TB2Jflows 0.1__py3-none-any.whl → 0.1.0__py3-none-any.whl

TB2Jflows/ase_siesta.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 import ase
 from ase.io.jsonio import decode, encode
-from pyDFTutils.siesta import MySiesta
+#from pyDFTutils.siesta import MySiesta
 from TB2J.interfaces import gen_exchange_siesta
 from TB2J.io_merge import merge
 from TB2J.rotate_atoms import rotate_atom_spin, rotate_atom_xyz
@@ -24,7 +24,6 @@ class SiestaFlow:
         restart=True,
         metadata={},
         fdf_arguments={},
-        relax_arguments={},
         split_soc=False,
         **kwargs,
     ):
@@ -51,7 +50,6 @@ class SiestaFlow:
         self.root_path = root_path
         self.restart = restart
         self.kwargs = kwargs
-        self.relax_args = relax_arguments
 
         # paths
         self.metadata_path = os.path.join(self.root_path, "metadata.json")
@@ -358,9 +356,9 @@ class SiestaFlow:
             write_path=os.path.join(self.root_path, "TB2J_results_merged"),
         )
 
-    def runall_collinear(self, atoms, relax=True, scf=True, TB2J=True,  **kwargs):
+    def runall_collinear(self, atoms, relax=True, scf=True, TB2J=True, **kwargs):
         if relax:
-            atoms = self.relax(atoms, **self.relax_args)
+            atoms = self.relax(atoms)
         if scf:
             self.scf_calculation_collinear(atoms, label="siesta")
         if TB2J:
@@ -370,7 +368,7 @@ class SiestaFlow:
         self, atoms, relax=True, scf=True, TB2J=True, rotate_type="structure", **kwargs
     ):
         if relax:
-            atoms = self.relax(atoms, **self.relax_args)
+            atoms = self.relax(atoms)
         if scf:
             self.scf_calculation_with_rotations(
                 atoms, rotate_type=rotate_type, label="siesta"
@@ -381,7 +379,7 @@ class SiestaFlow:
 
     def runall_split_soc(self, atoms, relax=True, scf=True, TB2J=True, **kwargs):
         if relax:
-            atoms = self.relax(atoms, **self.relax_args)
+            atoms = self.relax(atoms)
         if scf:
             self.scf_calculatoin_split_soc(atoms, label="siesta")
         if TB2J:

TB2Jflows/auto_siesta_TB2J.py

@@ -52,7 +52,6 @@ def auto_siesta_TB2J(
     TB2J=True,
     rotate_type="structure",
     fincore=True,
-    relax_arguments={},
     siesta_kwargs={},
     TB2J_kwargs={},
     fdf_kwargs={},
@@ -100,7 +99,6 @@ def auto_siesta_TB2J(
         fincore=fincore,
         Udict=Udict,
         split_soc=split_soc,
-        relax_arguments = relax_arguments,
         **siesta_kwargs,
     )
     flow.write_metadata()

TB2Jflows/find_pp.py

@@ -0,0 +1,67 @@
+import os
+from ase.data import chemical_symbols, atomic_numbers
+
+
+class PPFinder():
+    def __init__(self):
+        pass
+
+    def get_pp_path(self, element, xc, label, rel):
+        pass
+
+class DojoFinder():
+    def __init__(self, path=None):
+        if path is None:
+            self.path = os.environ['DOJO_PATH']
+        else:
+            self.path = path
+
+    def get_pp_path(self,
+                    xc : str,
+                    typ='NC',
+                    rel='sr',
+                    version='04',
+                    accuracy='standard',
+                    fmt='psml'):
+        typ=typ.lower()
+        xc=xc.lower()
+        if xc=="lda":
+            xc="pw"
+        dirname = os.path.join(self.path, f"{typ}-{rel}-{version}_{xc}_{accuracy}_{fmt}")
+        if not os.path.exists(dirname):
+            raise FileNotFoundError(f"File Not found: {dirname}")
+        return dirname
+
+    def get_pp_fname(self,
+                    element,
+                    xc : str,
+                    typ='NC',
+                    rel='sr',
+                    version='04',
+                    accuracy='standard',
+                    fincore=False,
+                    fmt='psml'):
+        if 57<atomic_numbers[element]<=70:
+            if fincore:
+                fname = os.path.join(self.get_pp_path(xc=xc, typ=typ, rel=rel,
+                  version=version, accuracy=accuracy, fmt=fmt), f"fincore/{element}.{fmt}")
+            else:
+                fname = os.path.join(self.get_pp_path(xc=xc, typ=typ, rel=rel,
+                  version=version, accuracy=accuracy, fmt=fmt), f"withf/{element}.{fmt}")
+
+        else:
+            fname = os.path.join(self.get_pp_path(xc=xc, typ=typ, rel=rel,
+                  version=version, accuracy=accuracy, fmt=fmt), f"{element}.{fmt}")
+        if not os.path.exists(fname):
+            raise FileNotFoundError(f"File Not found: {fname}")
+        return fname
+
+
+
+def test():
+    finder=DojoFinder(path=os.path.expanduser('~/projects/pp/dojo'))
+    fname=finder.get_pp_path(element='Sr', xc='pbesol')
+    fname=finder.get_pp_path(element='Srg', xc='pbe')
+
+if __name__=='__main__':
+    test()

