for ia, sp in enumerate(self.atom2sp):
self.sp2charge[sp] = gto.atom_charge(ia)
self.ao_log = ao_log_c().init_ao_log_gto_suggest_mesh(
gto, self, **kvargs)
self.atom2coord = np.zeros((self.natm, 3))
for ia, coord in enumerate(gto.atom_coords()):
self.atom2coord[ia, :] = coord # must be in Bohr already?
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom +
1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.norbs = self.norbs_sc = self.atom2s[-1]
self.nspin = 1
self.ucell = 20.0 * np.eye(3)
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
self._atom = gto._atom
self.basis = gto.basis
self.init_libnao()
self.state = 'should be useful for something'
return self
def init_siesta_xml(self, **kw):
from pyscf.nao.m_siesta_xml import siesta_xml
from pyscf.nao.m_siesta_wfsx import siesta_wfsx_c
from pyscf.nao.m_siesta_ion_xml import siesta_ion_xml
from pyscf.nao.m_siesta_hsx import siesta_hsx_c
from timeit import default_timer as timer
"""
Initialise system var using only the siesta files (siesta.xml in particular is needed)
System variables:
-----------------
label (string): calculation label
chdir (string): calculation directory
xml_dict (dict): information extracted from the xml siesta output, see m_siesta_xml
wfsx: class use to extract the information about wavefunctions, see m_siesta_wfsx
hsx: class to store a sparse representation of hamiltonian and overlap, see m_siesta_hsx
norbs_sc (integer): number of orbital
ucell (array, float): unit cell
sp2ion (list): species to ions, list of the species associated to the information from the ion files, see m_siesta_ion_xml
ao_log: Atomic orbital on an logarithmic grid, see m_ao_log
atom2coord (array, float): array containing the coordinates of each atom.
natm, natoms (integer): number of atoms
norbs (integer): number of orbitals
nspin (integer): number of spin
nkpoints (integer): number of kpoints
fermi_energy (float): Fermi energy
atom2sp (list): atom to specie, list associating the atoms to their specie number
atom2s: atom -> first atomic orbital in a global orbital counting
atom2mu_s: atom -> first multiplett (radial orbital) in a global counting of radial orbitals
sp2symbol (list): list associating the species to their symbol
sp2charge (list): list associating the species to their charge
state (string): this is an internal information on the current status of the class
"""
#label='siesta', cd='.', verbose=0,
self.label = label = kw['label'] if 'label' in kw else 'siesta'
self.cd = cd = kw['cd'] if 'cd' in kw else '.'
self.verbose = verbose = kw['verbose'] if 'verbose' in kw else 0
self.xml_dict = siesta_xml(cd + '/' + self.label + '.xml')
self.wfsx = siesta_wfsx_c(**kw)
self.hsx = siesta_hsx_c(fname=cd + '/' + self.label + '.HSX', **kw)
self.norbs_sc = self.wfsx.norbs if self.hsx.orb_sc2orb_uc is None else len(
self.hsx.orb_sc2orb_uc)
self.ucell = self.xml_dict["ucell"]
##### The parameters as fields
self.sp2ion = []
for sp in self.wfsx.sp2strspecie:
self.sp2ion.append(siesta_ion_xml(cd + '/' + sp + '.ion.xml'))
_siesta_ion_add_sp2(self, self.sp2ion)
self.ao_log = ao_log_c().init_ao_log_ion(self.sp2ion)
self.atom2coord = self.xml_dict['atom2coord']
self.natm = self.natoms = len(self.xml_dict['atom2sp'])
self.norbs = self.wfsx.norbs
self.nspin = self.wfsx.nspin
self.nkpoints = self.wfsx.nkpoints
self.fermi_energy = self.xml_dict['fermi_energy']
strspecie2sp = {}
# initialise a dictionary with species string as key
# associated to the specie number
for sp, strsp in enumerate(self.wfsx.sp2strspecie):
strspecie2sp[strsp] = sp
# list of atoms associated to them specie number
self.atom2sp = np.empty((self.natm), dtype=np.int64)
for o, atom in enumerate(self.wfsx.orb2atm):
self.atom2sp[atom - 1] = strspecie2sp[self.wfsx.orb2strspecie[o]]
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom +
1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
# atom2mu_s list of atom associated to them multipletts (radial orbitals)
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
orb2m = self.get_orb2m()
_siesta2blanko_csr(orb2m, self.hsx.s4_csr, self.hsx.orb_sc2orb_uc)
for s in range(self.nspin):
_siesta2blanko_csr(orb2m, self.hsx.spin2h4_csr[s],
self.hsx.orb_sc2orb_uc)
#t1 = timer()
for k in range(self.nkpoints):
for s in range(self.nspin):
for n in range(self.norbs):
_siesta2blanko_denvec(orb2m, self.wfsx.x[k, s, n, :, :])
#t2 = timer(); print(t2-t1, 'rsh wfsx'); t1 = timer()
self.sp2symbol = [
str(ion['symbol'].replace(' ', '')) for ion in self.sp2ion
]
self.sp2charge = self.ao_log.sp2charge
self.init_libnao()
self.state = 'should be useful for something'
# Trying to be similar to mole object from pySCF
self._xc_code = 'LDA,PZ' # estimate how ?
