TB2J 0.9.3rc0__tar.gz → 0.9.5rc0__tar.gz

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.9.3rc0
+Version: 0.9.5rc0
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,6 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: pre-commit
-Requires-Dist: HamiltonIO>=0.1.4
+Requires-Dist: HamiltonIO>=0.1.5
 
 TB2J is a Python package aimed to compute automatically the magnetic interactions (superexchange  and Dzyaloshinskii-Moriya) between atoms of magnetic crystals from DFT Hamiltonian based on Wannier functions or Linear combination of atomic orbitals. It uses the Green's function method and take the local rigid spin rotation as a perturbation. The package can take the output from Wannier90, which is interfaced with many density functional theory codes or from codes based on localised orbitals. A minimal user input is needed, which allows for an easily integration into a high-throughput workflows. 

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J/MAE.py

@@ -11,8 +11,9 @@ import matplotlib.pyplot as plt
 from pathlib import Path
 from TB2J.mathutils.rotate_spin import spherical_to_cartesian
 from HamiltonIO.model.occupations import Occupations
-from TB2J.abacus.abacus_wrapper import AbacusSplitSOCParser
-from HamiltonIO.siesta import SislWrapper
+#from TB2J.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.siesta import SislParser, SiestaHamiltonian
 import tqdm
 
 
@@ -75,7 +76,10 @@ class MAE:
         # e,rho = self.model.get_band_energy(dm=True)
         # self.calc_ref()
         # thetas = np.linspace(*angle_range, npoints)
-        for i, (theta, phi) in tqdm.tqdm(enumerate(zip(thetas, phis))):
+        nangles = len(thetas)
+        for i in tqdm.trange(nangles):
+            theta = thetas[i]
+            phi = phis[i]
             self.model.set_Hsoc_rotation_angle([theta, phi])
             e = self.get_band_energy()
             es.append(e)
@@ -96,28 +100,27 @@ def abacus_get_MAE(
         outpath_nosoc=path_nosoc, outpath_soc=path_soc, binary=False
     )
     model = parser.parse()
-    model.nel = 16
     ham = MAE(model, kmesh, gamma=gamma)
     es = ham.get_band_energy_vs_angles(thetas, psis)
     if outfile:
         with open(outfile, "w") as f:
             f.write("#theta, psi, energy\n")
             for theta, psi, e in zip(thetas, psis, es):
-                f.write(f"{theta}, {psi}, {e}\n")
+                f.write(f"{theta:5.3f}, {psi:5.3f}, {e:10.9f}\n")
     return es
 
 
 def siesta_get_MAE(fdf_fname, kmesh, thetas, phis, gamma=True, outfile="MAE.txt"):
     """ """
-    parser = SiestaParser(fdf_fname=fdf_fname, read_H_soc=True)
-    model = parser.parse()
+    model= SislParser(fdf_fname=fdf_fname, read_H_soc=True).get_model()
     ham = MAE(model, kmesh, gamma=gamma)
     es = ham.get_band_energy_vs_angles(thetas, phis)
     if outfile:
         with open(outfile, "w") as f:
             f.write("#theta, psi, energy\n")
             for theta, psi, e in zip(thetas, phis, es):
-                f.write(f"{theta}, {psi}, {e}\n")
+                #f.write(f"{theta}, {psi}, {e}\n")
+                f.write(f"{theta:5.3f}, {psi:5.3f}, {e:10.9f}\n")
     return es
 
 

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J/abacus/abacus_wrapper.py

@@ -36,6 +36,7 @@ class AbacusWrapper(AbstractTB):
             self.set_HR_soc(HR_soc=HR_soc, HR_nosoc=HR_nosoc, HR_full=HR)
         self.soc_rotation_angle = 0.0
 
+
     def set_HR_soc(self, HR_soc=None, HR_nosoc=None, HR_full=None):
         self.split_soc = True
         self.HR_soc = HR_soc
@@ -156,6 +157,9 @@ class AbacusParser:
         # read the information
         self.read_atoms()
         self.efermi = self.read_efermi()
+        self.nel = self.read_nel()
+        print(f"efermi: {self.efermi}")
+        print(f"nel: {self.nel}")
         self.read_basis()
 
     def read_spin(self):
@@ -254,10 +258,10 @@ class AbacusParser:
         nel = None
         with open(fname, "r") as myfile:
             for line in myfile:
-                if "NELECT" in line:
-                    nel = float(line.split()[2])
+                if "number of electrons" in line:
+                    nel = float(line.split()[-1])
         if nel is None:
-            raise ValueError(f"NELECT not found in the {str(fname)}  file.")
+            raise ValueError(f"number of electron not found in the {str(fname)}  file.")
         return nel
 
     def get_basis(self):
@@ -306,6 +310,7 @@ class AbacusSplitSOCParser:
             nspin=2,
             HR_soc=HR_soc,
             HR_nosoc=HR_nosoc,
+            nel=self.parser_nosoc.nel,
         )
         model.efermi = self.parser_soc.efermi
         model.basis = self.parser_nosoc.basis

