ramansep 0.2.1__tar.gz

ramansep-0.2.1/LICENSE

@@ -0,0 +1,202 @@
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ramansep-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ramansep
+Version: 0.2.1
+Summary: Separate strain from carrier density in 2D-material Raman maps using a two-mode linear inversion
+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/ramansep
+Project-URL: Issues, https://github.com/TaN-MM-Org/ramansep/issues
+Project-URL: Changelog, https://github.com/TaN-MM-Org/ramansep/releases
+Keywords: Raman spectroscopy,2D materials,MoS2,strain,carrier density,TMD
+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
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# ramansep
+
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.22014913-blue)](https://doi.org/10.5281/zenodo.22014913) [![tests](https://github.com/TaN-MM-Org/ramansep/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/ramansep/actions)
+
+Separate **strain** from **carrier density** in Raman maps of 2D materials,
+using two phonon modes whose lever arms differ.
+
+A single Raman frequency responds to strain and to carrier density at once,
+so one mode cannot tell the two apart. Two modes with sufficiently different
+responses form a linear, invertible probe: measure both shift maps, invert a
+2x2 matrix per pixel, and obtain a strain map and a carrier-density map with
+propagated uncertainties.
+
+## Status
+
+v0.2.0 (alpha). The inversion core, uncertainty propagation, conditioning
+diagnostics, a synthetic end-to-end example, and two cited coefficient
+sets for monolayer MoS2 are implemented and tested. The API may change
+before v1.0.
+
+## Cited coefficient sets (new in v0.2)
+
+Two example sets for monolayer 1H-MoS2 ship with full provenance, and the
+test-suite reproduces the published separation results of the source paper
+from them (edge charge of 2.3e12 cm^-2 from a 0.5 cm^-1 A'1 redshift with
+2LA(M) unmoved; 0.134% interior tension carrying no significant charge):
+
+- `mos2_a1_2la()`: the A'1 + 2LA(M) pair of the source paper. Strain lever
+  arms -5.1 and -20.9 cm^-1 per percent of biaxial strain (frozen-phonon
+  DFT, ratio 4.1); A'1 doping coefficient -2.2 cm^-1 per 1e13 cm^-2 of
+  electrons (measured, Chakraborty et al., Phys. Rev. B 85, 161403(R)
+  (2012)). The 2LA(M) doping coefficient is unmeasured and set to zero;
+  the source paper bounds the consequence of that choice at 16% of a
+  recovered edge charge.
+- `mos2_eprime_a1()`: the historically used all-optical E' + A'1 pair,
+  built from the measured biaxial Grueneisen parameters of Michail et al.,
+  ACS Appl. Mater. Interfaces 16, 49602 (2024). Both optical modes respond
+  weakly to strain, so for equal shift noise this pair returns about five
+  times the strain uncertainty of the A'1 + 2LA(M) pair; it is included
+  for comparison and for workflows where the overtone is not available.
+
+Each function's docstring states which number comes from which source and
+the conditions of applicability (1H monolayer, SiO2-supported, 300 K;
+532 nm for the disorder-activated calibration). Check that your sample
+matches before use.
+
+## What this package deliberately does not include
+
+No constants beyond the two documented MoS2 sets are shipped. Lever arms
+depend on material, mode pair, excitation wavelength and substrate; a
+measurement tool that ships unverified constants propagates wrong results.
+For any other system you provide a `ModeCoefficients` from the literature
+or your own calibration, and the `reference` field is mandatory so the
+provenance of every number travels with the analysis.
+
+## Install
+
+```
+pip install -e .
+```
+
+## Use
+
+```python
+import numpy as np
+from ramansep import SeparationModel, ModeCoefficients
+
+coeffs = ModeCoefficients(
+    mode1_name="A'1", mode2_name="2LA(M)",
+    k1_strain=...,   # cm^-1 per unit strain, from your calibration
+    k1_density=...,  # cm^-1 per unit carrier density
+    k2_strain=...,
+    k2_density=...,
+    reference="cite the source of these numbers",
+)
+model = SeparationModel(coeffs)
+result = model.invert(dw_mode1, dw_mode2, sigma1=0.1, sigma2=0.1)
+# result.strain, result.density, result.strain_sigma, result.density_sigma
+```
+
+`SeparationModel` warns when the mode pair is poorly conditioned, i.e. when
+the two modes respond too similarly for a reliable separation.
+
+## Method
+
+The method of using the first-order A'1 mode together with the
+disorder-activated 2LA(M) overtone, whose strain lever arms differ
+severalfold while only A'1 responds appreciably to carrier density, is
+developed in:
+
+> T. M. Mahim and M. M. Rahman, "Two Raman phonons quantify the fixed edge
+> charge left by patterning monolayer transition metal dichalcogenides"
+> (under review). Code for the paper itself:
+> https://github.com/Tanvir-Mahmud-Mahim/Width-scaling-in-monolayer-semiconductor-nanoribbon-transistors
+
+This package is the general-purpose, material-agnostic inversion tool; the
+paper repository reproduces the specific published study.
+
+## Roadmap
+
+- v0.2 (done): documented example coefficient sets with citations
+- v0.3: peak-fitting front end (load spectra, fit the two modes, feed the
+  inversion)
+- v0.4: joint Bayesian inversion with spatial priors
+
+## License
+
+Apache-2.0

