TB2J 0.9.12.10__tar.gz → 0.9.12.15__tar.gz

tb2j-0.9.12.15/.gitignore

@@ -0,0 +1,142 @@
+doc/refs/*.pdf
+
+
+# vim files
+*.swp
+
+# Latex
+*.aux
+
+
+# file for AI IDE
+# kiro
+.kiro/
+# cline
+.cline
+# roo coder
+.roo
+
+
+# xyz files
+
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# numpy results
+*.npy
+
+# png files
+
+# C extensions
+*.so
+*.a
+
+# Fortran extensions
+*.fpp
+*.mod
+*.o
+
+# F90wrap files
+*.plist
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+*.egg-info/*
+.installed.cfg
+*.egg
+
+# temporary files
+temp/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

tb2j-0.9.12.15/.readthedocs.yml

@@ -0,0 +1,27 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - requirements: docs/requirements.txt

tb2j-0.9.12.15/.travis.yml

@@ -0,0 +1,33 @@
+language: python
+python:
+  - "3.7"
+  - "3.8"
+  - "3.9"
+  - "3.10"
+  - "3.11"
+cache: pip
+
+addons:
+  apt:
+    packages: &common_packages
+      - gfortran
+      - libatlas-base-dev
+      - liblapack-dev
+      - libnetcdf-dev
+      - libnetcdff-dev
+      - eatmydata
+      - ccache
+before_install:
+ - if [[ $TRAVIS_PYTHON_VERSION == 3.7 ]]; then pip install -U importlib_metadata; fi
+
+install:
+  - pip install -r requirements.txt
+  - pip install sisl
+  - pip install -e .
+script:
+  - pwd
+  - cd examples/abinit-w90/SrMnO3
+  - ls -lah
+  - sh get_J.sh
+  - cd TB2J_results/Multibinit
+  - TB2J_magnon.py --figfname magnon.png

{tb2j-0.9.12.10 → tb2j-0.9.12.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.12.10
+Version: 0.9.12.15
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>
@@ -23,7 +23,6 @@ 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
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -33,9 +32,9 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.2.4
+Requires-Dist: HamiltonIO>=0.2.6
 Requires-Dist: pre-commit
-Requires-Dist: sympair>0.1.0
+Requires-Dist: sympair>0.1.1
 Requires-Dist: tomli>=2.0.0
 Requires-Dist: tomli-w>=1.0.0
 Requires-Dist: typing_extensions
@@ -43,11 +42,11 @@ Provides-Extra: siesta
 Requires-Dist: sisl>=0.9.0; extra == "siesta"
 Requires-Dist: netcdf4; extra == "siesta"
 Provides-Extra: lawaf
-Requires-Dist: lawaf==0.2.3; extra == "lawaf"
+Requires-Dist: lawaf>=0.2.3; extra == "lawaf"
 Provides-Extra: all
 Requires-Dist: sisl>=0.9.0; extra == "all"
 Requires-Dist: netcdf4; extra == "all"
-Requires-Dist: lawaf==0.2.3; extra == "all"
+Requires-Dist: lawaf>=0.2.3; extra == "all"
 Dynamic: license-file
 
 [![Python application](https://github.com/mailhexu/TB2J/actions/workflows/python-app.yml/badge.svg)](https://github.com/mailhexu/TB2J/actions/workflows/python-app.yml)

tb2j-0.9.12.15/TB2J/.gitignore

@@ -0,0 +1,5 @@
+*.o
+*.x
+*.mod
+exchanges.sublime-project
+exchanges.sublime-workspace

{tb2j-0.9.12.10 → tb2j-0.9.12.15}/TB2J/MAEGreen.py

@@ -51,7 +51,7 @@ class MAEGreen(ExchangeNCL):
 
         nangles = len(self.thetas)
         self.es = np.zeros(nangles, dtype=complex)
-        self.es_atom = np.zeros((nangles, self.natoms), dtype=complex)
+        self.es_matrix = np.zeros((nangles, self.natoms, self.natoms), dtype=complex)
         self.es_atom_orb = DefaultDict(lambda: 0)
 