TB2Jflows/mysiesta.py

@@ -0,0 +1,521 @@
+import os
+import math
+import numpy as np
+from ase import Atoms
+from ase.calculators.siesta import Siesta
+from ase.calculators.calculator import FileIOCalculator, ReadError
+from ase.calculators.siesta.parameters import format_fdf
+from ase.calculators.siesta.parameters import Species, PAOBasisBlock
+from ase.io import write
+import copy
+
+import shutil
+from os.path import join, isfile, islink
+import numpy as np
+from ase.units import Ry, eV, Bohr
+from ase.data import atomic_numbers
+#from ase.io.siesta import read_siesta_xv
+#from ase.calculators.siesta.import_functions import \
+#    get_valence_charge, read_vca_synth_block
+from ase.calculators.calculator import FileIOCalculator, ReadError
+from ase.calculators.calculator import Parameters, all_changes
+from ase.calculators.siesta.parameters import PAOBasisBlock, Species
+from ase.calculators.siesta.parameters import format_fdf
+#from pyDFTutils.siesta.pdos import gen_pdos_figure, plot_layer_pdos 
+
+from .siesta_basis  import get_basis, fincore_basis, withf_basis
+from .findpp import DojoFinder
+
+
+synthetic_atoms_dict_fincore={
+        "Yb":((6,5,5,5), (2,6,1,0))
+        }
+
+def read_siesta_xv(fd):
+    vectors = []
+    for i in range(3):
+        data = next(fd).split()
+        vectors.append([float(data[j]) * Bohr for j in range(3)])
+
+    # Read number of atoms (line 4)
+    natoms = int(next(fd).split()[0])
+
+    # Read remaining lines
+    speciesnumber, atomnumbers, xyz, V = [], [], [], []
+    for line in fd:
+        if len(line) > 5:  # Ignore blank lines
+            data = line.split()
+            speciesnumber.append(int(data[0]))
+            atomnumbers.append(int(data[1])%200)
+            xyz.append([float(data[2 + j]) * Bohr for j in range(3)])
+            V.append([float(data[5 + j]) * Bohr for j in range(3)])
+
+    vectors = np.array(vectors)
+    atomnumbers = np.array(atomnumbers)
+    xyz = np.array(xyz)
+    atoms = Atoms(numbers=atomnumbers, positions=xyz, cell=vectors,
+                  pbc=True)
+    assert natoms == len(atoms)
+    return atoms
+
+def read_xv(fname):
+    with open(fname) as myfile:
+        atoms=read_siesta_xv(myfile)
+    return atoms
+
+
+def get_species(atoms, xc, rel='sr', accuracy='standard'):
+    finder = DojoFinder()
+    elems = list(dict.fromkeys(atoms.get_chemical_symbols()).keys())
+    elem_dict = dict(zip(elems, range(1, len(elems) + 1)))
+    pseudo_path = finder.get_pp_path(xc=xc)
+    species = [
+        Species(symbol=elem,
+                pseudopotential=finder.get_pp_fname(
+                    elem, xc=xc, rel=rel, accuracy=accuracy, fincore=fincore),
+                ghost=False) for elem in elem_dict.keys()
+    ]
+    return pseudo_path, species
+
+
+def cart2sph(vec):
+    x, y, z = vec
+    r = np.linalg.norm(vec)               # r
+    if r < 1e-10:
+        theta, phi = 0.0, 0.0
+    else:
+        # note that there are many conventions, here is the ISO convention.
+        phi = math.atan2(y, x) * 180/math.pi                          # phi
+        theta = math.acos(z/r) * 180/math.pi                        # theta
+    return r, theta, phi
+
+
+class MySiesta(Siesta):
+    def __init__(self,
+                 atoms=None,
+                 command=None,
+                 xc='LDA',
+                 spin='non-polarized',
+                 basis_set='DZP',
+                 species=None,
+                 ghosts=[],
+                 synthetic_atoms={},
+                 input_basis_set={},
+                 pseudo_path=None,
+                 input_pp={},
+                 pp_accuracy='standard',
+                 fincore=False,
+                 **kwargs):
+        # non-perturnbative polarized orbital.
+        self.npt_elems = set()
+        self.synthetic_atoms=synthetic_atoms
+
+        if fincore:
+            input_basis_set.update(fincore_basis)
+        else:
+            input_basis_set.update(withf_basis)
+
+        if atoms is not None:
+            finder = DojoFinder()
+            elems = list(dict.fromkeys(atoms.get_chemical_symbols()).keys())
+            self.elem_dict = dict(zip(elems, range(1, len(elems) + 1)))
+            symbols = atoms.get_chemical_symbols()
+
+            # ghosts
+            ghost_symbols = [symbols[i] for i in ghosts]
+            ghost_elems = list(dict.fromkeys(ghost_symbols).keys())
+            tags = [1 if i in ghosts else 0 for i in range(len(atoms))]
+            atoms.set_tags(tags)
+
+            if pseudo_path is None:
+                pseudo_path = finder.get_pp_path(xc=xc, accuracy=pp_accuracy)
+
+            if spin == 'spin-orbit':
+                rel = 'fr'
+            else:
+                rel = 'sr'
+            species = []
+            for elem, index in self.elem_dict.items():
+                if elem not in input_basis_set:
