TB2Jflows 0.0.1__tar.gz → 0.2__tar.gz

tb2jflows-0.2/.gitignore

@@ -0,0 +1,129 @@
+doc/refs/*.pdf
+examples
+
+# Latex 
+*.aux
+
+# 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/

tb2jflows-0.2/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.5
+    hooks:
+      # Run the linter.
+      - id: ruff
+        # --select I sorts imports
+        args: [ --fix, --extend-select, I  ]
+      # Run the formatter.
+      - id: ruff-format

{tb2jflows-0.0.1 → tb2jflows-0.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: TB2Jflows
-Version: 0.0.1
+Version: 0.2
 Summary: TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -23,6 +23,7 @@ Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{tb2jflows-0.0.1 → tb2jflows-0.2}/TB2Jflows/ase_siesta.py

@@ -24,6 +24,7 @@ class SiestaFlow:
         restart=True,
         metadata={},
         fdf_arguments={},
+        relax_arguments={},
         split_soc=False,
         **kwargs,
     ):
@@ -50,6 +51,7 @@ 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")
@@ -158,6 +160,7 @@ class SiestaFlow:
         MaxStressTol=0.1,
         NumCGSteps=200,
     ):
+        print(f"Relaxation in {path}")
         if (
             self.restart
             and self.metadata["already_relaxed"]
@@ -169,20 +172,20 @@ class SiestaFlow:
             old_spin = self.spin
             if use_collinear:
                 self.spin = "collinear"
-                calc = self.get_calculator(atoms, path=self.relax_path, label=label)
-                calc.atoms = atoms
-                atoms = calc.relax(
-                    atoms,
-                    TypeOfRun=TypeOfRun,
-                    VariableCell=VariableCell,
-                    ConstantVolume=ConstantVolume,
-                    RelaxCellOnly=RelaxCellOnly,
-                    MaxForceTol=MaxForceTol,
-                    MaxStressTol=MaxStressTol,
-                    NumCGSteps=NumCGSteps,
-                )
-                self.spin = old_spin
-                self.relaxed_atoms = atoms
+            calc = self.get_calculator(atoms, path=self.relax_path, label=label)
+            calc.atoms = atoms
+            atoms = calc.relax(
+                atoms,
+                TypeOfRun=TypeOfRun,
+                VariableCell=VariableCell,
+                ConstantVolume=ConstantVolume,
+                RelaxCellOnly=RelaxCellOnly,
+                MaxForceTol=MaxForceTol,
+                MaxStressTol=MaxStressTol,
+                NumCGSteps=NumCGSteps,
+            )
+            self.spin = old_spin
+            self.relaxed_atoms = atoms
             self.update_metadata(
                 {
                     "already_relaxed": True,
@@ -227,19 +230,20 @@ class SiestaFlow:
     def scf_calculatoin_split_soc(self, atoms, label="siesta", nscf=False):
         fdf_args = {
             "SOC_split_SR_SO": True,
-            #"Spin.OrbitStrength": 3,
+            # "Spin.OrbitStrength": 3,
             "SaveHS.so": True,
             "SaveHS": True,
-            "Spin.Fix": False, 
+            "Spin.Fix": False,
+        }
+        nscf_args = {
+            "SCF.DM.Converge": True,
+            "SCF.DM.Tolerance": 1e4,
+            "SCF.H.Converge": False,
+            "SCF.EDM.Converge": False,
+            "SCF.Mix.First": False,
+            "SCF.Mix": "density",
+            "MaxSCFIterations": 1,
         }
-        nscf_args={"SCF.DM.Converge": True, 
-                "SCF.DM.Tolerance": 1e4, 
-                "SCF.H.Converge": False, 
-                "SCF.EDM.Converge": False, 
-                "SCF.Mix.First": False, 
-                "SCF.Mix": "density", 
-                "MaxSCFIterations": 1,
-                }
         if nscf:
             fdf_args.update(nscf_args)
 
@@ -288,14 +292,17 @@ class SiestaFlow:
         )
 
     def set_nonscf_params(self):
-        nscf_params={"SCF.DM.Converge": False, 
-                "SCF.DM.Tolerance": 1e4, 
-                "SCF.H.Converge": False, 
-                "SCF.EDM.Converge": False, 
-                "SCF.Mix.First": False, 
-                "SCF.Mix": "density", 
-                "MaxSCFIterations": 1,
-                }
+        nscf_params = {
+            "SCF.DM.Converge": False,
+            "SCF.DM.Tolerance": 1e4,
+            "SCF.H.Converge": False,
+            "SCF.EDM.Converge": False,
+            "SCF.Mix.First": False,
+            "SCF.Mix": "density",
+            "MaxSCFIterations": 1,
+        }
+
+        self.fdf_arguments.update(nscf_params)
 
     def run_TB2J_split_soc(self, **kwargs):
         path = os.path.join(self.scf_path, "split_soc")
@@ -352,9 +359,9 @@ 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)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculation_collinear(atoms, label="siesta")
         if TB2J:
@@ -364,7 +371,7 @@ class SiestaFlow:
         self, atoms, relax=True, scf=True, TB2J=True, rotate_type="structure", **kwargs
     ):
         if relax:
-            atoms = self.relax(atoms)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculation_with_rotations(
                 atoms, rotate_type=rotate_type, label="siesta"
@@ -375,7 +382,7 @@ class SiestaFlow:
 
     def runall_split_soc(self, atoms, relax=True, scf=True, TB2J=True, **kwargs):
         if relax:
-            atoms = self.relax(atoms)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculatoin_split_soc(atoms, label="siesta")
         if TB2J:

{tb2jflows-0.0.1 → tb2jflows-0.2}/TB2Jflows/auto_siesta_TB2J.py

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

{tb2jflows-0.0.1 → tb2jflows-0.2}/TB2Jflows.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: TB2Jflows
-Version: 0.0.1
+Version: 0.2
 Summary: TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -23,6 +23,7 @@ Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{tb2jflows-0.0.1 → tb2jflows-0.2}/TB2Jflows.egg-info/SOURCES.txt

@@ -1,6 +1,9 @@
+.gitignore
+.pre-commit-config.yaml
 LICENSE
 README.md
 setup.py
+upload_to_pip.sh
 TB2Jflows/__init__.py
 TB2Jflows/ase_siesta.py
 TB2Jflows/auto_siesta_TB2J.py
@@ -9,4 +12,6 @@ TB2Jflows.egg-info/PKG-INFO
 TB2Jflows.egg-info/SOURCES.txt
 TB2Jflows.egg-info/dependency_links.txt
 TB2Jflows.egg-info/requires.txt
-TB2Jflows.egg-info/top_level.txt
+TB2Jflows.egg-info/top_level.txt
+examples/SrMnO3/POSCAR
+examples/SrMnO3/SMO_example.py

tb2jflows-0.2/examples/SrMnO3/POSCAR

@@ -0,0 +1,13 @@
+Sr Mn  Ca O 
+ 1.0000000000000000
+     3.8099846261953436   -0.0000000000000000   -0.0000000000000000
+     0.0000000000000000    3.8099846261953436    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    3.8099846261953436
+  Sr Mn  O
+   1   1   3
+Cartesian
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  1.9049923130976718  1.9049923130976718  1.9049923130976718
+  1.9049923130976718  2.0049923130976718  0.0000000000000000
+  0.0000000000000000  1.9049923130976718  1.9049923130976718
+  1.9049923130976718  0.0000000000000000  1.9049923130976718

tb2jflows-0.2/examples/SrMnO3/SMO_example.py

@@ -0,0 +1,42 @@
+from ase.io import read
+import numpy as np
+from TB2Jflows import SiestaFlow
+
+
+def calculate_siesta_TB2J_SrMnO3():
+    atoms = read('POSCAR')
+    atoms.set_initial_magnetic_moments([0, 3, 0, 0, 0])
+    flow = SiestaFlow(atoms,
+                      spin='spin-orbit',
+                      restart=True,
+                      kpts=[6, 6, 6],
+                      root_path='SrMnO3')
+    flow.write_metadata()
+
+    #atoms = flow.relax(atoms)
+    mz = [0, 3, 0, 0, 0]
+    #m = np.zeros((5, 3), dtype=float)
+    #m[1] = np.array([3, 3, 3])/1.732
+    # m[1]=np.array([0,0,3])
+    # atoms.set_initial_magnetic_moments(None)
+    atoms.set_initial_magnetic_moments(mz)
+    # flow.scf_calculation_single_noncollinear(atoms)
+    # flow.run_TB2J_single_noncollinear(magnetic_elements='Mn',
+    #              nz=50,
+    #              kmesh=[5, 5, 5],
+    #              Rcut=18,
+    #              np=3,
+    #              use_cache=True)
+
+    flow.scf_calculation_with_rotations(atoms)
+    flow.run_TB2J(magnetic_elements='Mn',
+                  nz=50,
+                  kmesh=[7, 7, 7],
+                  Rcut=18,
+                  np=3,
+                  use_cache=True)
+    flow.run_TB2J_merge()
+
+
+if __name__ == '__main__':
+    calculate_siesta_TB2J_SrMnO3()

tb2jflows-0.2/setup.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+from setuptools import find_packages, setup
+
+__version__ = "0.2"
+
+long_description = """ TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J """
+
+setup(
+    name="TB2Jflows",
+    version=__version__,
+    description="TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J",
+    long_description=long_description,
+    author="Xu He",
+    author_email="mailhexu@gmail.com",
+    license="BSD-2-clause",
+    packages=find_packages(),
+    scripts=[],
+    install_requires=["TB2J", "ase", "sisl", "pyDFTutils"],
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Chemistry",
+        "Topic :: Scientific/Engineering :: Physics",
+        "License :: OSI Approved :: BSD License",
+    ],
+    python_requires=">=3.6",
+)

tb2jflows-0.2/upload_to_pip.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+rm ./dist/*
+#python3 setup.py sdist bdist_wheel
+python -m build
+python -m twine upload --repository pypi dist/* --verbose

tb2jflows-0.0.1/setup.py

@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-from setuptools import setup, find_packages
-
-__version__ = "0.0.1"
-
-long_description = """ TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J """
-
-setup(
-    name='TB2Jflows',
-    version=__version__,
-    description=
-    'TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J',
-    long_description=long_description,
-    author='Xu He',
-    author_email='mailhexu@gmail.com',
-    license='BSD-2-clause',
-    packages=find_packages(),
-    scripts=[
-    ],
-    install_requires=['TB2J', 'ase', 'sisl', 'pyDFTutils'],
-    classifiers=[
-        'Development Status :: 3 - Alpha',
-        'Programming Language :: Python :: 3',
-        'Operating System :: OS Independent',
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Scientific/Engineering :: Physics',
-        'License :: OSI Approved :: BSD License',
-    ],
-    python_requires='>=3.6',
-)