self._nelectron = self.hsx.nelec
self.cart = False
self.spin = self.nspin - 1
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self._built = True
self.max_memory = 20000
self.incore_anyway = False
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas + 1), dtype=np.int64)
for sp, mu_s in zip(self.atom2sp, self.atom2mu_s):
for mu, j in enumerate(self.ao_log.sp_mu2j[sp]):
self.mu2orb_s[mu_s + mu +
1] = self.mu2orb_s[mu_s + mu] + 2 * j + 1
self._atom = [(self.sp2symbol[sp], list(self.atom2coord[ia, :]))
for ia, sp in enumerate(self.atom2sp)]
return self
def init_ase_atoms(self, Atoms, **kvargs):
""" Initialise system vars using siesta file and Atom object from ASE."""
from pyscf.nao.m_siesta_xml import siesta_xml
from pyscf.nao.m_siesta_wfsx import siesta_wfsx_c
from pyscf.nao.m_siesta_ion_xml import siesta_ion_xml
from pyscf.nao.m_siesta_hsx import siesta_hsx_c
self.label = 'ase' if label is None else label
self.xml_dict = siesta_xml(self.label)
self.wfsx = siesta_wfsx_c(self.label)
self.hsx = siesta_hsx_c(self.label, **kvargs)
self.norbs_sc = self.wfsx.norbs if self.hsx.orb_sc2orb_uc is None else len(
self.hsx.orb_sc2orb_uc)
try:
import ase
except:
warn('no ASE installed: try via siesta.xml')
self.init_siesta_xml(**kvargs)
self.Atoms = Atoms
##### The parameters as fields
self.sp2ion = []
species = []
for sp in Atoms.get_chemical_symbols():
if sp not in species:
species.append(sp)
self.sp2ion.append(siesta_ion_xml(sp + '.ion.xml'))
_add_mu_sp2(self, self.sp2ion)
self.sp2ao_log = ao_log_c(self.sp2ion)
self.natm = self.natoms = Atoms.get_positions().shape[0]
self.norbs = self.wfsx.norbs
self.nspin = self.wfsx.nspin
self.nkpoints = self.wfsx.nkpoints
strspecie2sp = {}
for sp in range(len(self.wfsx.sp2strspecie)):
strspecie2sp[self.wfsx.sp2strspecie[sp]] = sp
self.atom2sp = np.empty((self.natoms), dtype='int64')
for i, sp in enumerate(Atoms.get_chemical_symbols()):
self.atom2sp[i] = strspecie2sp[sp]
self.atom2s = np.zeros((sv.natm + 1), dtype=np.int64)
for atom, sp in enumerate(sv.atom2sp):
atom2s[atom + 1] = atom2s[atom] + self.ao_log.sp2norbs[sp]
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
orb2m = get_orb2m(self)
_siesta2blanko_csr(orb2m, self.hsx.s4_csr, self.hsx.orb_sc2orb_uc)
for s in range(self.nspin):
_siesta2blanko_csr(orb2m, self.hsx.spin2h4_csr[s],
self.hsx.orb_sc2orb_uc)
for k in range(self.nkpoints):
for s in range(self.nspin):
for n in range(self.norbs):
_siesta2blanko_denvec(orb2m, self.wfsx.X[k, s, n, :, :])
self.sp2symbol = [
str(ion['symbol'].replace(' ', '')) for ion in self.sp2ion
]
self.sp2charge = self.ao_log.sp2charge
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas + 1), dtype=np.int64)
for sp, mu_s in zip(self.atom2sp, self.atom2mu_s):
for mu, j in enumerate(self.ao_log.sp_mu2j[sp]):