ramansep-0.2.1/README.md

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+# ramansep
+
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.22014913-blue)](https://doi.org/10.5281/zenodo.22014913) [![tests](https://github.com/TaN-MM-Org/ramansep/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/ramansep/actions)
+
+Separate **strain** from **carrier density** in Raman maps of 2D materials,
+using two phonon modes whose lever arms differ.
+
+A single Raman frequency responds to strain and to carrier density at once,
+so one mode cannot tell the two apart. Two modes with sufficiently different
+responses form a linear, invertible probe: measure both shift maps, invert a
+2x2 matrix per pixel, and obtain a strain map and a carrier-density map with
+propagated uncertainties.
+
+## Status
+
+v0.2.0 (alpha). The inversion core, uncertainty propagation, conditioning
+diagnostics, a synthetic end-to-end example, and two cited coefficient
+sets for monolayer MoS2 are implemented and tested. The API may change
+before v1.0.
+
+## Cited coefficient sets (new in v0.2)
+
+Two example sets for monolayer 1H-MoS2 ship with full provenance, and the
+test-suite reproduces the published separation results of the source paper
+from them (edge charge of 2.3e12 cm^-2 from a 0.5 cm^-1 A'1 redshift with
+2LA(M) unmoved; 0.134% interior tension carrying no significant charge):
+
+- `mos2_a1_2la()`: the A'1 + 2LA(M) pair of the source paper. Strain lever
+  arms -5.1 and -20.9 cm^-1 per percent of biaxial strain (frozen-phonon
+  DFT, ratio 4.1); A'1 doping coefficient -2.2 cm^-1 per 1e13 cm^-2 of
+  electrons (measured, Chakraborty et al., Phys. Rev. B 85, 161403(R)
+  (2012)). The 2LA(M) doping coefficient is unmeasured and set to zero;
+  the source paper bounds the consequence of that choice at 16% of a
+  recovered edge charge.
+- `mos2_eprime_a1()`: the historically used all-optical E' + A'1 pair,
+  built from the measured biaxial Grueneisen parameters of Michail et al.,
+  ACS Appl. Mater. Interfaces 16, 49602 (2024). Both optical modes respond
+  weakly to strain, so for equal shift noise this pair returns about five
+  times the strain uncertainty of the A'1 + 2LA(M) pair; it is included
+  for comparison and for workflows where the overtone is not available.
+
+Each function's docstring states which number comes from which source and
+the conditions of applicability (1H monolayer, SiO2-supported, 300 K;
+532 nm for the disorder-activated calibration). Check that your sample
+matches before use.
+
+## What this package deliberately does not include
+
+No constants beyond the two documented MoS2 sets are shipped. Lever arms
+depend on material, mode pair, excitation wavelength and substrate; a
+measurement tool that ships unverified constants propagates wrong results.
+For any other system you provide a `ModeCoefficients` from the literature
+or your own calibration, and the `reference` field is mandatory so the
+provenance of every number travels with the analysis.
+
+## Install
+
+```
+pip install -e .
+```
+
+## Use
+
+```python
+import numpy as np
+from ramansep import SeparationModel, ModeCoefficients
+
+coeffs = ModeCoefficients(
+    mode1_name="A'1", mode2_name="2LA(M)",
+    k1_strain=...,   # cm^-1 per unit strain, from your calibration
+    k1_density=...,  # cm^-1 per unit carrier density
+    k2_strain=...,
+    k2_density=...,
+    reference="cite the source of these numbers",
+)
+model = SeparationModel(coeffs)
+result = model.invert(dw_mode1, dw_mode2, sigma1=0.1, sigma2=0.1)
+# result.strain, result.density, result.strain_sigma, result.density_sigma
+```
+
+`SeparationModel` warns when the mode pair is poorly conditioned, i.e. when
+the two modes respond too similarly for a reliable separation.
+
+## Method
+
+The method of using the first-order A'1 mode together with the
+disorder-activated 2LA(M) overtone, whose strain lever arms differ
+severalfold while only A'1 responds appreciably to carrier density, is
+developed in:
+
+> T. M. Mahim and M. M. Rahman, "Two Raman phonons quantify the fixed edge
+> charge left by patterning monolayer transition metal dichalcogenides"
+> (under review). Code for the paper itself:
+> https://github.com/Tanvir-Mahmud-Mahim/Width-scaling-in-monolayer-semiconductor-nanoribbon-transistors
+
+This package is the general-purpose, material-agnostic inversion tool; the
+paper repository reproduces the specific published study.
+
+## Roadmap
+
+- v0.2 (done): documented example coefficient sets with citations
+- v0.3: peak-fitting front end (load spectra, fit the two modes, feed the
+  inversion)
+- v0.4: joint Bayesian inversion with spatial priors
+
+## License
+
+Apache-2.0

