hamop 0.1.0__tar.gz

hamop-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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hamop-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hamop
+Version: 0.1.0
+Summary: One tight-binding Hamiltonian, every observable: bands, DOS, Kubo optical conductivity and NEGF transmission from the same real-space blocks, nonorthogonal bases included
+Author-email: "Tanvir M. Mahim" <tanvir.mahim@bracu.ac.bd>
+License: Apache-2.0
+Project-URL: Homepage, https://tanvir-mahmud-mahim.github.io/software/
+Project-URL: Repository, https://github.com/TaN-MM-Org/hamop
+Project-URL: Issues, https://github.com/TaN-MM-Org/hamop/issues
+Project-URL: Changelog, https://github.com/TaN-MM-Org/hamop/releases
+Keywords: tight binding,Kubo-Greenwood,NEGF,Landauer,optical conductivity,quantum transport,LCAO
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.8
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# hamop
+
+[![Tests](https://github.com/TaN-MM-Org/hamop/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/hamop/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/hamop?label=PyPI&color=blue)](https://pypi.org/project/hamop/)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+**One tight-binding Hamiltonian, every observable, strictly
+consistent.** Build a Hamiltonian once, as real-space blocks in an
+orthogonal or nonorthogonal basis, and compute its band structure,
+density of states, Kubo-Greenwood optical conductivity and Landauer
+(NEGF) transmission from the same matrices.
+
+The point of the package is the consistency, not any single solver.
+When the optics of a model and its spectrum are computed by different
+codes with different conventions, they drift: a different gauge for the
+velocity operator, a different treatment of the overlap matrix, a
+different broadening, and suddenly the absorption edge no longer sits
+at the band gap. Here every observable diagonalizes the same Bloch
+matrices through the same canonically orthogonalized solver, and the
+Kubo velocity operator is built from the exact k-derivative of the same
+assembly, so spectral, optical and transport statements about one model
+cannot disagree with each other.
+
+## What it does
+
+- **`TightBindingModel`**: sites with any number of orbitals, directed
+  hopping blocks with automatic Hermitian completion, optional overlap
+  blocks (LCAO-style nonorthogonal bases), periodic in any dimension or
+  finite. Assembles H(k), S(k) and their exact k-derivatives in the
+  atomic gauge.
+- **Spectrum** (`bands`, `dos`, `fermi_level`, `band_edges`): band
+  structures along arbitrary k-lists, Gaussian-broadened densities of
+  states, chemical potential at a given filling by bisection, band
+  edges and gap about a chemical potential.
+- **Optics** (`sigma_optical`): Kubo-Greenwood real sheet conductivity
+  in units of e²/(4ℏ), with the nonorthogonal velocity correction
+  `v = dH/dk − (eₙ+eₘ)/2 dS/dk` that makes the result exactly
+  invariant under a shift of the energy zero.
+- **Transport** (`sancho_rubio`, `transmission`,
+  `transmission_direct`): two-probe Landauer transmission with
+  Sancho-Rubio lead surface Green functions and a recursive Green
+  function sweep, nonorthogonal bases included, plus a dense
+  direct-inversion reference implementation of the same quantity.
+- **`gen_eigh`**: generalized eigensolver with canonical
+  orthogonalization (Szabo and Ostlund, *Modern Quantum Chemistry*,
+  sec. 3.4.5), so mildly overcomplete overlaps cannot blow up the
+  spectrum — the standard remedy used inside electronic-structure
+  codes.
+
+Dependencies: NumPy and SciPy. Nothing else.
+
+## Validation against closed forms
+
+Every physical claim in the package is pinned by a test against an
+exact result, not a stored number:
+
+- the single-orbital chain reproduces E(k) = e₀ + 2t cos ka to machine
+  precision, and its nonorthogonal variant reproduces
+  E(k) = 2t cos ka / (1 + 2s cos ka);
+- the chain density of states matches 1/(π√(4t² − E²)) and integrates
+  to the orbital count;
+- graphene's nearest-neighbour model gives Dirac-point closure at K
+  exactly, ±3|t| at Γ exactly, and the **universal optical sheet
+  conductivity e²/(4ℏ)** on the interband plateau (Kuzmenko et al.,
+  Phys. Rev. Lett. 100, 117401 (2008)) — which is also the absolute
+  anchor for the package's conductivity unit;
+- the two-site molecule absorbs at exactly 2|t| with the hand-derived
+  velocity matrix element |M| = |a t|;
+- σ(ω) is invariant to 10⁻¹⁰ under H → H + cS with μ → μ + c, which
+  pins the nonorthogonal velocity term;
+- the chain's lead surface Green function matches its closed form
+  (E − i√(4t² − E²))/(2t²); a pristine chain transmits exactly one
+  channel inside the band and nothing outside; two decoupled chains
+  transmit two; an on-site impurity ε reproduces
+  T = (4t² − E²)/((4t² − E²) + ε²);
+- the recursive Green function sweep agrees with dense direct inversion
+  to machine precision, disorder and overlap included.