self.mu2orb_s[mu_s + mu +
1] = self.mu2orb_s[mu_s + mu] + 2 * j + 1
self.state = 'should be useful for something'
return self
def init_label(self, **kw):
from pyscf.nao.m_siesta_xml import siesta_xml
from pyscf.nao.m_siesta_wfsx import siesta_wfsx_c
from pyscf.nao.m_siesta_ion_xml import siesta_ion_xml
from pyscf.nao.m_siesta_hsx import siesta_hsx_c
from timeit import default_timer as timer
"""
Initialise system var using only the siesta files (siesta.xml in particular is needed)
System variables:
-----------------
label (string): calculation label
chdir (string): calculation directory
xml_dict (dict): information extracted from the xml siesta output, see m_siesta_xml
wfsx: class use to extract the information about wavefunctions, see m_siesta_wfsx
hsx: class to store a sparse representation of hamiltonian and overlap, see m_siesta_hsx
norbs_sc (integer): number of orbital
ucell (array, float): unit cell
sp2ion (list): species to ions, list of the species associated to the information from the ion files, see m_siesta_ion_xml
ao_log: Atomic orbital on an logarithmic grid, see m_ao_log
atom2coord (array, float): array containing the coordinates of each atom.
natm, natoms (integer): number of atoms
norbs (integer): number of orbitals
nspin (integer): number of spin
nkpoints (integer): number of kpoints
fermi_energy (float): Fermi energy
atom2sp (list): atom to specie, list associating the atoms to their specie number
atom2s: atom -> first atomic orbital in a global orbital counting
atom2mu_s: atom -> first multiplett (radial orbital) in a global counting of radial orbitals
sp2symbol (list): list associating the species to their symbol
sp2charge (list): list associating the species to their charge
state (string): this is an internal information on the current status of the class
"""
#label='siesta', cd='.', verbose=0, **kvargs
self.label = label = kw['label'] if 'label' in kw else 'siesta'
self.cd = cd = kw['cd'] if 'cd' in kw else '.'
self.xml_dict = siesta_xml(cd+'/'+self.label+'.xml')
self.wfsx = siesta_wfsx_c(**kw)
self.hsx = siesta_hsx_c(fname=cd+'/'+self.label+'.HSX', **kw)
self.norbs_sc = self.wfsx.norbs if self.hsx.orb_sc2orb_uc is None else len(self.hsx.orb_sc2orb_uc)
self.ucell = self.xml_dict["ucell"]
##### The parameters as fields
self.sp2ion = []
for sp in self.wfsx.sp2strspecie: self.sp2ion.append(siesta_ion_xml(cd+'/'+sp+'.ion.xml'))
_siesta_ion_add_sp2(self, self.sp2ion)
self.ao_log = ao_log_c().init_ao_log_ion(self.sp2ion, **kw)
self.atom2coord = self.xml_dict['atom2coord']
self.natm=self.natoms=len(self.xml_dict['atom2sp'])
self.norbs = self.wfsx.norbs
self.nspin = self.wfsx.nspin
self.nkpoints = self.wfsx.nkpoints
self.fermi_energy = self.xml_dict['fermi_energy']
strspecie2sp = {}