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J/abacus/gen_exchange_abacus.py

@@ -6,7 +6,8 @@ The main function to compute exchange interaction from abacus data
 
 import os
 from pathlib import Path
-from TB2J.abacus.abacus_wrapper import AbacusParser
+#from TB2J.abacus.abacus_wrapper import AbacusParser
+from HamiltonIO.abacus import AbacusParser
 from TB2J.exchange import ExchangeNCL, ExchangeCL
 from TB2J.exchangeCL2 import ExchangeCL2
 

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J/manager.py

@@ -7,11 +7,15 @@ from TB2J.exchange_qspace import ExchangeCLQspace
 from TB2J.utils import read_basis, auto_assign_basis_name
 from ase.io import read
 
-#from TB2J.sisl_wrapper import SislWrapper
+# from TB2J.sisl_wrapper import SislWrapper
+
+from HamiltonIO.siesta import SislParser
 try:
-    from HamiltonIO.siesta import SislWrapper
+    from HamiltonIO.siesta import SislParser
 except ImportError:
-    print("Cannot import SislWrapper from HamiltonIO.siesta. Please install HamiltonIO first.")
+    print(
+        "Cannot import SislWrapper from HamiltonIO.siesta. Please install HamiltonIO first."
+    )
     from TB2J.sisl_wrapper import SislWrapper
 from TB2J.gpaw_wrapper import GPAWWrapper
 from TB2J.wannier import parse_atoms
@@ -283,14 +287,16 @@ def gen_exchange_siesta(
             include_orbs[element] = None
     magnetic_elements = list(include_orbs.keys())
 
-    fdf = sisl.get_sile(fdf_fname)
+    #fdf = sisl.get_sile(fdf_fname)
     # geom = fdf.read_geometry()
-    H = fdf.read_hamiltonian()
-    geom = H.geometry
-    if H.spin.is_colinear:
+    #H = fdf.read_hamiltonian()
+    #geom = H.geometry
+    parser=SislParser(fdf_fname=fdf_fname, ispin=None, read_H_soc=False)
+    if parser.spin.is_colinear:
         print("Reading Siesta hamiltonian: colinear spin.")
-        tbmodel_up = SislWrapper(fdf_fname=None,sisl_hamiltonian=H, spin=0, geom=geom)
-        tbmodel_dn = SislWrapper(fdf_fname=None, sisl_hamiltonian=H, spin=1, geom=geom)
+        #tbmodel_up = SislWrapper(fdf_fname=None, sisl_hamiltonian=H, spin=0, geom=geom)
+        #tbmodel_dn = SislWrapper(fdf_fname=None, sisl_hamiltonian=H, spin=1, geom=geom)
+        tbmodel_up, tbmodel_dn = parser.get_model()
         basis = dict(zip(tbmodel_up.orbs, list(range(tbmodel_up.norb))))
         print("Starting to calculate exchange.")
         description = f""" Input from collinear Siesta data.
@@ -320,7 +326,7 @@ def gen_exchange_siesta(
         print("\n")
         print(f"All calculation finsihed. The results are in {output_path} directory.")
 
-    elif H.spin.is_colinear and False:
+    elif parser.spin.is_colinear and False:
         print(
             "Reading Siesta hamiltonian: colinear spin. Treat as non-colinear. For testing only."
         )
@@ -355,10 +361,10 @@ def gen_exchange_siesta(
         print("\n")
         print(f"All calculation finsihed. The results are in {output_path} directory.")
 
-    elif H.spin.is_spinorbit or H.spin.is_noncolinear:
+    elif parser.spin.is_spinorbit or H.spin.is_noncolinear:
         print("Reading Siesta hamiltonian: non-colinear spin.")
-        tbmodel = SislWrapper(fdf_fname=None, sisl_hamiltonian=H, spin=None, geom=geom)
-        basis = dict(zip(tbmodel.orbs, list(range(tbmodel.nbasis))))
+        model = parser.get_model()
+        basis = dict(zip(model.orbs, list(range(model.nbasis))))
         print("Starting to calculate exchange.")
         description = f""" Input from non-collinear Siesta data.
  working directory: {os.getcwd()}
@@ -368,8 +374,8 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
  If you need these component, try to do three calculations with spin along x, y, z,  or use structure with z rotated to x, y and z. And then use TB2J_merge.py to get the full set of parameters.
 \n"""
         exchange = ExchangeNCL(
-            tbmodels=tbmodel,
-            atoms=tbmodel.atoms,
+            tbmodels=model,
+            atoms=model.atoms,
             basis=basis,
             efermi=0.0,
             magnetic_elements=magnetic_elements,