+
+Run them yourself: `pip install -e .[test]` then `pytest`.
+
+## Install and use
+
+```
+pip install hamop
+```
+
+```python
+import numpy as np
+from hamop import graphene, bands, dos, sigma_optical
+
+g = graphene(t=-2.7, a=2.46)          # eV, Angstrom
+omega = np.linspace(0.5, 2.0, 60)
+sigma = sigma_optical(g, omega, mu=0.0, mesh=120, eta=0.12)
+# sigma is ~1.0 on the plateau: the universal e^2/(4 hbar)
+```
+
+Building your own model:
+
+```python
+from hamop import TightBindingModel, band_edges
+
+m = TightBindingModel(positions=[[0.0], [0.7]], norb=1, cell=[[2.0]])
+m.add_hop(0, 1, (0,), [[-1.0]])       # intra-cell bond
+m.add_hop(1, 0, (1,), [[-0.6]])       # inter-cell bond
+print(band_edges(m, mu=0.0, mesh=2001))   # the SSH gap, 2|t1 - t2|
+```
+
+Conventions, stated once: energies in eV, positions in Angstrom, k in
+1/Angstrom, Cartesian. Each directed hopping block is added once and
+its Hermitian partner is implied. Optical conductivity is the real
+sheet conductivity in units of e²/(4ℏ) with spin degeneracy as an
+explicit factor (default 2). The velocity operator uses the standard
+atomistic position gauge (position operator diagonal at the sites);
+the intra-atomic dipole contribution is neglected, the common
+approximation in tight-binding optics.
+
+## Relation to existing tools
+
+Excellent tools cover parts of this space: [PythTB](https://www.physics.rutgers.edu/pythtb/) and [pybinding](https://docs.pybinding.site/) build tight-binding models and their spectra, and [Kwant](https://kwant-project.org/) is the standard for quantum transport. hamop does not replace any of them, and for their core use cases they are more capable. Its niche is the combination they leave open: nonorthogonal (LCAO-style) overlap matrices as first-class citizens across *all* observables, optics and transport computed from the same Bloch assembly as the spectrum so the three can never disagree, and a deliberately small NumPy/SciPy-only core validated line by line against closed forms -- the shape of engine an LCAO electronic-structure pipeline exports its Hamiltonians into.
+
+## Status
+
+v0.1.0 (alpha). Implemented and tested: the model container with exact
+k-derivatives, canonical-orthogonalization eigensolver, band
+structures, densities of states, filling-resolved chemical potentials,
+band edges, Kubo-Greenwood optical conductivity for periodic and finite
+systems, Sancho-Rubio surface Green functions, and recursive plus
+direct-inversion Landauer transmission.
+
+Not yet implemented, stated plainly: k-space symmetry reduction (grids
+are full Monkhorst-Pack), Lorentzian and adaptive broadenings, the
+Drude (intraband) term of the conductivity, spin-orbit-coupled blocks
+as a first-class convention (complex blocks work, but no helper),
+Hall/off-diagonal conductivity tensors, and interaction self-energies
+in the transport module. Sparse or very large models are out of scope
+for now: matrices are dense.
+
+## Where it comes from
+
+Methodological basis:
+
+> "Learning the quantum Hamiltonian of defective monolayer MoS2
+> reveals collective vacancy brightness decoupled from defect count";
+> code for the paper:
+> https://github.com/Tanvir-Mahmud-Mahim/mos2-vacancy-optics
+
+That study computes the optics, the electronic structure and the
+transport of vacancy-disordered MoS2 supercells from one
+density-functional Hamiltonian, so that a defect configuration's
+optical and electronic signatures are strictly consistent — and its
+conclusions depend on that consistency. This package is the
+general-purpose engine distilled from that pipeline: the same
+observables for any Hamiltonian a user supplies, with the
+material-specific machinery (DFT extraction, machine-learned
+Hamiltonians, MoS2 structures) left in the paper repository.