# initialise a dictionary with species string as key
# associated to the specie number
for sp,strsp in enumerate(self.wfsx.sp2strspecie): strspecie2sp[strsp] = sp
# list of atoms associated to them specie number
self.atom2sp = np.empty((self.natm), dtype=np.int64)
for o,atom in enumerate(self.wfsx.orb2atm):
self.atom2sp[atom-1] = strspecie2sp[self.wfsx.orb2strspecie[o]]
self.atom2s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp):
self.atom2s[atom+1]=self.atom2s[atom]+self.ao_log.sp2norbs[sp]
# atom2mu_s list of atom associated to them multipletts (radial orbitals)
self.atom2mu_s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp):
self.atom2mu_s[atom+1]=self.atom2mu_s[atom]+self.ao_log.sp2nmult[sp]
orb2m = self.get_orb2m()
_siesta2blanko_csr(orb2m, self.hsx.s4_csr, self.hsx.orb_sc2orb_uc)
for s in range(self.nspin):
_siesta2blanko_csr(orb2m, self.hsx.spin2h4_csr[s], self.hsx.orb_sc2orb_uc)
#t1 = timer()
for k in range(self.nkpoints):
for s in range(self.nspin):
for n in range(self.norbs):
_siesta2blanko_denvec(orb2m, self.wfsx.x[k,s,n,:,:])
#t2 = timer(); print(t2-t1, 'rsh wfsx'); t1 = timer()
self.sp2symbol = [str(ion['symbol'].replace(' ', '')) for ion in self.sp2ion]
self.sp2charge = self.ao_log.sp2charge
self.state = 'should be useful for something'
# Trying to be similar to mole object from pySCF
self._xc_code = 'LDA,PZ' # estimate how ?
self._nelectron = self.hsx.nelec
self.cart = False
self.spin = self.nspin-1
self.stdout = sys.stdout
self.symmetry = False
self.symmetry_subgroup = None
self._built = True
self.max_memory = 20000
self.incore_anyway = False
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas+1), dtype=np.int64)
for sp,mu_s in zip(self.atom2sp,self.atom2mu_s):
for mu,j in enumerate(self.ao_log.sp_mu2j[sp]): self.mu2orb_s[mu_s+mu+1] = self.mu2orb_s[mu_s+mu] + 2*j+1
self._atom = [(self.sp2symbol[sp], list(self.atom2coord[ia,:])) for ia,sp in enumerate(self.atom2sp)]
return self
def fireball_import(self, **kw):
""" Calls """
from pyscf.nao.m_ao_log import ao_log_c
from pyscf.nao.m_fireball_get_cdcoeffs_dat import fireball_get_ucell_cdcoeffs_dat
#label, cd
self.label = label = kw['fireball'] if 'fireball' in kw else 'out'
self.cd = cd = kw['cd'] if 'cd' in kw else '.'
#print('self.label', self.label)
fstdout = open(self.cd + '/' + self.label, "r")
s = fstdout.readlines()
fstdout.close()
try:
fl = [l for l in s if 'tempfe =' in l][0]
self.telec = float(fl.split(
'=')[1]) / 11604.0 / 27.2114 # Electron temperature in Hartree
except:
raise RuntimeError(
"tempfe = is not found in Fireball's standard output. Stop...")
try:
fl = [l for l in s if 'Fermi Level = ' in l][-1]
self.fermi_energy = float(
fl.split('=')[1]) / 27.2114 # Fermi energy in Hartree
except:
raise RuntimeError(
"Fermi Level = is not found in Fireball's standard output. Stop..."
