easyspyn 0.2.0__tar.gz

easyspyn-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Alexej Jerschow
+
+Spynach is a Python reimplementation of the Spinach spin dynamics kernel
+(https://spindynamics.org). This licence derives from the Spinach MIT
+licence of Ilya Kuprov (see below).
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+
+Spinach
+=======
+
+The sources, tests, molecule data, isotope table, spherical grids and
+example scripts of Spynach were written by reading and translating Spinach. Spinach is distributed under the MIT License with the following
+notice, which is reproduced here as that licence requires and must be kept
+with any copy or substantial portion of this software.
+
+Copyright (c) 2005-2025 ILYA KUPROV
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+EasySpin
+========
+
+The `epreasy` package (src/epreasy), its tests and its isotope table were
+written by reading and translating EasySpin (https://easyspin.org), which
+is distributed under the MIT License with the following notice, reproduced
+here as that licence requires and to be kept with any copy or substantial
+portion of this software.
+
+Copyright (c) 2006-2024 Stefan Stoll and other contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+Use of AI in the translation
+============================
+
+The translation of Spinach from MATLAB to Python was carried out largely by
+an AI coding agent (Claude, Anthropic) working under the direction of
+Alexej Jerschow, who set the goals, reviewed the results and holds the
+copyright above. Commits made by the agent are marked as such in the git
+history. Correctness rests on the test suite, which compares Spynach with
+reference data computed by Spinach, not on the method of authorship.

easyspyn-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: easyspyn
+Version: 0.2.0
+Summary: EasySpin's EPR simulators in Python (EPReasy): cw EPR, ENDOR, slow motion, pulse EPR, fitting
+Author: Alexej Jerschow
+License-Expression: MIT
+Project-URL: Homepage, https://ajerschow.github.io/spynach/easyspin.html
+Project-URL: Documentation, https://github.com/ajerschow/spynach/blob/main/docs/epreasy.md
+Project-URL: Source, https://github.com/ajerschow/spynach
+Project-URL: Changelog, https://github.com/ajerschow/spynach/blob/main/CHANGELOG.md
+Keywords: EPR,ESR,EasySpin,spectral simulation,ENDOR,spin dynamics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.11
+Provides-Extra: fast
+Requires-Dist: numba>=0.60; extra == "fast"
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Requires-Dist: spynach; extra == "test"
+Requires-Dist: h5py>=3.10; extra == "test"
+Dynamic: license-file
+
+# EasySpyn (EPReasy): EasySpin's EPR simulators in Python
+
+A Python port of [EasySpin](https://easyspin.org), the MATLAB toolbox for EPR spectral simulation by Stefan Stoll
+and co-workers (MIT licence), keeping EasySpin's interface: spin systems as dictionaries with EasySpin's field
+names, fields in mT, couplings in MHz, 1-based spin numbers.
+
+    pip install easyspyn          # the import name is epreasy
+    pip install "easyspyn[fast]"  # adds Numba for the line-summation and projection kernels
+
+```python
+import epreasy as es
+
+nitroxide = {"g": [2.0088, 2.0061, 2.0027], "Nucs": "14N", "A": [16, 16, 86], "lwpp": 0.3}
+powder = es.pepper(nitroxide, {"mwFreq": 9.5, "Range": [330, 350], "nPoints": 1024})
+print(powder.x.shape, powder.spec.shape)
+```
+
+What is ported: `pepper` and `garlic` (cw EPR of powders, crystals and solutions), `esfit` (fitting), `salt` and
+`endorfrq` (ENDOR), `curry` (magnetometry), `chili` (slow motion), `saffron` (pulse EPR: ESEEM, HYSCORE, Mims
+ENDOR), and the foundation underneath (`sop`, `ham`, `levels`, `resfields`, line shapes, grids). Results are
+compared with EasySpin 6.0.15's own output on about 280 reference cases. Not ported: `saffron`'s `thyme` engine
+and `spidyan`, the GUIs, and some options; the guide lists them.
+
+EPReasy is part of the [Spynach](https://github.com/ajerschow/spynach) project, which also ports the Spinach
+spin dynamics kernel. It is an early release (0.2.0); corrections and bug reports are welcome on GitHub.
+
+- Guides: https://github.com/ajerschow/spynach/blob/main/docs/epreasy.md
+- Differences from EasySpin: https://github.com/ajerschow/spynach/blob/main/docs/coming-from-easyspin.md
+- Try it in the browser, with timings against EasySpin: https://ajerschow.github.io/spynach/easyspin.html
+
+Attribution: EPReasy is a translation of EasySpin and keeps its notice; see `LICENSE`.