ramansep-0.2.1/pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ramansep"
+version = "0.2.1"
+description = "Separate strain from carrier density in 2D-material Raman maps using a two-mode linear inversion"
+readme = "README.md"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Tanvir M. Mahim", email = "tanvir.mahim@bracu.ac.bd" }]
+requires-python = ">=3.9"
+keywords = ["Raman spectroscopy", "2D materials", "MoS2", "strain", "carrier density", "TMD"]
+dependencies = ["numpy>=1.22"]
+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]
+plot = ["matplotlib"]
+test = ["pytest"]
+
+[project.urls]
+Homepage = "https://tanvir-mahmud-mahim.github.io/software/"
+Repository = "https://github.com/TaN-MM-Org/ramansep"
+Issues = "https://github.com/TaN-MM-Org/ramansep/issues"
+Changelog = "https://github.com/TaN-MM-Org/ramansep/releases"
+
+[tool.setuptools.packages.find]
+where = ["src"]

ramansep-0.2.1/setup.cfg

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

ramansep-0.2.1/src/ramansep/__init__.py

@@ -0,0 +1,19 @@
+"""ramansep: separate strain from carrier density in 2D-material Raman maps.
+
+Two Raman modes with different strain lever arms and different doping
+responses form a linear, invertible probe of the (strain, carrier density)
+state at each map pixel. This package implements that inversion with full
+uncertainty propagation and conditioning diagnostics.
+
+Methodological basis: T. M. Mahim and M. M. Rahman, "Two Raman phonons
+quantify the fixed edge charge left by patterning monolayer transition
+metal dichalcogenides" (under review). The solver is material-agnostic:
+you supply the coefficient matrix for your material and mode pair.
+"""
+from .core import SeparationModel, SeparationResult
+from .materials import (ModeCoefficients, mos2_a1_2la, mos2_eprime_a1,
+                        synthetic_demo)
+
+__version__ = "0.2.1"
+__all__ = ["SeparationModel", "SeparationResult", "ModeCoefficients",
+           "synthetic_demo", "mos2_a1_2la", "mos2_eprime_a1"]