+                    bselem = basis_set
+                    if elem in ['Li', 'Be', 'Na', 'Mg', 'Sm']:
+                        self.npt_elems.add(f"{elem}.{index}")
+                else:
+                    bselem = PAOBasisBlock(input_basis_set[elem])
+                if elem not in input_pp:
+                    pseudopotential = finder.get_pp_fname(
+                        elem, xc=xc, rel=rel, accuracy=pp_accuracy, fincore=fincore)
+                else:
+                    pseudopotential = os.path.join(
+                        pseudo_path, input_pp[elem])
+
+                if elem in self.synthetic_atoms:
+                    excess_charge = 0
+                else:
+                    excess_charge = None
+
+                species.append(Species(symbol=elem,
+                                       pseudopotential=pseudopotential,
+                                       basis_set=bselem,
+                                       ghost=False, 
+                                       excess_charge=excess_charge))
+            for elem in ghost_elems:
+                species.append(
+                    Species(symbol=elem,
+                            pseudopotential=finder.get_pp_fname(
+                                elem, xc=xc, rel=rel, accuracy=pp_accuracy, 
+                                fincore=fincore),
+                            tag=1,
+                            ghost=True))
+
+
+        Siesta.__init__(self,
+                        xc=xc,
+                        spin=spin,
+                        atoms=atoms,
+                        pseudo_path=pseudo_path,
+                        species=species,
+                        **kwargs)
+        self.set_npt_elements()
+        self.set_synthetic_atoms()
+
+    def _write_species(self, fd, atoms):
+        """Write input related the different species.
+
+        Parameters:
+            - f:     An open file object.
+            - atoms: An atoms object.
+        """
+        species, species_numbers = self.species(atoms)
+
+        if self['pseudo_path'] is not None:
+            pseudo_path = self['pseudo_path']
+        elif 'SIESTA_PP_PATH' in os.environ:
+            pseudo_path = os.environ['SIESTA_PP_PATH']
+        else:
+            mess = "Please set the environment variable 'SIESTA_PP_PATH'"
+            raise Exception(mess)
+
+        fd.write(format_fdf('NumberOfSpecies', len(species)))
+        fd.write(format_fdf('NumberOfAtoms', len(atoms)))
+
+        pao_basis = []
+        chemical_labels = []
+        basis_sizes = []
+        synth_blocks = []
+        for species_number, spec in enumerate(species):
+            species_number += 1
+            symbol = spec['symbol']
+            atomic_number = atomic_numbers[symbol]
+
+            if spec['pseudopotential'] is None:
+                if self.pseudo_qualifier() == '':
+                    label = symbol
+                    pseudopotential = label + '.psf'
+                else:
+                    label = '.'.join([symbol, self.pseudo_qualifier()])
+                    pseudopotential = label + '.psf'
+            else:
+                pseudopotential = spec['pseudopotential']
+                label = os.path.basename(pseudopotential)
+                label = '.'.join(label.split('.')[:-1])
+
+            if not os.path.isabs(pseudopotential):
+                pseudopotential = join(pseudo_path, pseudopotential)
+
+            if not os.path.exists(pseudopotential):
+                mess = "Pseudopotential '%s' not found" % pseudopotential
+                raise RuntimeError(mess)
+
+            name = os.path.basename(pseudopotential)
+            name = name.split('.')
+            name.insert(-1, str(species_number))
+            if spec['ghost']:
+                name.insert(-1, 'ghost')
+                atomic_number = -atomic_number
+
+            name = '.'.join(name)
+            pseudo_targetpath = self.getpath(name)
+
+            if join(os.getcwd(), name) != pseudopotential:
+                if islink(pseudo_targetpath) or isfile(pseudo_targetpath):
+                    os.remove(pseudo_targetpath)
+                symlink_pseudos = self['symlink_pseudos']
+
+                symlink_pseudos = False
+
+                if symlink_pseudos is None:
+                    symlink_pseudos = not os.name == 'nt'
+
+                if symlink_pseudos:
+                    os.symlink(pseudopotential, pseudo_targetpath)
+                else:
+                    shutil.copy(pseudopotential, pseudo_targetpath)
+            if not spec['excess_charge'] is None:
+                atomic_number += 200
+                n_atoms = sum(np.array(species_numbers) == species_number)
+
+                if spec['excess_charge'] != 0:
+                    paec = float(spec['excess_charge']) / n_atoms
+                    vc = get_valence_charge(pseudopotential)