     def set_angles_xyz(self):
@@ -153,7 +153,7 @@ class MAEGreen(ExchangeNCL):
         Hsoc_k = self.tbmodel.get_Hk_soc(self.G.kpts)
         na = len(thetas)
         dE_angle = np.zeros(na, dtype=complex)
-        dE_angle_atom = np.zeros((na, self.natoms), dtype=complex)
+        dE_angle_matrix = np.zeros((na, self.natoms, self.natoms), dtype=complex)
         # dE_angle_orbitals = np.zeros((na, self.natoms, self.norb, self.norb), dtype=complex)
         dE_angle_atom_orb = DefaultDict(lambda: 0)
         for iangle, (theta, phi) in enumerate(zip(thetas, phis)):
@@ -178,23 +178,30 @@ class MAEGreen(ExchangeNCL):
                 # dE_angle[iangle] += np.trace(GdH@GdH) * self.G.kweights[ik]
                 # dE_angle[iangle] += np.trace(GdH@G0K[ik].T.conj()@dHi ) * self.G.kweights[ik]
                 dE_angle[iangle] += dG2sum * self.G.kweights[ik]
+
+                # Calculate atom-atom matrix interactions
                 for iatom in range(self.natoms):
                     iorb = self.iorb(iatom)
-                    # dG2= dG2[::2, ::2] + dG2[1::2, 1::2] + dG2[1::2, ::2] + dG2[::2, 1::2]
-                    dE_atom_orb = dG2[np.ix_(iorb, iorb)] * self.G.kweights[ik]
-                    dE_atom_orb = (
-                        dE_atom_orb[::2, ::2]
-                        + dE_atom_orb[1::2, 1::2]
-                        + dE_atom_orb[1::2, ::2]
-                        + dE_atom_orb[::2, 1::2]
-                    )
-                    dE_atom = np.sum(dE_atom_orb)
-                    mmat = self.mmats[iatom]
-                    dE_atom_orb = mmat.T @ dE_atom_orb @ mmat
-                    dE_angle_atom_orb[(iangle, iatom)] += dE_atom_orb
-                    # dE_atom = np.sum(dG2diag[iorb]) * self.G.kweights[ik]
-                    dE_angle_atom[iangle, iatom] += dE_atom
-        return dE_angle, dE_angle_atom, dE_angle_atom_orb
+                    for jatom in range(self.natoms):
+                        jorb = self.iorb(jatom)
+                        # Calculate cross terms between atoms i and j
+                        dE_ij_orb = dG2[np.ix_(iorb, jorb)] * self.G.kweights[ik]
+                        dE_ij_orb = (
+                            dE_ij_orb[::2, ::2]
+                            + dE_ij_orb[1::2, 1::2]
+                            + dE_ij_orb[1::2, ::2]
+                            + dE_ij_orb[::2, 1::2]
+                        )
+                        dE_ij = np.sum(dE_ij_orb)
+                        # Transform to local orbital basis
+                        mmat_i = self.mmats[iatom]
+                        mmat_j = self.mmats[jatom]
+                        dE_ij_orb = mmat_i.T @ dE_ij_orb @ mmat_j
+                        dE_angle_matrix[iangle, iatom, jatom] += dE_ij
+                        # Store orbital-resolved data for diagonal terms
+                        if iatom == jatom:
+                            dE_angle_atom_orb[(iangle, iatom)] += dE_ij_orb
+        return dE_angle, dE_angle_matrix, dE_angle_atom_orb
 
     def get_perturbed_R(self, e, thetas, phis):
         self.tbmodel.set_so_strength(0.0)
@@ -232,16 +239,16 @@ class MAEGreen(ExchangeNCL):
             npole = len(self.contour.path)
             results = map(func, tqdm.tqdm(self.contour.path, total=npole))
         for i, result in enumerate(results):
-            dE_angle, dE_angle_atom, dE_angle_atom_orb = result
+            dE_angle, dE_angle_matrix, dE_angle_atom_orb = result
             self.es += dE_angle * self.contour.weights[i]
-            self.es_atom += dE_angle_atom * self.contour.weights[i]
+            self.es_matrix += dE_angle_matrix * self.contour.weights[i]
             for key, value in dE_angle_atom_orb.items():
                 self.es_atom_orb[key] += (
                     dE_angle_atom_orb[key] * self.contour.weights[i]
                 )
 
         self.es = -np.imag(self.es) / (2 * np.pi)
-        self.es_atom = -np.imag(self.es_atom) / (2 * np.pi)
+        self.es_matrix = -np.imag(self.es_matrix) / (2 * np.pi)
         for key, value in self.es_atom_orb.items():
             self.es_atom_orb[key] = -np.imag(value) / (2 * np.pi)
 
@@ -259,6 +266,7 @@ class MAEGreen(ExchangeNCL):
         Path(output_path).mkdir(exist_ok=True)
         fname = f"{output_path}/MAE.dat"
         fname_orb = f"{output_path}/MAE_orb.dat"
+        fname_matrix = f"{output_path}/MAE_matrix.dat"
         # fname_tensor = f"{output_path}/MAE_tensor.dat"
         # if figure3d is not None:
         #    fname_fig3d = f"{output_path}/{figure3d}"
@@ -269,24 +277,32 @@ class MAEGreen(ExchangeNCL):
         if with_eigen:
             fname_eigen = f"{output_path}/MAE_eigen.dat"
             with open(fname_eigen, "w") as f:
-                f.write("# theta, phi, MAE(total), MAE(atom-wise) Unit: meV\n")
-                for i, (theta, phi, e, es) in enumerate(
-                    zip(self.thetas, self.phis, self.es2, self.es_atom)
+                f.write("# theta, phi, MAE(total) Unit: meV\n")
+                for i, (theta, phi, e) in enumerate(
+                    zip(self.thetas, self.phis, self.es2)
                 ):
-                    f.write(f"{theta:.5f} {phi:.5f} {e*1e3:.8f} ")
-                    for ea in es:
-                        f.write(f"{ea*1e3:.8f} ")
-                    f.write("\n")
+                    f.write(f"{theta:.5f} {phi:.5f} {e*1e3:.8f}\n")
 