+
+## Support and governance
+
+The package is written and maintained by Tanvir Mahmud Mahim
+(Department of Electrical and Electronic Engineering, BRAC University),
+who reviews every change and takes the final decision on scope and
+releases. There is no separate governance body; design questions are
+discussed in the open in issues and pull requests, and the standing
+rule of [CONTRIBUTING.md](CONTRIBUTING.md) binds the maintainer exactly
+as it binds contributors: a change that touches physics arrives with a
+test, and a constant arrives with its source.
+
+Support runs through the issue tracker at
+https://github.com/TaN-MM-Org/hamop/issues. Usage questions are welcome
+there alongside bug reports; a docstring that left a unit or a sign
+convention unclear is treated as a documentation bug, not as user
+error. The maintainer aims to respond within a week.
+
+While the version is below 1.0 the API may still move between minor
+versions; such changes are called out in the release notes. The
+limitations named under Status are deliberate scope, recorded there
+precisely so that a user can tell a designed-out feature from an
+oversight.
+
+## License
+
+Apache-2.0 (see [LICENSE](LICENSE)). Citation metadata is in
+[CITATION.cff](CITATION.cff).

hamop-0.1.0/README.md

@@ -0,0 +1,183 @@
+# hamop
+
+[![Tests](https://github.com/TaN-MM-Org/hamop/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/hamop/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/hamop?label=PyPI&color=blue)](https://pypi.org/project/hamop/)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+**One tight-binding Hamiltonian, every observable, strictly
+consistent.** Build a Hamiltonian once, as real-space blocks in an
+orthogonal or nonorthogonal basis, and compute its band structure,
+density of states, Kubo-Greenwood optical conductivity and Landauer
+(NEGF) transmission from the same matrices.
+
+The point of the package is the consistency, not any single solver.
+When the optics of a model and its spectrum are computed by different
+codes with different conventions, they drift: a different gauge for the
+velocity operator, a different treatment of the overlap matrix, a
+different broadening, and suddenly the absorption edge no longer sits
+at the band gap. Here every observable diagonalizes the same Bloch
+matrices through the same canonically orthogonalized solver, and the
+Kubo velocity operator is built from the exact k-derivative of the same
+assembly, so spectral, optical and transport statements about one model
+cannot disagree with each other.
+
+## What it does
+
+- **`TightBindingModel`**: sites with any number of orbitals, directed
+  hopping blocks with automatic Hermitian completion, optional overlap
+  blocks (LCAO-style nonorthogonal bases), periodic in any dimension or
+  finite. Assembles H(k), S(k) and their exact k-derivatives in the
+  atomic gauge.
+- **Spectrum** (`bands`, `dos`, `fermi_level`, `band_edges`): band
+  structures along arbitrary k-lists, Gaussian-broadened densities of
+  states, chemical potential at a given filling by bisection, band
+  edges and gap about a chemical potential.
+- **Optics** (`sigma_optical`): Kubo-Greenwood real sheet conductivity
+  in units of e²/(4ℏ), with the nonorthogonal velocity correction
+  `v = dH/dk − (eₙ+eₘ)/2 dS/dk` that makes the result exactly
+  invariant under a shift of the energy zero.
+- **Transport** (`sancho_rubio`, `transmission`,
+  `transmission_direct`): two-probe Landauer transmission with
+  Sancho-Rubio lead surface Green functions and a recursive Green
+  function sweep, nonorthogonal bases included, plus a dense
+  direct-inversion reference implementation of the same quantity.
+- **`gen_eigh`**: generalized eigensolver with canonical
+  orthogonalization (Szabo and Ostlund, *Modern Quantum Chemistry*,
+  sec. 3.4.5), so mildly overcomplete overlaps cannot blow up the
+  spectrum — the standard remedy used inside electronic-structure
+  codes.
+
+Dependencies: NumPy and SciPy. Nothing else.