+                    fraction = float(vc + paec) / vc
+                    pseudo_head = name[:-4]
+                    fractional_command = os.environ['SIESTA_UTIL_FRACTIONAL']
+                    cmd = '%s %s %.7f' % (fractional_command,
+                                          pseudo_head,
+                                          fraction)
+                    os.system(cmd)
+
+                    pseudo_head += '-Fraction-%.5f' % fraction
+                    synth_pseudo = pseudo_head + '.psf'
+                    synth_block_filename = pseudo_head + '.synth'
+                    os.remove(name)
+                    shutil.copyfile(synth_pseudo, name)
+                    synth_block = read_vca_synth_block(
+                        synth_block_filename,
+                        species_number=species_number)
+                    synth_blocks.append(synth_block)
+                else:
+                    synth_block = self.synthetic_atoms[symbol]
+
+
+
+            if len(synth_blocks) > 0:
+                fd.write(format_fdf('SyntheticAtoms', list(synth_blocks)))
+
+            label = '.'.join(np.array(name.split('.'))[:-1])
+            string = '    %d %d %s' % (species_number, atomic_number, label)
+            chemical_labels.append(string)
+            if isinstance(spec['basis_set'], PAOBasisBlock):
+                pao_basis.append(spec['basis_set'].script(label))
+            else:
+                basis_sizes.append(("    " + label, spec['basis_set']))
+        fd.write((format_fdf('ChemicalSpecieslabel', chemical_labels)))
+        fd.write('\n')
+        fd.write((format_fdf('PAO.Basis', pao_basis)))
+        fd.write((format_fdf('PAO.BasisSizes', basis_sizes)))
+        fd.write('\n')
+
+
+    def set_npt_elements(self):
+        if len(self.npt_elems) > 0:
+            npt_text = []
+            for name in self.npt_elems:
+                npt_text.append(
+                    f"{name} non-perturbative ")
+            # npt_text += "%endblock PAO.PolarizationScheme\n"
+            self['fdf_arguments'].update({"PAO.PolarizationScheme": npt_text})
+
+    def set_synthetic_atoms(self):
+        print("setting syn")
+        nsyn=len(self.synthetic_atoms)
+        if  nsyn> 0:
+            syntext = []
+            #syntext.append(f"{nsyn}")
+            for name, content in self.synthetic_atoms.items():
+                syntext.append(
+                    f"{self.elem_dict[name]}")
+                syntext.append(
+                    " ".join([str(x) for x in content[0]]))
+                syntext.append(
+                    " ".join([str(x) for x in content[1]]))
+            self['fdf_arguments'].update({"SyntheticAtoms": syntext})
+
+        #print("setting syn:", syntext)
+
+    def set_fdf_arguments(self, fdf_arguments):
+        self['fdf_arguments'].update(fdf_arguments)
+
+    def set_mixer(self,
+                  method='pulay',
+                  weight=0.05,
+                  history=10,
+                  restart=25,
+                  restart_save=4,
+                  linear_after=0,
+                  linear_after_weight=0.1):
+        pass
+
+    def update_fdf_arguments(self, fdf_arguments):
+        fdf = self['fdf_arguments'].update(fdf_arguments)
+
+    def add_Hubbard_U(self,
+                      specy,
+                      n=3,
+                      l=2,
+                      U=0,
+                      J=0,
+                      rc=0.0,
+                      Fermi_cut=0.0,
+                      scale_factor='0.95'):
+        if not 'Udict' in self.__dict__:
+            self.Udict = dict()
+        idx=self.elem_dict[specy]
+        specy_label=f"{specy}.{idx}"
+        self.Udict[specy_label] = {
+            'n': n,
+            'l': l,
+            'U': U,
+            'J': J,
+            'rc': rc,
+            'Fermi_cut': Fermi_cut,
+            'scale_factor': scale_factor
+        }
+        self.set_Hubbard_U(self.Udict)
+
+    def set_Hubbard_U(self, Udict):
+        """
+        Udict: {'Fe': {'n':n, 'l':l, 'U':U, 'J', J, 'rc':rc, 'Fermi_cut':Fermi_cut }}
+        """
+        Ublock = []
+        for key, val in Udict.items():
+            Ublock.append('  %s %s ' % (key, 1))
+            if val['n'] is not None:
+                Ublock.append('  n=%s %s' % (val['n'], val['l']))
+            else:
+                Ublock.append('%s' % (val['l']))
+            Ublock.append('  %s  %s' % (val['U'], val['J']))
+            if 'rc' in val:
+                Ublock.append('  %s  %s' % (val['rc'], val['Fermi_cut']))
+            Ublock.append('    %s' % val['scale_factor'])
+
+        self.update_fdf_arguments(
+            {'LDAU.Proj': Ublock, 'LDAU.ProjectorGenerationMethod': 2})
+
+    def set_Udict(self, Udict):
+        """
+        Udict: e.g. {"Fe":{"n":3, "l":2, "U":3.0, "J":0.0}, ...}