         with open(fname, "w") as f:
-            f.write("# theta (rad), phi(rad), MAE(total), MAE(atom-wise) Unit: meV\n")
-            for i, (theta, phi, e, es) in enumerate(
-                zip(self.thetas, self.phis, self.es, self.es_atom)
-            ):
-                f.write(f"{theta%np.pi:.5f} {phi%(2*np.pi):.5f} {e*1e3:.8f} ")
-                for ea in es:
-                    f.write(f"{ea*1e3:.8f} ")
-                f.write("\n")
+            f.write("# theta (rad), phi(rad), MAE(total) Unit: meV\n")
+            for i, (theta, phi, e) in enumerate(zip(self.thetas, self.phis, self.es)):
+                f.write(f"{theta%np.pi:.5f} {phi%(2*np.pi):.5f} {e*1e3:.8f}\n")
+
+        # Write matrix data to MAE_matrix.dat
+        with open(fname_matrix, "w") as fmat:
+            fmat.write("# MAE atom-atom interaction matrices\n")
+            fmat.write("# Format: angle_index theta phi atom_i atom_j MAE_ij(meV)\n")
+            fmat.write("# Units: theta and phi in radians, MAE in meV\n")
+            for iangle, (theta, phi) in enumerate(zip(self.thetas, self.phis)):
+                for iatom in range(self.natoms):
+                    for jatom in range(self.natoms):
+                        mae_ij = (
+                            self.es_matrix[iangle, iatom, jatom] * 1e3
+                        )  # Convert to meV
+                        fmat.write(
+                            f"{iangle:4d} {theta:.5f} {phi:.5f} {iatom:4d} {jatom:4d} {mae_ij:.8f}\n"
+                        )
+                fmat.write("\n")  # Empty line between angles for readability
 
         # self.ani = self.fit_anisotropy_tensor()
         # with open(fname_tensor, "w") as f:
@@ -312,34 +328,37 @@ class MAEGreen(ExchangeNCL):
                 for orb in self.orbital_names[iatom]:
                     f.write(f"{orb} ")
                 f.write("\n")
-            for i, (theta, phi, e, eatom) in enumerate(
-                zip(self.thetas, self.phis, self.es, self.es_atom)
-            ):
+            for i, (theta, phi, e) in enumerate(zip(self.thetas, self.phis, self.es)):
                 f.write("-" * 60 + "\n")
                 f.write(f"Angle {i:03d}:   theta={theta:.5f} phi={phi:.5f} \n ")
                 f.write(f"E: {e*1e3:.8f} \n")
-                for iatom, ea in enumerate(eatom):
-                    f.write(f"Atom {iatom:03d}: {ea*1e3:.8f} \n")
-                    f.write("Orbital: ")
-                    eorb = self.es_atom_orb[(i, iatom)]
-
-                    # write numpy matrix to file
-                    f.write(
-                        np.array2string(
-                            eorb * 1e3, precision=4, separator=",", suppress_small=True
-                        )
-                    )
-
-                    eorb_diff = eorb - self.es_atom_orb[(0, iatom)]
-                    f.write("Diference to the first angle: ")
-                    f.write(
-                        np.array2string(
-                            eorb_diff * 1e3,
-                            precision=4,
-                            separator=",",
-                            suppress_small=True,
+                for iatom in range(self.natoms):
+                    f.write(f"Atom {iatom:03d} orbital matrix:\n")
+                    if (i, iatom) in self.es_atom_orb:
+                        eorb = self.es_atom_orb[(i, iatom)]
+                        # write numpy matrix to file
+                        f.write(
+                            np.array2string(
+                                eorb * 1e3,
+                                precision=4,
+                                separator=",",
+                                suppress_small=True,
+                            )
                         )
-                    )
+                        f.write("\n")
+
+                        if (0, iatom) in self.es_atom_orb:
+                            eorb_diff = eorb - self.es_atom_orb[(0, iatom)]
+                            f.write("Difference to the first angle: ")
+                            f.write(
+                                np.array2string(
+                                    eorb_diff * 1e3,
+                                    precision=4,
+                                    separator=",",
+                                    suppress_small=True,
+                                )
+                            )
+                            f.write("\n")
                 f.write("\n")
 
     def run(self, output_path="TB2J_anisotropy", with_eigen=False):

{tb2j-0.9.12.10 → tb2j-0.9.12.15}/TB2J/contour.py

@@ -27,8 +27,9 @@ class Contour:
         integrate f along the path
         """
         ret = 0
-        for i in range(len(values)):
-            ret += values[i] * self.weights[i]
+        ret = np.einsum("i...,i->...", values, self.weights)
+        # for i in range(len(values)):
+        #    ret += values[i] * self.weights[i]
         return ret
 
     def build_path_semicircle(self, npoints, endpoint=True):