)
# Read information about species from the standard output
ssll = [i for i, l in enumerate(s)
if "Information for this species" in l] # starting lines in stdout
self.nspecies = len(ssll)
self.sp2ion = []
for sl in ssll:
ion = {}
scut = s[sl:sl + 20]
for iline, line in enumerate(scut):
if "- Element" in line: ion["symbol"] = line.split()[0]
elif "- Atomic energy" in line:
ion["atomic_energy"] = float(line.split()[0])
elif "- Nuclear Z" in line:
ion["z"] = int(line.split()[0])
elif "- Atomic Mass" in line:
ion["mass"] = float(line.split()[0])
elif "- Number of shells" in line and "(Pseudopotential)" not in line:
ion["npao"] = int(line.split()[0])
ion["pao2j"] = list(map(int, scut[iline + 1].split()))
elif "- Number of shells (Pseudopotential)" in line:
ion["nshpp"] = int(line.split()[0])
ion["shpp2j"] = list(map(int, scut[iline + 1].split()))
elif "- Radial cutoffs (Pseudopotential)" in line:
ion["rcutpp"] = float(line.split()[0])
ion["pao2occ"] = list(map(float, scut[iline + 1].split()))
ion["pao2rcut"] = list(map(float, scut[iline + 2].split()))
ion["pao2fname"] = scut[iline + 3].split()
elif "============" in line:
break
self.sp2ion.append(ion)
self.sp2charge = [ion["z"] for ion in self.sp2ion]
self.sp2valence = [sum(ion["pao2occ"]) for ion in self.sp2ion]
# Read the radial functions from the Fdata/basis/fname.*wf*
for sp, ion in enumerate(self.sp2ion):
pao2npts = []
pao2delta = []
pao2ff = []
for pao, [fname, j, occp] in enumerate(
zip(ion["pao2fname"], ion["pao2j"], ion["pao2occ"])):
f = open(self.cd + '/Fdata/' + fname, "r")
ll = f.readlines()
f.close()
#print(fname.split('/')[2].split(".")[0], ll[0].split('.')[0].strip())
#print(fname.split('/')[2].split(".")[1], ll[0].split('.')[1].strip())
assert fname.split('/')[2].split(".")[0] == ll[0].split(
'.')[0].strip()
assert fname.split('/')[2].split(".")[1][0:3] == ll[0].split(
'.')[1].strip()[0:3]
z = int(ll[1].split()[0])
assert z == ion["z"]
atom_name = ll[1].split()[1].strip()
npts = int(ll[2])
pao2npts.append(npts)
[rc1, rc2, occ] = list(map(float, ll[3].split()))
assert rc1 > 0.0
assert rc2 > 0.0
assert occ == occp
delta = rc1 / npts
pao2delta.append(delta)
assert int(ll[4]) == j
ff = []
for line in ll[5:]:
ff += list(map(float, line.replace("D", "E").split()))
pao2ff.append(ff)
#print(z, rc1, rc2, occ, atom_name, fname, ion["pao2rcut"][pao],delta)
self.sp2ion[sp]["pao2npts"] = pao2npts
self.sp2ion[sp]["pao2delta"] = pao2delta
self.sp2ion[sp]["pao2ff"] = pao2ff
# Convert to init_ao_log_ion-compatible
for sp, ion in enumerate(self.sp2ion):
ioncompat = ion
data = []
for i, [d, ff, npts, j] in enumerate(
zip(ion["pao2delta"], ion["pao2ff"], ion["pao2npts"],
ion["pao2j"])):
rr = np.linspace(0.0, npts * d, npts)
norm = (np.array(ff)**2 * rr**2).sum() * (rr[1] - rr[0])
ff = [ff[0] / np.sqrt(norm)
] + [f / r / np.sqrt(norm) for f, r in zip(ff, rr) if r > 0]
data.append(np.array([rr, ff]).T)
norm = (np.array(ff)**2 * rr**2).sum() * (rr[1] - rr[0])
print(__name__, 'norm', norm)
paos = {
"npaos":
ion["npao"],
"delta":
ion["pao2delta"],
"cutoff":
ion["pao2rcut"],
"npts":
ion["pao2npts"],
"data":
data,
"orbital": [{
"l": j,
"population": occ
} for occ, j in zip(ion["pao2occ"], ion["pao2j"])]
}
ioncompat["paos"] = paos
ioncompat["vna"] = None
ioncompat["valence"] = sum(ion["pao2occ"])
self.sp2ion[sp] = ioncompat
self.ao_log = ao_log_c().init_ao_log_ion(self.sp2ion, **kw)
self.sp_mu2j = [mu2j for mu2j in self.ao_log.sp_mu2j]
#self.ao_log.view()