ramansep-0.2.1/src/ramansep/core.py

@@ -0,0 +1,126 @@
+"""Linear two-mode separation of strain and carrier density."""
+from __future__ import annotations
+
+import dataclasses
+import warnings
+
+import numpy as np
+
+from .materials import ModeCoefficients
+
+
+@dataclasses.dataclass
+class SeparationResult:
+    """Result of a two-mode inversion.
+
+    Attributes
+    ----------
+    strain : ndarray
+        Strain field, in the strain unit of the coefficient matrix
+        (percent biaxial strain unless your coefficients say otherwise).
+    density : ndarray
+        Carrier-density field, in the density unit of the coefficient
+        matrix (cm^-2 unless your coefficients say otherwise).
+    strain_sigma, density_sigma : ndarray or None
+        One-standard-deviation uncertainties propagated from the peak-shift
+        uncertainties, if those were provided.
+    correlation : ndarray or None
+        Pixelwise correlation coefficient between the strain and density
+        estimates. Values near +/-1 mean the two modes barely separate the
+        two causes at that pixel.
+    condition_number : float
+        Condition number of the coefficient matrix. Large values mean the
+        mode pair is poorly chosen for separation.
+    """
+
+    strain: np.ndarray
+    density: np.ndarray
+    strain_sigma: np.ndarray | None
+    density_sigma: np.ndarray | None
+    correlation: np.ndarray | None
+    condition_number: float
+
+
+class SeparationModel:
+    """Invert two peak-shift maps into strain and carrier-density maps.
+
+    Parameters
+    ----------
+    coefficients : ModeCoefficients
+        The 2x2 lever-arm matrix K such that
+
+            [dw_mode1]   [k1_strain  k1_density] [strain ]
+            [dw_mode2] = [k2_strain  k2_density] [density]
+
+        where dw are peak shifts relative to the pristine reference.
+    condition_warn : float
+        Warn if the condition number of K exceeds this value.
+    """
+
+    def __init__(self, coefficients: ModeCoefficients, condition_warn: float = 30.0):
+        self.coefficients = coefficients
+        self.K = np.asarray(coefficients.matrix(), dtype=float)
+        if self.K.shape != (2, 2):
+            raise ValueError("coefficient matrix must be 2x2")
+        det = np.linalg.det(self.K)
+        if det == 0.0:
+            raise ValueError(
+                "coefficient matrix is singular: the two modes respond "
+                "identically and cannot separate strain from density"
+            )
+        self.condition_number = float(np.linalg.cond(self.K))
+        if self.condition_number > condition_warn:
+            warnings.warn(
+                f"coefficient matrix condition number is "
+                f"{self.condition_number:.1f}; the mode pair is poorly "
+                "conditioned and small shift errors will produce large "
+                "strain/density errors",
+                stacklevel=2,
+            )
+        self.Kinv = np.linalg.inv(self.K)
+
+    def invert(self, dw1, dw2, sigma1=None, sigma2=None) -> SeparationResult:
+        """Invert peak-shift maps (any matching numpy shapes) pixelwise.
+
+        dw1, dw2 : peak shifts of mode 1 and mode 2 (cm^-1), relative to the
+            pristine-material reference frequency of each mode.
+        sigma1, sigma2 : optional 1-sigma uncertainties of the shifts,
+            scalar or arrays broadcastable to the map shape.
+        """
+        dw1 = np.asarray(dw1, dtype=float)
+        dw2 = np.asarray(dw2, dtype=float)
+        if dw1.shape != dw2.shape:
+            raise ValueError("the two shift maps must have the same shape")
+
+        strain = self.Kinv[0, 0] * dw1 + self.Kinv[0, 1] * dw2
+        density = self.Kinv[1, 0] * dw1 + self.Kinv[1, 1] * dw2
+
+        strain_sigma = density_sigma = correlation = None
+        if sigma1 is not None and sigma2 is not None:
+            s1 = np.broadcast_to(np.asarray(sigma1, dtype=float), dw1.shape)
+            s2 = np.broadcast_to(np.asarray(sigma2, dtype=float), dw2.shape)
+            var_strain = (self.Kinv[0, 0] * s1) ** 2 + (self.Kinv[0, 1] * s2) ** 2
+            var_density = (self.Kinv[1, 0] * s1) ** 2 + (self.Kinv[1, 1] * s2) ** 2
+            cov = (self.Kinv[0, 0] * self.Kinv[1, 0] * s1**2
+                   + self.Kinv[0, 1] * self.Kinv[1, 1] * s2**2)
+            strain_sigma = np.sqrt(var_strain)
+            density_sigma = np.sqrt(var_density)
+            with np.errstate(invalid="ignore", divide="ignore"):
+                correlation = cov / (strain_sigma * density_sigma)
+
+        return SeparationResult(
+            strain=strain,
+            density=density,
+            strain_sigma=strain_sigma,
+            density_sigma=density_sigma,
+            correlation=correlation,
+            condition_number=self.condition_number,
+        )
+
+    def forward(self, strain, density):
+        """Predict the two peak shifts from strain and density maps."""
+        strain = np.asarray(strain, dtype=float)
+        density = np.asarray(density, dtype=float)
+        dw1 = self.K[0, 0] * strain + self.K[0, 1] * density
+        dw2 = self.K[1, 0] * strain + self.K[1, 1] * density
+        return dw1, dw2