+
+## Validation against closed forms
+
+Every physical claim in the package is pinned by a test against an
+exact result, not a stored number:
+
+- the single-orbital chain reproduces E(k) = e₀ + 2t cos ka to machine
+  precision, and its nonorthogonal variant reproduces
+  E(k) = 2t cos ka / (1 + 2s cos ka);
+- the chain density of states matches 1/(π√(4t² − E²)) and integrates
+  to the orbital count;
+- graphene's nearest-neighbour model gives Dirac-point closure at K
+  exactly, ±3|t| at Γ exactly, and the **universal optical sheet
+  conductivity e²/(4ℏ)** on the interband plateau (Kuzmenko et al.,
+  Phys. Rev. Lett. 100, 117401 (2008)) — which is also the absolute
+  anchor for the package's conductivity unit;
+- the two-site molecule absorbs at exactly 2|t| with the hand-derived
+  velocity matrix element |M| = |a t|;
+- σ(ω) is invariant to 10⁻¹⁰ under H → H + cS with μ → μ + c, which
+  pins the nonorthogonal velocity term;
+- the chain's lead surface Green function matches its closed form
+  (E − i√(4t² − E²))/(2t²); a pristine chain transmits exactly one
+  channel inside the band and nothing outside; two decoupled chains
+  transmit two; an on-site impurity ε reproduces
+  T = (4t² − E²)/((4t² − E²) + ε²);
+- the recursive Green function sweep agrees with dense direct inversion
+  to machine precision, disorder and overlap included.
+
+Run them yourself: `pip install -e .[test]` then `pytest`.
+
+## Install and use
+
+```
+pip install hamop
+```
+
+```python
+import numpy as np
+from hamop import graphene, bands, dos, sigma_optical
+
+g = graphene(t=-2.7, a=2.46)          # eV, Angstrom
+omega = np.linspace(0.5, 2.0, 60)
+sigma = sigma_optical(g, omega, mu=0.0, mesh=120, eta=0.12)
+# sigma is ~1.0 on the plateau: the universal e^2/(4 hbar)
+```
+
+Building your own model:
+
+```python
+from hamop import TightBindingModel, band_edges
+
+m = TightBindingModel(positions=[[0.0], [0.7]], norb=1, cell=[[2.0]])
+m.add_hop(0, 1, (0,), [[-1.0]])       # intra-cell bond
+m.add_hop(1, 0, (1,), [[-0.6]])       # inter-cell bond
+print(band_edges(m, mu=0.0, mesh=2001))   # the SSH gap, 2|t1 - t2|
+```
+
+Conventions, stated once: energies in eV, positions in Angstrom, k in
+1/Angstrom, Cartesian. Each directed hopping block is added once and
+its Hermitian partner is implied. Optical conductivity is the real
+sheet conductivity in units of e²/(4ℏ) with spin degeneracy as an
+explicit factor (default 2). The velocity operator uses the standard
+atomistic position gauge (position operator diagonal at the sites);
+the intra-atomic dipole contribution is neglected, the common
+approximation in tight-binding optics.
+
+## Relation to existing tools
+
+Excellent tools cover parts of this space: [PythTB](https://www.physics.rutgers.edu/pythtb/) and [pybinding](https://docs.pybinding.site/) build tight-binding models and their spectra, and [Kwant](https://kwant-project.org/) is the standard for quantum transport. hamop does not replace any of them, and for their core use cases they are more capable. Its niche is the combination they leave open: nonorthogonal (LCAO-style) overlap matrices as first-class citizens across *all* observables, optics and transport computed from the same Bloch assembly as the spectrum so the three can never disagree, and a deliberately small NumPy/SciPy-only core validated line by line against closed forms -- the shape of engine an LCAO electronic-structure pipeline exports its Hamiltonians into.
+
+## Status
+
+v0.1.0 (alpha). Implemented and tested: the model container with exact
+k-derivatives, canonical-orthogonalization eigensolver, band
+structures, densities of states, filling-resolved chemical potentials,
+band edges, Kubo-Greenwood optical conductivity for periodic and finite
+systems, Sancho-Rubio surface Green functions, and recursive plus
+direct-inversion Landauer transmission.
+
+Not yet implemented, stated plainly: k-space symmetry reduction (grids
+are full Monkhorst-Pack), Lorentzian and adaptive broadenings, the
+Drude (intraband) term of the conductivity, spin-orbit-coupled blocks
+as a first-class convention (complex blocks work, but no helper),
+Hall/off-diagonal conductivity tensors, and interaction self-energies
+in the transport module. Sparse or very large models are out of scope
+for now: matrices are dense.