+        or {"Fe":{[3, 2, 3, 0]}
+
+        """
+        for specy, val in Udict.items():
+            if isinstance(val, dict):
+                self.add_Hubbard_U(specy, **val)
+            else:
+                self.add_Hubbard_U(specy, *val)
+
+    def write_Hubbard_block(self, f):
+        pass
+
+    def relax(
+        self,
+        atoms,
+        TypeOfRun='Broyden',
+        VariableCell=True,
+        ConstantVolume=False,
+        RelaxCellOnly=False,
+        MaxForceTol=0.001,
+        MaxStressTol=1,
+        NumCGSteps=40,
+        relaxed_file="relaxed.vasp"
+    ):
+        pbc = atoms.get_pbc()
+        initial_magnetic_moments = atoms.get_initial_magnetic_moments()
+        self.update_fdf_arguments({
+            'MD.TypeOfRun': TypeOfRun,
+            'MD.VariableCell': VariableCell,
+            'MD.ConstantVolume': ConstantVolume,
+            'MD.RelaxCellOnly': RelaxCellOnly,
+            'MD.MaxForceTol': "%s eV/Ang" % MaxForceTol,
+            'MD.MaxStressTol': "%s GPa" % MaxStressTol,
+            'MD.NumCGSteps': NumCGSteps,
+        })
+        self.calculate(atoms)
+        #self.read(self.prefix + '.XV')
+        self.atoms=read_xv(os.path.join(self.directory, self.prefix + '.XV'))
+        self.atoms.set_pbc(pbc)
+        self.atoms.set_initial_magnetic_moments(initial_magnetic_moments)
+        atoms = self.atoms
+        self.update_fdf_arguments({
+            'MD.NumCGSteps': 0,
+        })
+        if relaxed_file is not None:
+            write(relaxed_file, atoms, vasp5=True, sort=False)
+        return self.atoms
+
+    def scf_calculation(self, atoms, dos=True, kpts=[7,7,7], **kwargs):
+        if dos:
+            k1, k2, k3 = kpts
+            self.update_fdf_arguments({'WriteEigenvalues': '.true.', 
+        		'ProjectedDensityOfStates': ['-70.00 30.0 0.015 3000 eV'],
+                'PDOS.kgrid_Monkhorst_Pack': [f'{k1} 0 0 0.0',
+                                              f'0 {k2} 0 0.0',
+                                              f'0 0 {k3} 0.0']})
+        self.calculate(atoms, **kwargs)
+
+    def _write_structure(self, f, atoms):
+        """Translate the Atoms object to fdf-format.
+
+        Parameters:
+            - f:     An open file object.
+            - atoms: An atoms object.
+        """
+        cell = atoms.cell
+        f.write('\n')
+
+        if cell.rank in [1, 2]:
+            raise ValueError('Expected 3D unit cell or no unit cell.  You may '
+                             'wish to add vacuum along some directions.')
+
+        # Write lattice vectors
+        if np.any(cell):
+            f.write(format_fdf('LatticeConstant', '1.0 Ang'))
+            f.write('%block LatticeVectors\n')
+            for i in range(3):
+                for j in range(3):
+                    s = ('    %.15f' % cell[i, j]).rjust(16) + ' '
+                    f.write(s)
+                f.write('\n')
+            f.write('%endblock LatticeVectors\n')
+            f.write('\n')
+
+        self._write_atomic_coordinates(f, atoms)
+
+        # Write magnetic moments.
+        magmoms = atoms.get_initial_magnetic_moments()
+
+        # The DM.InitSpin block must be written to initialize to
+        # no spin. SIESTA default is FM initialization, if the
+        # block is not written, but  we must conform to the
+        # atoms object.
+        if magmoms is not None:
+            if len(magmoms) == 0:
+                f.write('#Empty block forces ASE initialization.\n')
+
+            f.write('%block DM.InitSpin\n')
+            if len(magmoms) != 0 and isinstance(magmoms[0], np.ndarray):
+                for n, Mcart in enumerate(magmoms):
+                    M = cart2sph(Mcart)
+                    if M[0] != 0:
+                        f.write('    %d %.14f %.14f %.14f \n' %
+                                (n + 1, M[0], M[1], M[2]))
+            elif len(magmoms) != 0 and isinstance(magmoms[0], float):
+                for n, M in enumerate(magmoms):
+                    if M != 0:
+                        f.write('    %d %.14f \n' % (n + 1, M))
+            f.write('%endblock DM.InitSpin\n')
+            f.write('\n')
+
+    def my_read_results(self):
+        """Read the results.
+        """
+        #self.read_number_of_grid_points()
+        self.read_energy()
+        self.read_forces_stress()
+        # self.read_eigenvalues()
+        self.read_kpoints()
+        self.read_dipole()
+        self.read_pseudo_density()
+        # self.read_hsx()
+        self.read_dim()
+        # if self.results['hsx'] is not None:
+        #    self.read_pld(self.results['hsx'].norbitals,
+        #                  len(self.atoms))
+        #    self.atoms.cell = self.results['pld'].cell * Bohr
+        # else:
+        #    self.results['pld'] = None
+
+        # self.read_wfsx()
+        self.read_ion(self.atoms)
+
+        self.read_bands()