ramansep-0.2.1/src/ramansep/materials.py

@@ -0,0 +1,156 @@
+"""Coefficient sets for mode pairs.
+
+This module ships two CITED example coefficient sets for monolayer 1H-MoS2
+(see mos2_a1_2la and mos2_eprime_a1 below), plus a synthetic set for the
+test-suite. Every number in the cited sets is traceable to a published
+measurement or to the first-principles calculation of the reference given
+in its `reference` field; the docstring of each function states which
+numbers come from where.
+
+The warning of v0.1 still applies in general: peak-shift lever arms depend
+on material, mode pair, excitation wavelength and substrate. Before using
+either MoS2 set on your own spectra, check that your sample, excitation
+and substrate match the conditions stated in the sources. For any other
+material or mode pair, populate a ModeCoefficients from the literature or
+from your own calibration; the mandatory `reference` field keeps the
+provenance attached to the analysis.
+
+Units used by both MoS2 sets:
+    strain  : percent biaxial strain (positive = tension)
+    density : electron sheet density in units of 1e13 cm^-2
+    shifts  : cm^-1 (softening, i.e. redshift, is negative)
+"""
+from __future__ import annotations
+
+import dataclasses
+
+
+@dataclasses.dataclass
+class ModeCoefficients:
+    """Lever arms of two Raman modes.
+
+    Units are your choice but must be consistent; the inversion returns
+    strain and density in whatever units these coefficients imply.
+
+    mode1_name, mode2_name : labels, e.g. "A'1" and "2LA(M)".
+    k1_strain : shift of mode 1 per unit strain          (e.g. cm^-1 / %)
+    k1_density : shift of mode 1 per unit carrier density (e.g. cm^-1 / 1e13 cm^-2)
+    k2_strain, k2_density : same for mode 2.
+    reference : where the numbers come from. Required, on purpose.
+    """
+
+    mode1_name: str
+    mode2_name: str
+    k1_strain: float
+    k1_density: float
+    k2_strain: float
+    k2_density: float
+    reference: str
+
+    def matrix(self):
+        return [[self.k1_strain, self.k1_density],
+                [self.k2_strain, self.k2_density]]
+
+
+def synthetic_demo() -> ModeCoefficients:
+    """An arbitrary, NON-PHYSICAL coefficient set for tests and demos.
+
+    The values are chosen only to be well-conditioned. Do not use for
+    analysis of real spectra.
+    """
+    return ModeCoefficients(
+        mode1_name="demo-mode-1",
+        mode2_name="demo-mode-2",
+        k1_strain=-2.0,
+        k1_density=-0.8,
+        k2_strain=-6.0,
+        k2_density=-0.1,
+        reference="synthetic demonstration values; not physical",
+    )
+
+
+def mos2_a1_2la() -> ModeCoefficients:
+    """Monolayer 1H-MoS2, A'1 + 2LA(M) pair (the pair of the source paper).
+
+    Strain lever arms are the frozen-phonon DFT values computed in the
+    source paper: the A'1 mode softens by 5.1 cm^-1 per percent of biaxial
+    tension and the disorder-activated 2LA(M) overtone by 20.9 cm^-1 per
+    percent (acoustic Grueneisen parameter gamma_LA = 2.30), a lever-arm
+    ratio of 4.1. The A'1 doping coefficient is the gated-Raman measurement
+    of Chakraborty et al.: a softening of 2.2 cm^-1 per 1e13 cm^-2 of
+    electrons, from the symmetry-selective coupling of the out-of-plane
+    mode to the K-valley density; the E'-symmetry channel, and with it the
+    2LA(M) overtone, couples only weakly.
+
+    CAVEAT carried over from the source paper: no gated measurement of the
+    2LA(M) doping coefficient exists, so it is set to zero here rather than
+    known to be zero. The source paper bounds the consequence: letting the
+    overtone renormalize at up to half the frequency-scaled A'1 rate
+    changes a recovered edge charge by 16 percent.
+
+    Units: percent biaxial strain; electron density in 1e13 cm^-2.
+    Applicability: 1H monolayer, 532 nm excitation, SiO2-supported, 300 K.
+    """
+    return ModeCoefficients(
+        mode1_name="A'1",
+        mode2_name="2LA(M)",
+        k1_strain=-5.1,
+        k1_density=-2.2,
+        k2_strain=-20.9,
+        k2_density=0.0,
+        reference=(
+            "Strain lever arms (DFT, frozen phonon): T. M. Mahim and "
+            "M. M. Rahman, 'Two Raman phonons quantify the fixed edge "
+            "charge left by patterning monolayer transition metal "
+            "dichalcogenides' (under review); code and data: "
+            "github.com/Tanvir-Mahmud-Mahim/Width-scaling-in-monolayer-"
+            "semiconductor-nanoribbon-transistors, "
+            "doi:10.5281/zenodo.21778170. A'1 doping coefficient "
+            "(measured): B. Chakraborty et al., Phys. Rev. B 85, "
+            "161403(R) (2012). 2LA(M) doping coefficient set to zero "
+            "(unmeasured; see docstring caveat)."
+        ),
+    )
+
+
+def mos2_eprime_a1() -> ModeCoefficients:
+    """Monolayer 1H-MoS2, E' + A'1 pair, from direct biaxial measurements.
+
+    Strain lever arms follow from the measured biaxial-strain mode
+    Grueneisen parameters of Michail et al. (gamma_E' = 0.56,
+    gamma_A'1 = 0.31, in the convention gamma = -(1/2w) dw/deps) applied
+    to the mode frequencies w(E') = 385.0 cm^-1 and w(A'1) = 403.0 cm^-1:
+    dw/deps = -2 gamma w = -4.31 (E') and -2.50 (A'1) cm^-1 per percent
+    of biaxial strain. Doping coefficients are the gated-Raman
+    measurements of Chakraborty et al.: -0.33 (E') and -2.2 (A'1) cm^-1
+    per 1e13 cm^-2 of electrons.
+
+    This is the historically used all-optical pair (Michail et al. 2016).
+    Both optical modes respond weakly to strain (lever arms of -4.31 and
+    -2.50 cm^-1 per percent, against -20.9 for the 2LA(M) overtone), so
+    for equal peak-shift noise this pair returns a strain uncertainty
+    about five times larger than mos2_a1_2la(); propagate sigmas through
+    invert() and compare strain_sigma before choosing it.
+
+    Units: percent biaxial strain; electron density in 1e13 cm^-2.
+    Applicability: 1H monolayer, SiO2-supported, 300 K.
+    """
+    return ModeCoefficients(
+        mode1_name="E'",
+        mode2_name="A'1",
+        k1_strain=-4.31,
+        k1_density=-0.33,
+        k2_strain=-2.50,
+        k2_density=-2.2,
+        reference=(
+            "Strain: measured biaxial Grueneisen parameters, A. Michail "
+            "et al., ACS Appl. Mater. Interfaces 16, 49602 (2024) "
+            "(gamma_E'=0.56, gamma_A'1=0.31), converted with "
+            "w(E')=385.0 cm^-1 and w(A'1)=403.0 cm^-1 (Mignuzzi et al., "
+            "Phys. Rev. B 91, 195411 (2015); Michail et al., Appl. Phys. "
+            "Lett. 108, 173102 (2016)). Doping (measured): B. Chakraborty "
+            "et al., Phys. Rev. B 85, 161403(R) (2012). Compiled as in "
+            "T. M. Mahim and M. M. Rahman (under review), "
+            "doi:10.5281/zenodo.21778170."
+        ),
+    )