f = open(self.cd + '/answer.bas', "r")
lsa = f.readlines()
f.close()
self.natm = self.natoms = int(lsa[0]) # number of atoms
atom2znuc = [int(l.split()[0]) for l in lsa[1:]] # atom --> nuclear charge
self.atom2coord = [list(map(float,
l.split()[1:]))
for l in lsa[1:]] # coordinates
self.atom2coord = np.array(self.atom2coord)
assert self.natoms == len(atom2znuc)
assert self.natoms == len(self.atom2coord)
self.atom2sp = [self.sp2charge.index(znuc)
for znuc in atom2znuc] # atom --> nuclear charge
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom + 1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.norbs = self.atom2s[-1]
self.norbs_sc = self.norbs
self.ucell = fireball_get_ucell_cdcoeffs_dat(self.cd)
# atom2mu_s list of atom associated to them multipletts (radial orbitals)
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
nelec = 0.0
for sp in self.atom2sp:
nelec += self.sp2valence[sp]
self._nelectron = nelec
#print(self.atom2sp)
#print(self.sp2charge)
#print(self.atom2coord)
#print(self.telec)
#print(self.atom2s)
#print(self.atom2mu_s)
self.nspin = 1 # just a guess
return self
def system_vars_gpaw(self, calc, label="gpaw", chdir='.', **kvargs):
"""
Initialise system variables with gpaw inputs:
Input parameters:
-----------------
calc: GPAW object
kvargs: optional arguments, need a list of precise arguments somewhere
"""
from pyscf.lib import logger
from pyscf.lib.parameters import ELEMENTS as chemical_symbols
from pyscf.nao.m_gpaw_wfsx import gpaw_wfsx_c
from pyscf.nao.m_gpaw_hsx import gpaw_hsx_c
from pyscf.nao.m_ao_log import ao_log_c
import ase.units as units
self.label = label
self.chdir = '.'
self.verbose = logger.NOTE
self.ao_log = ao_log_c().init_ao_log_gpaw(calc.setups)
self.atom2coord = calc.get_atoms().get_positions() / units.Bohr
self.natm = self.natoms = len(self.atom2coord)
self.atom2sp = np.array(
[self.ao_log.sp2key.index(key) for key in calc.setups.id_a],
dtype=np.int64)
self.ucell = calc.atoms.get_cell() / units.Bohr
self.norbs = calc.setups.nao
self.norbs_sc = self.norbs
self.nspin = calc.get_number_of_spins()
self.nkpoints = 1
self.fermi_energy = float(
calc.get_fermi_level() /
units.Ha) # ensure that fermi_energy is float type
self.atom2s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom + 1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.atom2mu_s = np.zeros((self.natm + 1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom +
1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
self.sp2symbol = [chemical_symbols[Z] for Z in self.ao_log.sp2charge]
self.sp2charge = self.ao_log.sp2charge
self.wfsx = gpaw_wfsx_c(calc)
self.hsx = gpaw_hsx_c(self, calc)
#print(self.atom2coord)
#print(self.natoms)
#print(self.atom2sp)
#print(self.norbs)
#print(self.nspin)
#print(self.nkpoints)
#print(self.fermi_energy)
#print(self.atom2s)
#print(self.atom2mu_s)
#print(self.sp2symbol)
#print(self.sp2charge)
self.state = 'should be useful for something'
return self
# pointer to sp_mu2rcut
svn[i] = s + 1
i += 1
f = s + nrt
svn[s:f] = conc(self.psi_log).reshape(nrt)
s = f
# pointer to psi_log
svn[i] = s + 1
i += 1
f = s + nms
svn[s:f] = conc(self.sp_mu2s)
s = f
# pointer to sp_mu2s
svn[i] = s + 1
# this is a terminator to simple operation
return svn
#
#
#
if __name__ == "__main__":
from pyscf import gto
from pyscf.nao.m_ao_log import ao_log_c
""" Interpreting small Gaussian calculation """
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0',
basis='ccpvdz') # coordinates in Angstrom!