TB2Jflows/siesta_basis.py

@@ -0,0 +1,50 @@
+
+withf_basis = {
+    #"La": "5\nn=5  0  1\n3.889 \n1.0 \nn=6  0  2\n9.113 6.906 \n1.0 1.0 \nn=5  1  1\n4.548 \n1.0 \nn=6  1  1\n9.113 \n1.0 \nn=5  2  2\n7.55 5.398 \n1.0 1.0 \n",
+    "Ce": "6\nn=5  0  1\n3.805 \n1.0 \nn=6  0  2\n9.041 6.837 \n1.0 1.0 \nn=5  1  1\n4.458 \n1.0 \nn=6  1  1\n9.041 \n1.0 \nn=5  2  2\n7.489 5.339 \n1.0 1.0 \nn=4  3  2\n4.114 2.494 \n1.0 1.0 \n",
+    "Pr": "6\nn=5  0  1\n3.737 \n1.0 \nn=6  0  2\n8.879 6.702 \n1.0 1.0 \nn=5  1  1\n4.387 \n1.0 \nn=6  1  1\n8.879 \n1.0 \nn=5  2  2\n7.46 5.307 \n1.0 1.0 \nn=4  3  2\n3.944 2.369 \n1.0 1.0 \n",
+    "Nd": "6\nn=5  0  1\n3.67 \n1.0 \nn=6  0  2\n8.808 6.641 \n1.0 1.0 \nn=5  1  1\n4.317 \n1.0 \nn=6  1  1\n8.808 \n1.0 \nn=5  2  2\n7.445 5.285 \n1.0 1.0 \nn=4  3  2\n3.805 2.271 \n1.0 1.0 \n",
+    "Pm": "6\nn=5  0  1\n3.611 \n1.0 \nn=6  0  2\n8.756 6.588 \n1.0 1.0 \nn=5  1  1\n4.257 \n1.0 \nn=6  1  1\n8.756 \n1.0 \nn=5  2  2\n7.43 5.269 \n1.0 1.0 \nn=4  3  2\n3.692 2.189 \n1.0 1.0 \n",
+    "Sm": "6\nn=5  0  1\n3.554 \n1.0 \nn=6  0  2\n8.668 6.516 \n1.0 1.0 \nn=5  1  1\n4.197 \n1.0 \nn=6  1  1\n8.668 \n1.0 \nn=5  2  2\n7.445 5.269 \n1.0 1.0 \nn=4  3  2\n3.59 2.115 \n1.0 1.0 \n",
+    "Eu": "6\nn=5  0  1\n3.497 \n1.0 \nn=6  0  2\n8.599 6.458 \n1.0 1.0 \nn=5  1  1\n4.139 \n1.0 \nn=6  1  1\n8.599 \n1.0 \nn=5  2  2\n7.46 5.275 \n1.0 1.0 \nn=4  3  2\n3.504 2.052 \n1.0 1.0 \n",
+    "Gd": "6\nn=5  0  1\n3.442 \n1.0 \nn=6  0  2\n8.514 6.374 \n1.0 1.0 \nn=5  1  1\n4.089 \n1.0 \nn=6  1  1\n8.514 \n1.0 \nn=5  2  2\n7.489 5.285 \n1.0 1.0 \nn=4  3  2\n3.435 1.997 \n1.0 1.0 \n",
+    "Tb": "6\nn=5  0  1\n3.394 \n1.0 \nn=6  0  2\n8.395 6.279 \n1.0 1.0 \nn=5  1  1\n4.04 \n1.0 \nn=6  1  1\n8.395 \n1.0 \nn=5  2  2\n7.52 5.301 \n1.0 1.0 \nn=4  3  2\n3.366 1.948 \n1.0 1.0 \n",
+    "Dy": "6\nn=5  0  1\n3.346 \n1.0 \nn=6  0  2\n8.295 6.186 \n1.0 1.0 \nn=5  1  1\n3.992 \n1.0 \nn=6  1  1\n8.295 \n1.0 \nn=5  2  2\n7.565 5.323 \n1.0 1.0 \nn=4  3  2\n3.306 1.901 \n1.0 1.0 \n",
+    "Ho": "6\nn=5  0  1\n3.293 \n1.0 \nn=6  0  2\n8.179 6.093 \n1.0 1.0 \nn=5  1  1\n3.944 \n1.0 \nn=6  1  1\n8.179 \n1.0 \nn=5  2  2\n7.61 5.349 \n1.0 1.0 \nn=4  3  2\n3.254 1.86 \n1.0 1.0 \n",
+    "Er": "6\nn=5  0  1\n3.247 \n1.0 \nn=6  0  2\n8.049 5.972 \n1.0 1.0 \nn=5  1  1\n3.897 \n1.0 \nn=6  1  1\n8.049 \n1.0 \nn=5  2  2\n7.656 5.387 \n1.0 1.0 \nn=4  3  2\n3.208 1.821 \n1.0 1.0 \n",
+    "Tm": "6\nn=5  0  1\n3.202 \n1.0 \nn=6  0  2\n7.921 5.872 \n1.0 1.0 \nn=5  1  1\n3.858 \n1.0 \nn=6  1  1\n7.921 \n1.0 \nn=5  2  2\n7.718 5.419 \n1.0 1.0 \nn=4  3  2\n3.163 1.785 \n1.0 1.0 \n",
+    "Yb": "6\nn=5  0  1\n3.163 \n1.0 \nn=6  0  2\n7.796 5.761 \n1.0 1.0 \nn=5  1  1\n3.812 \n1.0 \nn=6  1  1\n7.796 \n1.0 \nn=5  2  2\n7.78 5.468 \n1.0 1.0 \nn=4  3  2\n3.119 1.753 \n1.0 1.0 \n"