ramansep-0.2.1/src/ramansep.egg-info/PKG-INFO

@@ -0,0 +1,134 @@
+Metadata-Version: 2.4
+Name: ramansep
+Version: 0.2.1
+Summary: Separate strain from carrier density in 2D-material Raman maps using a two-mode linear inversion
+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/ramansep
+Project-URL: Issues, https://github.com/TaN-MM-Org/ramansep/issues
+Project-URL: Changelog, https://github.com/TaN-MM-Org/ramansep/releases
+Keywords: Raman spectroscopy,2D materials,MoS2,strain,carrier density,TMD
+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
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# ramansep
+
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.22014913-blue)](https://doi.org/10.5281/zenodo.22014913) [![tests](https://github.com/TaN-MM-Org/ramansep/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/ramansep/actions)
+
+Separate **strain** from **carrier density** in Raman maps of 2D materials,
+using two phonon modes whose lever arms differ.
+
+A single Raman frequency responds to strain and to carrier density at once,
+so one mode cannot tell the two apart. Two modes with sufficiently different
+responses form a linear, invertible probe: measure both shift maps, invert a
+2x2 matrix per pixel, and obtain a strain map and a carrier-density map with
+propagated uncertainties.
+
+## Status
+
+v0.2.0 (alpha). The inversion core, uncertainty propagation, conditioning
+diagnostics, a synthetic end-to-end example, and two cited coefficient
+sets for monolayer MoS2 are implemented and tested. The API may change
+before v1.0.
+
+## Cited coefficient sets (new in v0.2)
+
+Two example sets for monolayer 1H-MoS2 ship with full provenance, and the
+test-suite reproduces the published separation results of the source paper
+from them (edge charge of 2.3e12 cm^-2 from a 0.5 cm^-1 A'1 redshift with
+2LA(M) unmoved; 0.134% interior tension carrying no significant charge):
+
+- `mos2_a1_2la()`: the A'1 + 2LA(M) pair of the source paper. Strain lever
+  arms -5.1 and -20.9 cm^-1 per percent of biaxial strain (frozen-phonon
+  DFT, ratio 4.1); A'1 doping coefficient -2.2 cm^-1 per 1e13 cm^-2 of
+  electrons (measured, Chakraborty et al., Phys. Rev. B 85, 161403(R)
+  (2012)). The 2LA(M) doping coefficient is unmeasured and set to zero;
+  the source paper bounds the consequence of that choice at 16% of a
+  recovered edge charge.
+- `mos2_eprime_a1()`: the historically used all-optical E' + A'1 pair,
+  built from the measured biaxial Grueneisen parameters of Michail et al.,
+  ACS Appl. Mater. Interfaces 16, 49602 (2024). Both optical modes respond
+  weakly to strain, so for equal shift noise this pair returns about five
+  times the strain uncertainty of the A'1 + 2LA(M) pair; it is included
+  for comparison and for workflows where the overtone is not available.
+
+Each function's docstring states which number comes from which source and
+the conditions of applicability (1H monolayer, SiO2-supported, 300 K;
+532 nm for the disorder-activated calibration). Check that your sample
+matches before use.
+
+## What this package deliberately does not include
+
+No constants beyond the two documented MoS2 sets are shipped. Lever arms
+depend on material, mode pair, excitation wavelength and substrate; a
+measurement tool that ships unverified constants propagates wrong results.
+For any other system you provide a `ModeCoefficients` from the literature
+or your own calibration, and the `reference` field is mandatory so the
+provenance of every number travels with the analysis.
+
+## Install
+
+```
+pip install -e .
+```
+
+## Use
+
+```python
+import numpy as np
+from ramansep import SeparationModel, ModeCoefficients
+
+coeffs = ModeCoefficients(
+    mode1_name="A'1", mode2_name="2LA(M)",
+    k1_strain=...,   # cm^-1 per unit strain, from your calibration
+    k1_density=...,  # cm^-1 per unit carrier density
+    k2_strain=...,
+    k2_density=...,
+    reference="cite the source of these numbers",
+)
+model = SeparationModel(coeffs)
+result = model.invert(dw_mode1, dw_mode2, sigma1=0.1, sigma2=0.1)
+# result.strain, result.density, result.strain_sigma, result.density_sigma
+```
+
+`SeparationModel` warns when the mode pair is poorly conditioned, i.e. when
+the two modes respond too similarly for a reliable separation.
+
+## Method
+
+The method of using the first-order A'1 mode together with the
+disorder-activated 2LA(M) overtone, whose strain lever arms differ
+severalfold while only A'1 responds appreciably to carrier density, is
+developed in:
+
+> T. M. Mahim and M. M. Rahman, "Two Raman phonons quantify the fixed edge
+> charge left by patterning monolayer transition metal dichalcogenides"
+> (under review). Code for the paper itself:
+> https://github.com/Tanvir-Mahmud-Mahim/Width-scaling-in-monolayer-semiconductor-nanoribbon-transistors
+
+This package is the general-purpose, material-agnostic inversion tool; the
+paper repository reproduces the specific published study.
+
+## Roadmap
+
+- v0.2 (done): documented example coefficient sets with citations
+- v0.3: peak-fitting front end (load spectra, fit the two modes, feed the
+  inversion)
+- v0.4: joint Bayesian inversion with spatial priors
+
+## License
+
+Apache-2.0

