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_wfsx_fname(self, **kw):
""" Initialise system var starting with a given WFSX file """
from pyscf.nao.m_tools import read_xyz
from pyscf.nao.m_fermi_energy import fermi_energy
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
self.label = label = kw['label'] if 'label' in kw else 'siesta'
self.cd = cd = kw['cd'] if 'cd' in kw else '.'
fname = kw['wfsx_fname'] if 'wfsx_fname' in kw else None
self.wfsx = siesta_wfsx_c(fname=fname, **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.natm = self.natoms = max(self.wfsx.orb2atm)
self.norbs = len(self.wfsx.orb2atm)
self.norbs_sc = self.norbs
self.nspin = self.wfsx.nspin
self.ucell = 30.0 * np.eye(3)
self.nkpoints = self.wfsx.nkpoints
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.ao_log = ao_log(sp2ion=self.sp2ion, **kw)
self.kb_log = ao_log(sp2ion=self.sp2ion, fname='kbs', **kw)
strspecie2sp = {}
# initialise a dictionary with species string as a 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]
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
#t1 = timer()
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)
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()
# Get self.atom2coord via .xml or .xyz files
try:
self.xml_dict = siesta_xml(cd + '/' + self.label + '.xml')
self.atom2coord = self.xml_dict['atom2coord']
self.fermi_energy = self.xml_dict['fermi_energy']
except:
print(__name__,
'no siesta.xml file --> excepting with siesta.xyz file')
a2sym, a2coord = read_xyz(cd + '/' + self.label + '.xyz')
self.atom2coord = a2coord * 1.8897259886
# cross-check of loaded .xyz file:
atom2sym_ref = np.array([
self.sp2ion[sp]['symbol'].strip()
for atom, sp in enumerate(self.atom2sp)
])
for ia, (a1, a2) in enumerate(zip(a2sym, atom2sym_ref)):
if a1 != a2:
raise RuntimeError('.xyz wrong? %d %s %s ' % (ia, a1, a2))
self.fermi_energy = fermi_energy(self.wfsx.ksn2e, self.hsx.nelec,
self.hsx.telec)
self.sp2symbol = [
str(ion['symbol'].replace(' ', '')) for ion in self.sp2ion
]
self.sp2charge = self.ao_log.sp2charge
# 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._atom = [(self.sp2symbol[sp], list(self.atom2coord[ia, :]))
for ia, sp in enumerate(self.atom2sp)]
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 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