+
+## Where it comes from
+
+Methodological basis:
+
+> "Learning the quantum Hamiltonian of defective monolayer MoS2
+> reveals collective vacancy brightness decoupled from defect count";
+> code for the paper:
+> https://github.com/Tanvir-Mahmud-Mahim/mos2-vacancy-optics
+
+That study computes the optics, the electronic structure and the
+transport of vacancy-disordered MoS2 supercells from one
+density-functional Hamiltonian, so that a defect configuration's
+optical and electronic signatures are strictly consistent — and its
+conclusions depend on that consistency. This package is the
+general-purpose engine distilled from that pipeline: the same
+observables for any Hamiltonian a user supplies, with the
+material-specific machinery (DFT extraction, machine-learned
+Hamiltonians, MoS2 structures) left in the paper repository.
+
+## Support and governance
+
+The package is written and maintained by Tanvir Mahmud Mahim
+(Department of Electrical and Electronic Engineering, BRAC University),
+who reviews every change and takes the final decision on scope and
+releases. There is no separate governance body; design questions are
+discussed in the open in issues and pull requests, and the standing
+rule of [CONTRIBUTING.md](CONTRIBUTING.md) binds the maintainer exactly
+as it binds contributors: a change that touches physics arrives with a
+test, and a constant arrives with its source.
+
+Support runs through the issue tracker at
+https://github.com/TaN-MM-Org/hamop/issues. Usage questions are welcome
+there alongside bug reports; a docstring that left a unit or a sign
+convention unclear is treated as a documentation bug, not as user
+error. The maintainer aims to respond within a week.
+
+While the version is below 1.0 the API may still move between minor
+versions; such changes are called out in the release notes. The
+limitations named under Status are deliberate scope, recorded there
+precisely so that a user can tell a designed-out feature from an
+oversight.
+
+## License
+
+Apache-2.0 (see [LICENSE](LICENSE)). Citation metadata is in
+[CITATION.cff](CITATION.cff).

hamop-0.1.0/pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hamop"
+version = "0.1.0"
+description = "One tight-binding Hamiltonian, every observable: bands, DOS, Kubo optical conductivity and NEGF transmission from the same real-space blocks, nonorthogonal bases included"
+readme = "README.md"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Tanvir M. Mahim", email = "tanvir.mahim@bracu.ac.bd" }]
+requires-python = ">=3.9"
+keywords = ["tight binding", "Kubo-Greenwood", "NEGF", "Landauer", "optical conductivity", "quantum transport", "LCAO"]
+dependencies = ["numpy>=1.22", "scipy>=1.8"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Physics",
+]
+
+[project.optional-dependencies]
+test = ["pytest"]
+
+[project.urls]
+Homepage = "https://tanvir-mahmud-mahim.github.io/software/"
+Repository = "https://github.com/TaN-MM-Org/hamop"
+Issues = "https://github.com/TaN-MM-Org/hamop/issues"
+Changelog = "https://github.com/TaN-MM-Org/hamop/releases"
+
+[tool.setuptools.packages.find]
+where = ["src"]

hamop-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

hamop-0.1.0/src/hamop/__init__.py

@@ -0,0 +1,29 @@
+"""hamop: one tight-binding Hamiltonian, every observable, strictly consistent.
+
+Build a Hamiltonian once, as real-space blocks in an orthogonal or
+nonorthogonal basis, and compute its band structure, density of states,
+Kubo-Greenwood optical conductivity and Landauer transmission from the
+same matrices, so that spectral, optical and transport statements about
+one model can never drift apart.
+
+Methodological basis: the study "Learning the quantum Hamiltonian of
+defective monolayer MoS2 reveals collective vacancy brightness
+decoupled from defect count" (code:
+https://github.com/Tanvir-Mahmud-Mahim/mos2-vacancy-optics); this
+package is the general-purpose engine distilled from that pipeline.
+"""
+from .eigsolve import gen_eigh
+from .kubo import carrier_count, sigma_optical
+from .lattices import chain_lead_blocks, graphene, linear_chain, two_site
+from .model import TightBindingModel
+from .negf import sancho_rubio, transmission, transmission_direct
+from .spectrum import band_edges, bands, dos, fermi_level
+
+__version__ = "0.1.0"
+__all__ = [
+    "TightBindingModel", "gen_eigh",
+    "bands", "dos", "fermi_level", "band_edges",
+    "sigma_optical", "carrier_count",
+    "sancho_rubio", "transmission", "transmission_direct",
+    "linear_chain", "two_site", "graphene", "chain_lead_blocks",
+]