ramansep-0.2.1/src/ramansep.egg-info/SOURCES.txt

@@ -0,0 +1,13 @@
+LICENSE
+README.md
+pyproject.toml
+src/ramansep/__init__.py
+src/ramansep/core.py
+src/ramansep/materials.py
+src/ramansep.egg-info/PKG-INFO
+src/ramansep.egg-info/SOURCES.txt
+src/ramansep.egg-info/dependency_links.txt
+src/ramansep.egg-info/requires.txt
+src/ramansep.egg-info/top_level.txt
+tests/test_core.py
+tests/test_mos2_sets.py

ramansep-0.2.1/src/ramansep.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

ramansep-0.2.1/src/ramansep.egg-info/requires.txt

@@ -0,0 +1,7 @@
+numpy>=1.22
+
+[plot]
+matplotlib
+
+[test]
+pytest

ramansep-0.2.1/src/ramansep.egg-info/top_level.txt

@@ -0,0 +1 @@
+ramansep

ramansep-0.2.1/tests/test_core.py

@@ -0,0 +1,54 @@
+import numpy as np
+import pytest
+
+from ramansep import SeparationModel, ModeCoefficients, synthetic_demo
+
+
+def test_round_trip_recovers_fields():
+    model = SeparationModel(synthetic_demo())
+    rng = np.random.default_rng(0)
+    strain = rng.normal(0.0, 0.1, size=(32, 32))
+    density = rng.normal(0.0, 1.0, size=(32, 32))
+    dw1, dw2 = model.forward(strain, density)
+    out = model.invert(dw1, dw2)
+    np.testing.assert_allclose(out.strain, strain, atol=1e-12)
+    np.testing.assert_allclose(out.density, density, atol=1e-12)
+
+
+def test_uncertainty_propagation_scales_linearly():
+    model = SeparationModel(synthetic_demo())
+    out1 = model.invert(np.zeros((4, 4)), np.zeros((4, 4)), sigma1=0.1, sigma2=0.1)
+    out2 = model.invert(np.zeros((4, 4)), np.zeros((4, 4)), sigma1=0.2, sigma2=0.2)
+    np.testing.assert_allclose(out2.strain_sigma, 2.0 * out1.strain_sigma)
+    np.testing.assert_allclose(out2.density_sigma, 2.0 * out1.density_sigma)
+
+
+def test_uncertainty_matches_monte_carlo():
+    model = SeparationModel(synthetic_demo())
+    rng = np.random.default_rng(1)
+    s1, s2 = 0.05, 0.08
+    n = 200_000
+    dw1 = rng.normal(0.0, s1, n)
+    dw2 = rng.normal(0.0, s2, n)
+    out = model.invert(dw1, dw2, sigma1=s1, sigma2=s2)
+    # analytic sigma (constant across pixels) vs empirical spread
+    assert np.isclose(out.strain.std(), out.strain_sigma[0], rtol=2e-2)
+    assert np.isclose(out.density.std(), out.density_sigma[0], rtol=2e-2)
+
+
+def test_singular_matrix_rejected():
+    bad = ModeCoefficients("m1", "m2", 1.0, 2.0, 2.0, 4.0, reference="test")
+    with pytest.raises(ValueError):
+        SeparationModel(bad)
+
+
+def test_poor_conditioning_warns():
+    nearly = ModeCoefficients("m1", "m2", 1.0, 1.0, 1.0, 1.001, reference="test")
+    with pytest.warns(UserWarning):
+        SeparationModel(nearly)
+
+
+def test_shape_mismatch_rejected():
+    model = SeparationModel(synthetic_demo())
+    with pytest.raises(ValueError):
+        model.invert(np.zeros(3), np.zeros(4))