+}
+
+fincore_basis ={
+    #"La": "4\nn=5  0  1\n3.889 \n1.0 \nn=6  0  2\n9.113 6.906 \n1.0 1.0 \nn=5  1  1\n4.548 \n1.0 \nn=6  1  1\n9.113 \n1.0 \nn=5  2  2\n7.55 5.398 \n1.0 1.0 \n",
+    "Ce": "5\nn=5  0  1\n3.805 \n1.0 \nn=6  0  2\n8.968 6.776 \n1.0 1.0 \nn=5  1  1\n4.458 \n1.0 \nn=6  1  1\n8.968 \n1.0 \nn=5  2  2\n7.489 5.339 \n1.0 1.0 \n",
+    "Pr": "5\nn=5  0  1\n3.737 \n1.0 \nn=6  0  2\n8.791 6.621 \n1.0 1.0 \nn=5  1  1\n4.387 \n1.0 \nn=6  1  1\n8.791 \n1.0 \nn=5  2  2\n7.46 5.307 \n1.0 1.0 \n",
+    "Nd": "5\nn=5  0  1\n3.67 \n1.0 \nn=6  0  2\n8.634 6.49 \n1.0 1.0 \nn=5  1  1\n4.317 \n1.0 \nn=6  1  1\n8.634 \n1.0 \nn=5  2  2\n7.445 5.285 \n1.0 1.0 \n",
+    "Pm": "5\nn=5  0  1\n3.611 \n1.0 \nn=6  0  2\n8.446 6.33 \n1.0 1.0 \nn=5  1  1\n4.257 \n1.0 \nn=6  1  1\n8.446 \n1.0 \nn=5  2  2\n7.43 5.269 \n1.0 1.0 \n",
+    "Sm": "5\nn=5  0  1\n3.554 \n1.0 \nn=6  0  2\n8.328 6.223 \n1.0 1.0 \nn=5  1  1\n4.197 \n1.0 \nn=6  1  1\n8.328 \n1.0 \nn=5  2  2\n7.445 5.269 \n1.0 1.0 \n",
+    "Eu": "5\nn=5  0  1\n3.497 \n1.0 \nn=6  0  2\n8.278 6.186 \n1.0 1.0 \nn=5  1  1\n4.139 \n1.0 \nn=6  1  1\n8.278 \n1.0 \nn=5  2  2\n7.46 5.275 \n1.0 1.0 \n",
+    "Gd": "5\nn=5  0  1\n3.442 \n1.0 \nn=6  0  2\n8.278 6.179 \n1.0 1.0 \nn=5  1  1\n4.089 \n1.0 \nn=6  1  1\n8.278 \n1.0 \nn=5  2  2\n7.489 5.285 \n1.0 1.0 \n",
+    "Tb": "5\nn=5  0  1\n3.394 \n1.0 \nn=6  0  2\n8.147 6.063 \n1.0 1.0 \nn=5  1  1\n4.04 \n1.0 \nn=6  1  1\n8.147 \n1.0 \nn=5  2  2\n7.52 5.301 \n1.0 1.0 \n",
+    "Dy": "5\nn=5  0  1\n3.346 \n1.0 \nn=6  0  2\n7.969 5.919 \n1.0 1.0 \nn=5  1  1\n3.992 \n1.0 \nn=6  1  1\n7.969 \n1.0 \nn=5  2  2\n7.565 5.323 \n1.0 1.0 \n",
+    "Ho": "5\nn=5  0  1\n3.293 \n1.0 \nn=6  0  2\n7.827 5.79 \n1.0 1.0 \nn=5  1  1\n3.944 \n1.0 \nn=6  1  1\n7.827 \n1.0 \nn=5  2  2\n7.61 5.349 \n1.0 1.0 \n",
+    "Er": "5\nn=5  0  1\n3.247 \n1.0 \nn=6  0  2\n7.626 5.624 \n1.0 1.0 \nn=5  1  1\n3.897 \n1.0 \nn=6  1  1\n7.626 \n1.0 \nn=5  2  2\n7.656 5.387 \n1.0 1.0 \n",
+    "Tm": "5\nn=5  0  1\n3.202 \n1.0 \nn=6  0  2\n7.474 5.49 \n1.0 1.0 \nn=5  1  1\n3.858 \n1.0 \nn=6  1  1\n7.474 \n1.0 \nn=5  2  2\n7.718 5.419 \n1.0 1.0 \n",
+    "Yb": "5\nn=5  0  1\n3.163 \n1.0 \nn=6  0  2\n7.312 5.36 \n1.0 1.0 \nn=5  1  1\n3.812 \n1.0 \nn=6  1  1\n7.312 \n1.0 \nn=5  2  2\n7.78 5.468 \n1.0 1.0 \n"
+}
+
+def get_basis(element, fincore=False):
+    if not fincore:
+        return withf_basis[element]
+    elif basis == "fincore":
+        return fincore_basis[element]
+    else:
+        raise ValueError("Invalid basis set: {}".format(basis))
+
+if __name__ == "__main__":
+    print(get_basis("La"))
+    print(get_basis("La", fincore=True))
+    print(get_basis("Ce"))
+    print(get_basis("Ce", fincore=True))
+
+