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J/pauli.py

@@ -143,11 +143,39 @@ def pauli_block_all(M):
     return MI, Mx, My, Mz
 
 
-def gather_pauli_blocks(MI, Mx, My, Mz):
+def gather_pauli_blocks(MI, Mx, My, Mz, coeffs=[1.0, 1.0, 1.0, 1.0]):
     """
     Gather the I, x, y, z component of a matrix.
     """
-    return np.kron(MI, s0) + np.kron(Mx, s1) + np.kron(My, s2) + np.kron(Mz, s3)
+    cI, cx, cy, cz = coeffs
+    return cI*np.kron(MI, s0) + cx*np.kron(Mx, s1) + cy*np.kron(My, s2) + cz*np.kron(Mz, s3)
+
+def pauli_part(M, coeffs=[1.0, 1.0, 1.0, 1.0]):
+    """
+    Get the I, x, y, z part of a matrix.
+    """
+    MI, Mx, My, Mz = pauli_block_all(M)
+    return gather_pauli_blocks(MI, Mx, My, Mz, coeffs=coeffs)
+
+def chargepart(M):
+    """
+    Get the charge part of a matrix.
+    """
+    MI = (M[::2, ::2] + M[1::2, 1::2]) / 2.0
+    Mcopy = np.zeros_like(M)
+    Mcopy[::2, ::2]  = MI
+    Mcopy[1::2, 1::2] = MI
+    return Mcopy
+
+def spinpart(M):
+    """
+    Get the spin part of a matrix.
+    """
+    MI = (M[::2, ::2] + M[1::2, 1::2]) / 2.0
+    Mcopy = M.copy()
+    Mcopy[::2, ::2]  -= MI
+    Mcopy[1::2, 1::2] -= MI
+    return Mcopy
 
 
 def test_gather_pauli_blocks():

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.9.3rc0
+Version: 0.9.5rc0
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,6 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: pre-commit
-Requires-Dist: HamiltonIO>=0.1.4
+Requires-Dist: HamiltonIO>=0.1.5
 
 TB2J is a Python package aimed to compute automatically the magnetic interactions (superexchange  and Dzyaloshinskii-Moriya) between atoms of magnetic crystals from DFT Hamiltonian based on Wannier functions or Linear combination of atomic orbitals. It uses the Green's function method and take the local rigid spin rotation as a perturbation. The package can take the output from Wannier90, which is interfaced with many density functional theory codes or from codes based on localised orbitals. A minimal user input is needed, which allows for an easily integration into a high-throughput workflows. 

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J.egg-info/SOURCES.txt

@@ -24,7 +24,6 @@ TB2J/kpoints.py
 TB2J/manager.py
 TB2J/myTB.py
 TB2J/orbmap.py
-TB2J/patch.py
 TB2J/pauli.py
 TB2J/pert.py
 TB2J/plot.py

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/TB2J.egg-info/requires.txt

@@ -5,5 +5,4 @@ ase>=3.19
 tqdm
 pathos
 packaging>=20.0
-pre-commit
-HamiltonIO>=0.1.4
+HamiltonIO>=0.1.5

{tb2j-0.9.3rc0 → tb2j-0.9.5rc0}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import setup, find_packages
 
-__version__ = "0.9.3_pre"
+__version__ = "0.9.5_pre"
 
 long_description = """TB2J is a Python package aimed to compute automatically the magnetic interactions (superexchange  and Dzyaloshinskii-Moriya) between atoms of magnetic crystals from DFT Hamiltonian based on Wannier functions or Linear combination of atomic orbitals. It uses the Green's function method and take the local rigid spin rotation as a perturbation. The package can take the output from Wannier90, which is interfaced with many density functional theory codes or from codes based on localised orbitals. A minimal user input is needed, which allows for an easily integration into a high-throughput workflows. """
 
@@ -34,8 +34,7 @@ setup(
         "tqdm",
         "pathos",
         "packaging>=20.0",
-        "pre-commit",
-        "HamiltonIO>=0.1.4"
+        "HamiltonIO>=0.1.5",
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",
@@ -47,4 +46,5 @@ setup(
         "License :: OSI Approved :: BSD License",
     ],
     python_requires=">=3.6",
+
 )

tb2j-0.9.3rc0/TB2J/patch.py

@@ -1,50 +0,0 @@
-import types
-from unittest import mock
-
-class A(object):#but seems to work for old style objects too
-    def funcx(self,x):
-        print("x1=",x)
-        print("called from", self)
-
-    def method(self,x):
-        print("xmethod=",x)
-        print("called from", self)
-
-def patch_me(target):
-    def method(target,x):
-        print("x=",x)
-        print("called from", target)
-        target.method = types.MethodType(method,target)
-
-def method(self,x):
-    print("x=",x)
-    print("called from", self)
-
-@mock.patch("__main__.A")
-def funcx(self,x):
-    print("new x=",x)
-    print("called from", self)
-        
-A.method=method
-#add more if needed
-a = A()
-print(A.__dict__)
-print(a)
-#out: <__main__.A object at 0x2b73ac88bfd0>  
-
-@mock.patch("__main__.a")
-def funcx(self,x):
-    print("x=",x)
-    print("called from", self)
- 
-a.funcx(3)
-patch_me(a)    #patch instance
-a.method=method
-#a.method(5)
-#out: x= 5
-#out: called from <__main__.A object at 0x2b73ac88bfd0>
-patch_me(A)
-
-a.method(6)        #can patch class too
-#out: x= 6
-#out: called from <class '__main__.A'>