ao_log = ao_log_c(gto=mol)
print(ao_log.sp2norbs)
svn[i] = self.jmx; i+=1;
svn[i] = conc(self.psi_log).sum(); i+=1;
# Pointers to data
i = 99
s = 199
svn[i] = s+1; i+=1; f=s+nr; svn[s:f] = self.rr; s=f; # pointer to rr
svn[i] = s+1; i+=1; f=s+nr; svn[s:f] = self.pp; s=f; # pointer to pp
svn[i] = s+1; i+=1; f=s+nsp; svn[s:f] = self.sp2nmult; s=f; # pointer to sp2nmult
svn[i] = s+1; i+=1; f=s+nsp; svn[s:f] = self.sp2rcut; s=f; # pointer to sp2rcut
svn[i] = s+1; i+=1; f=s+nsp; svn[s:f] = self.sp2norbs; s=f; # pointer to sp2norbs
svn[i] = s+1; i+=1; f=s+nsp; svn[s:f] = self.sp2charge; s=f; # pointer to sp2charge
svn[i] = s+1; i+=1; f=s+nmt; svn[s:f] = conc(self.sp_mu2j); s=f; # pointer to sp_mu2j
svn[i] = s+1; i+=1; f=s+nmt; svn[s:f] = conc(self.sp_mu2rcut); s=f; # pointer to sp_mu2rcut
svn[i] = s+1; i+=1; f=s+nrt; svn[s:f] = conc(self.psi_log).reshape(nrt); s=f; # pointer to psi_log
svn[i] = s+1; i+=1; f=s+nms; svn[s:f] = conc(self.sp_mu2s); s=f; # pointer to sp_mu2s
svn[i] = s+1; # this is a terminator to simple operation
return svn
#
#
#
if __name__=="__main__":
from pyscf import gto
from pyscf.nao.m_ao_log import ao_log_c
""" Interpreting small Gaussian calculation """
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0', basis='ccpvdz') # coordinates in Angstrom!
ao_log = ao_log_c(gto=mol)
print(ao_log.sp2norbs)
def init_ase_atoms(self, Atoms, **kvargs):
""" Initialise system vars using siesta file and Atom object from ASE."""
from pyscf.nao.m_siesta_xml import siesta_xml
from pyscf.nao.m_siesta_wfsx import siesta_wfsx_c
from pyscf.nao.m_siesta_ion_xml import siesta_ion_xml
from pyscf.nao.m_siesta_hsx import siesta_hsx_c
self.label = 'ase' if label is None else label
self.xml_dict = siesta_xml(self.label)
self.wfsx = siesta_wfsx_c(self.label)
self.hsx = siesta_hsx_c(self.label, **kvargs)
self.norbs_sc = self.wfsx.norbs if self.hsx.orb_sc2orb_uc is None else len(self.hsx.orb_sc2orb_uc)
try:
import ase
except:
warn('no ASE installed: try via siesta.xml')
self.init_siesta_xml(**kvargs)
self.Atoms = Atoms
##### The parameters as fields
self.sp2ion = []
species = []
for sp in Atoms.get_chemical_symbols():
if sp not in species:
species.append(sp)
self.sp2ion.append(siesta_ion_xml(sp+'.ion.xml'))
_add_mu_sp2(self, self.sp2ion)
self.sp2ao_log = ao_log_c(self.sp2ion)
self.natm=self.natoms= Atoms.get_positions().shape[0]
self.norbs = self.wfsx.norbs
self.nspin = self.wfsx.nspin
self.nkpoints = self.wfsx.nkpoints
strspecie2sp = {}
for sp in range(len(self.wfsx.sp2strspecie)): strspecie2sp[self.wfsx.sp2strspecie[sp]] = sp
self.atom2sp = np.empty((self.natoms), dtype='int64')
for i, sp in enumerate(Atoms.get_chemical_symbols()):
self.atom2sp[i] = strspecie2sp[sp]
self.atom2s = np.zeros((sv.natm+1), dtype=np.int64)
for atom,sp in enumerate(sv.atom2sp): atom2s[atom+1]=atom2s[atom]+self.ao_log.sp2norbs[sp]
self.atom2mu_s = np.zeros((self.natm+1), dtype=np.int64)