ramansep-0.2.1/tests/test_mos2_sets.py

@@ -0,0 +1,95 @@
+"""Tests of the cited MoS2 coefficient sets.
+
+The two headline tests reproduce, from the shipped coefficients and the
+peak shifts reported in the source paper (Mahim and Rahman, under review;
+tip-enhanced maps of Krayev et al., Appl. Phys. Lett. 128, 203102 (2026)),
+the paper's published separation results:
+
+  * at the ribbon edge, A'1 redshifts by 0.5 cm^-1 while 2LA(M) does not
+    move -> an electron excess of 2.3e12 cm^-2 with strain below 0.03%;
+  * at an interior spot, 2LA(M) redshifts by 2.8 cm^-1 and A'1 by
+    0.6 cm^-1 -> 0.134% of tension carrying no significant charge
+    (the paper's quoted uncertainty on the edge charge is 7.6e11 cm^-2).
+
+If a transcription error ever enters the coefficient tables, these tests
+fail against the published numbers.
+"""
+import numpy as np
+import pytest
+
+from ramansep import SeparationModel, mos2_a1_2la, mos2_eprime_a1
+
+
+def test_values_locked_a1_2la():
+    c = mos2_a1_2la()
+    assert c.mode1_name == "A'1" and c.mode2_name == "2LA(M)"
+    assert c.k1_strain == -5.1      # cm^-1 per % biaxial (DFT, source paper)
+    assert c.k1_density == -2.2     # cm^-1 per 1e13 cm^-2 (Chakraborty 2012)
+    assert c.k2_strain == -20.9     # cm^-1 per % biaxial (DFT, source paper)
+    assert c.k2_density == 0.0      # unmeasured, set to zero (documented)
+    assert "Chakraborty" in c.reference
+    assert "10.5281/zenodo.21778170" in c.reference
+
+
+def test_values_locked_eprime_a1():
+    c = mos2_eprime_a1()
+    # dw/deps = -2 gamma w / 100 per percent of biaxial strain
+    assert c.k1_strain == pytest.approx(-2 * 0.56 * 385.0 / 100, abs=0.005)
+    assert c.k2_strain == pytest.approx(-2 * 0.31 * 403.0 / 100, abs=0.005)
+    assert c.k1_density == -0.33
+    assert c.k2_density == -2.2
+    assert "Michail" in c.reference and "Chakraborty" in c.reference
+
+
+def test_lever_arm_ratio_of_paper_pair():
+    c = mos2_a1_2la()
+    # "a computed ratio of 4.1" (source paper, Sec. II)
+    assert c.k2_strain / c.k1_strain == pytest.approx(4.1, abs=0.05)
+
+
+def test_edge_charge_reproduces_paper():
+    model = SeparationModel(mos2_a1_2la())
+    res = model.invert(np.array([-0.5]), np.array([0.0]))
+    density_cm2 = res.density[0] * 1e13
+    strain_pct = res.strain[0]
+    # 2LA(M) unmoved forces zero recovered strain in this pair
+    assert strain_pct == pytest.approx(0.0, abs=1e-12)
+    # exact linear inversion: 0.5 / 2.2 = 0.227e13
+    assert density_cm2 == pytest.approx(0.5 / 2.2 * 1e13, rel=1e-12)
+    # agrees with the published rounded value 2.3e12 cm^-2
+    assert abs(density_cm2 - 2.3e12) < 0.5e11
+
+
+def test_interior_strain_reproduces_paper():
+    model = SeparationModel(mos2_a1_2la())
+    res = model.invert(np.array([-0.6]), np.array([-2.8]))
+    strain_pct = res.strain[0]
+    density_cm2 = res.density[0] * 1e13
+    # published: 0.134% tension
+    assert strain_pct == pytest.approx(0.134, abs=0.0005)
+    # published: no significant charge (edge-charge 1-sigma is 7.6e11)
+    assert abs(density_cm2) < 7.6e11
+
+
+def test_optical_pair_amplifies_strain_noise_more():
+    """With equal shift noise, the all-optical pair is the noisier probe
+    of strain, because both optical modes respond weakly to strain. The
+    raw matrix condition number does not capture this (it is sensitive to
+    row scaling), so the comparison is made on the propagated sigma."""
+    dw = np.array([0.0])
+    sig = 0.1
+    r_paper = SeparationModel(mos2_a1_2la()).invert(dw, dw, sig, sig)
+    r_optical = SeparationModel(mos2_eprime_a1()).invert(dw, dw, sig, sig)
+    ratio = r_optical.strain_sigma[0] / r_paper.strain_sigma[0]
+    assert ratio > 4.0
+
+
+def test_forward_inverse_roundtrip_cited_sets():
+    for coeffs in (mos2_a1_2la(), mos2_eprime_a1()):
+        model = SeparationModel(coeffs)
+        strain = np.array([0.05, -0.02, 0.134])
+        density = np.array([0.23, 0.0, 0.038])
+        dw1, dw2 = model.forward(strain, density)
+        res = model.invert(dw1, dw2)
+        np.testing.assert_allclose(res.strain, strain, atol=1e-12)
+        np.testing.assert_allclose(res.density, density, atol=1e-12)