tb2jflows-0.1.0.dist-info/METADATA

@@ -0,0 +1,77 @@
+Metadata-Version: 2.4
+Name: TB2Jflows
+Version: 0.1.0
+Summary: TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J
+Author-email: Xu He <mailhexu@gmail.com>
+License: BSD-2-clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.6
+Requires-Dist: ase
+Requires-Dist: sisl
+Requires-Dist: tb2j
+Description-Content-Type: text/markdown
+
+# TB2Jflows
+Workflows for automatically calculation of exchange parameters from DFT
+
+## Installation
+
+First download the package from the github page. Run the following command in the TB2Jflows directory
+
+```
+pip install . --user
+```
+
+will install TB2Jflows and the dependencies.
+
+You need the following things to 
+
+- Siesta built with psml and netcdf.
+- Pseudopotentials from PseudoDojo Dataset. 
+- Configure the command to run siesta and the path to the pseudopotentials, e.g.
+
+```
+export ASE_IESTA_COMMAND="mpirun siesta < PREFIX.fdf > PREFIX.out 2> PREFIX.err"
+export DOJO_PATH='$HOME/.local/pp/dojo'
+```
+
+## Usage
+
+Below is an example of calculating the exchange parameters of SrMnO3:
+
+```python
+from ase.io import read
+from TB2Jflows import SiestaFlow
+
+
+def calculate_siesta_TB2J_SrMnO3():
+    atoms = read('SrMnO3.STRUCT_OUT')
+    atoms.set_initial_magnetic_moments([0, 3, 0, 0, 0])
+    flow = SiestaFlow(atoms,
+                      spin='spin-orbit',
+                      restart=True,
+                      root_path='SrMnO3')
+    flow.write_metadata()
+    atoms = flow.relax(atoms)
+    flow.scf_calculation_with_rotations(atoms)
+    flow.run_TB2J(magnetic_elements='Mn',
+                  nz=50,
+                  kmesh=[7, 7, 7],
+                  Rcut=18,
+                  np=10,
+                  use_cache=True)
+    flow.run_TB2J_merge()
+
+
+if __name__ == '__main__':
+    calculate_siesta_TB2J_SrMnO3()
+~                                     
+```
+

tb2jflows-0.1.0.dist-info/RECORD

@@ -0,0 +1,11 @@
+TB2Jflows/__init__.py,sha256=0aRVj9v-u64LxJl7Cyxcr4YUjpeMkBGPuv-nJbxbHOg,100
+TB2Jflows/ase_siesta.py,sha256=1b6j0dFNnXCeLnCTWoLAJ158JQul8UcORIttGOhNydw,14366
+TB2Jflows/auto_siesta_TB2J.py,sha256=c5dviznEbXyO3BJbh-LNBlC9efT7YbdC7ydWxyCJZ5E,3113
+TB2Jflows/find_pp.py,sha256=iTqxLPuR88Jsuh4lc7hPEzFczhoOB0x6K5MWqYTEeiQ,2134
+TB2Jflows/mysiesta.py,sha256=DV9dnYibrpPzegKy_MvoMOOrmoom2NPKblhVNBUZkeg,18943
+TB2Jflows/run_abacus.py,sha256=96tZ2n02FFLl8IZf4W_4TvkCcsd6oS1FVEIqhZpY76o,2692
+TB2Jflows/siesta_basis.py,sha256=UIO0VF_558jIK6kGctqEwHyyV_t7KEWGOtv4Obw4fyg,5408
+tb2jflows-0.1.0.dist-info/METADATA,sha256=mnUu8VXO3Dndka3rbgqWJ0hiWxOXmWyF9AjauzpVQZk,2170
+tb2jflows-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+tb2jflows-0.1.0.dist-info/licenses/LICENSE,sha256=KNu68sa-XR_2jZJKhDcSnxoNve8jtHgkw_w9PjP1YOk,1315
+tb2jflows-0.1.0.dist-info/RECORD,,

{tb2jflows-0.1.dist-info → tb2jflows-0.1.0.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any
-

tb2jflows-0.1.dist-info/METADATA

@@ -1,31 +0,0 @@
-Metadata-Version: 2.4
-Name: TB2Jflows
-Version: 0.1
-Summary: TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J
-Author: Xu He
-Author-email: mailhexu@gmail.com
-License: BSD-2-clause
-Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.6
-License-File: LICENSE
-Requires-Dist: TB2J
-Requires-Dist: ase
-Requires-Dist: sisl
-Requires-Dist: pyDFTutils
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: license
-Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
-
- TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J 

tb2jflows-0.1.dist-info/RECORD

@@ -1,9 +0,0 @@
-TB2Jflows/__init__.py,sha256=0aRVj9v-u64LxJl7Cyxcr4YUjpeMkBGPuv-nJbxbHOg,100
-TB2Jflows/ase_siesta.py,sha256=zvKfKPidFvndfMQH0PHDprnFpwirk4yKdqwWDBe-_EI,14493
-TB2Jflows/auto_siesta_TB2J.py,sha256=hrnJos-Rkx1bngFOSr4wATUr0NVyBXmSOsrvscfMLmg,3180
-TB2Jflows/run_abacus.py,sha256=96tZ2n02FFLl8IZf4W_4TvkCcsd6oS1FVEIqhZpY76o,2692
-tb2jflows-0.1.dist-info/licenses/LICENSE,sha256=KNu68sa-XR_2jZJKhDcSnxoNve8jtHgkw_w9PjP1YOk,1315
-tb2jflows-0.1.dist-info/METADATA,sha256=BFLB9Ngpq9iLlEAxF245S9snQgmTFTp3FBypy5azHkY,967
-tb2jflows-0.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-tb2jflows-0.1.dist-info/top_level.txt,sha256=iYRLHB7ZeHb59fEZLnbqJDymBKWPqfVgmvqd9S51Txw,10
-tb2jflows-0.1.dist-info/RECORD,,

tb2jflows-0.1.dist-info/top_level.txt

@@ -1 +0,0 @@
-TB2Jflows