for atom,sp in enumerate(self.atom2sp): self.atom2mu_s[atom+1]=self.atom2mu_s[atom]+self.ao_log.sp2nmult[sp]
orb2m = get_orb2m(self)
_siesta2blanko_csr(orb2m, self.hsx.s4_csr, self.hsx.orb_sc2orb_uc)
for s in range(self.nspin):
_siesta2blanko_csr(orb2m, self.hsx.spin2h4_csr[s], self.hsx.orb_sc2orb_uc)
for k in range(self.nkpoints):
for s in range(self.nspin):
for n in range(self.norbs):
_siesta2blanko_denvec(orb2m, self.wfsx.X[k,s,n,:,:])
self.sp2symbol = [str(ion['symbol'].replace(' ', '')) for ion in self.sp2ion]
self.sp2charge = self.ao_log.sp2charge
self.nbas = self.atom2mu_s[-1] # total number of radial orbitals
self.mu2orb_s = np.zeros((self.nbas+1), dtype=np.int64)
for sp,mu_s in zip(self.atom2sp,self.atom2mu_s):
for mu,j in enumerate(self.ao_log.sp_mu2j[sp]): self.mu2orb_s[mu_s+mu+1] = self.mu2orb_s[mu_s+mu] + 2*j+1
self.state = 'should be useful for something'
return self
def system_vars_gpaw(self, **kw):
"""
Initialise system variables with gpaw inputs:
Input parameters:
-----------------
calc: GPAW object
kvargs: optional arguments, need a list of precise arguments somewhere
"""
from pyscf.lib import logger
from pyscf.lib.parameters import ELEMENTS as chemical_symbols
from pyscf.nao.m_gpaw_wfsx import gpaw_wfsx_c
from pyscf.nao.m_gpaw_hsx import gpaw_hsx_c
from pyscf.nao.m_ao_log import ao_log_c
import ase.units as units
#gpaw=calc, label="gpaw", chdir='.', **kvargs
self.gpaw = calc = kw['gpaw']
self.label = kw['label'] if 'label' in kw else 'gpaw'
self.chdir = kw['cd'] if 'cd' in kw else '.'
self.verbose = logger.NOTE
self.ao_log = ao_log_c().init_ao_log_gpaw(calc.setups)
self.atom2coord = calc.get_atoms().get_positions()/units.Bohr
self.natm = self.natoms = len(self.atom2coord)
self.atom2sp = np.array([list(self.ao_log.sp2key).index(key) for key in calc.setups.id_a], dtype=np.int64)
self.ucell = calc.atoms.get_cell()/units.Bohr
self.norbs = calc.setups.nao
self.norbs_sc = self.norbs
self.nspin = calc.get_number_of_spins()
self.nkpoints = 1
self.fermi_energy = float(calc.get_fermi_level()/units.Ha) # ensure that fermi_energy is float type
self.atom2s = np.zeros((self.natm+1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2s[atom+1] = self.atom2s[atom] + self.ao_log.sp2norbs[sp]
self.atom2mu_s = np.zeros((self.natm+1), dtype=np.int64)
for atom, sp in enumerate(self.atom2sp):
self.atom2mu_s[atom+1] = self.atom2mu_s[atom] + self.ao_log.sp2nmult[sp]
self.sp2symbol = [chemical_symbols[Z] for Z in self.ao_log.sp2charge]
self.sp2charge = self.ao_log.sp2charge
self.wfsx = gpaw_wfsx_c(calc)
self.hsx = gpaw_hsx_c(self, calc)
#print(self.atom2coord)
#print(self.natoms)
#print(self.atom2sp)
#print(self.norbs)
#print(self.nspin)
#print(self.nkpoints)
#print(self.fermi_energy)
#print(self.atom2s)
#print(self.atom2mu_s)
#print(self.sp2symbol)
#print(self.sp2charge)
self.state = 'should be useful for something'
return self