easyspyn-0.2.0/README.md

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+# EasySpyn (EPReasy): EasySpin's EPR simulators in Python
+
+A Python port of [EasySpin](https://easyspin.org), the MATLAB toolbox for EPR spectral simulation by Stefan Stoll
+and co-workers (MIT licence), keeping EasySpin's interface: spin systems as dictionaries with EasySpin's field
+names, fields in mT, couplings in MHz, 1-based spin numbers.
+
+    pip install easyspyn          # the import name is epreasy
+    pip install "easyspyn[fast]"  # adds Numba for the line-summation and projection kernels
+
+```python
+import epreasy as es
+
+nitroxide = {"g": [2.0088, 2.0061, 2.0027], "Nucs": "14N", "A": [16, 16, 86], "lwpp": 0.3}
+powder = es.pepper(nitroxide, {"mwFreq": 9.5, "Range": [330, 350], "nPoints": 1024})
+print(powder.x.shape, powder.spec.shape)
+```
+
+What is ported: `pepper` and `garlic` (cw EPR of powders, crystals and solutions), `esfit` (fitting), `salt` and
+`endorfrq` (ENDOR), `curry` (magnetometry), `chili` (slow motion), `saffron` (pulse EPR: ESEEM, HYSCORE, Mims
+ENDOR), and the foundation underneath (`sop`, `ham`, `levels`, `resfields`, line shapes, grids). Results are
+compared with EasySpin 6.0.15's own output on about 280 reference cases. Not ported: `saffron`'s `thyme` engine
+and `spidyan`, the GUIs, and some options; the guide lists them.
+
+EPReasy is part of the [Spynach](https://github.com/ajerschow/spynach) project, which also ports the Spinach
+spin dynamics kernel. It is an early release (0.2.0); corrections and bug reports are welcome on GitHub.
+
+- Guides: https://github.com/ajerschow/spynach/blob/main/docs/epreasy.md
+- Differences from EasySpin: https://github.com/ajerschow/spynach/blob/main/docs/coming-from-easyspin.md
+- Try it in the browser, with timings against EasySpin: https://ajerschow.github.io/spynach/easyspin.html
+
+Attribution: EPReasy is a translation of EasySpin and keeps its notice; see `LICENSE`.

easyspyn-0.2.0/easyspyn.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: easyspyn
+Version: 0.2.0
+Summary: EasySpin's EPR simulators in Python (EPReasy): cw EPR, ENDOR, slow motion, pulse EPR, fitting
+Author: Alexej Jerschow
+License-Expression: MIT
+Project-URL: Homepage, https://ajerschow.github.io/spynach/easyspin.html
+Project-URL: Documentation, https://github.com/ajerschow/spynach/blob/main/docs/epreasy.md
+Project-URL: Source, https://github.com/ajerschow/spynach
+Project-URL: Changelog, https://github.com/ajerschow/spynach/blob/main/CHANGELOG.md
+Keywords: EPR,ESR,EasySpin,spectral simulation,ENDOR,spin dynamics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.11
+Provides-Extra: fast
+Requires-Dist: numba>=0.60; extra == "fast"
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Requires-Dist: spynach; extra == "test"
+Requires-Dist: h5py>=3.10; extra == "test"
+Dynamic: license-file
+
+# EasySpyn (EPReasy): EasySpin's EPR simulators in Python
+
+A Python port of [EasySpin](https://easyspin.org), the MATLAB toolbox for EPR spectral simulation by Stefan Stoll
+and co-workers (MIT licence), keeping EasySpin's interface: spin systems as dictionaries with EasySpin's field
+names, fields in mT, couplings in MHz, 1-based spin numbers.
+
+    pip install easyspyn          # the import name is epreasy
+    pip install "easyspyn[fast]"  # adds Numba for the line-summation and projection kernels
+
+```python
+import epreasy as es
+
+nitroxide = {"g": [2.0088, 2.0061, 2.0027], "Nucs": "14N", "A": [16, 16, 86], "lwpp": 0.3}
+powder = es.pepper(nitroxide, {"mwFreq": 9.5, "Range": [330, 350], "nPoints": 1024})
+print(powder.x.shape, powder.spec.shape)
+```
+
+What is ported: `pepper` and `garlic` (cw EPR of powders, crystals and solutions), `esfit` (fitting), `salt` and
+`endorfrq` (ENDOR), `curry` (magnetometry), `chili` (slow motion), `saffron` (pulse EPR: ESEEM, HYSCORE, Mims
+ENDOR), and the foundation underneath (`sop`, `ham`, `levels`, `resfields`, line shapes, grids). Results are
+compared with EasySpin 6.0.15's own output on about 280 reference cases. Not ported: `saffron`'s `thyme` engine
+and `spidyan`, the GUIs, and some options; the guide lists them.
+
+EPReasy is part of the [Spynach](https://github.com/ajerschow/spynach) project, which also ports the Spinach
+spin dynamics kernel. It is an early release (0.2.0); corrections and bug reports are welcome on GitHub.
+
+- Guides: https://github.com/ajerschow/spynach/blob/main/docs/epreasy.md
+- Differences from EasySpin: https://github.com/ajerschow/spynach/blob/main/docs/coming-from-easyspin.md
+- Try it in the browser, with timings against EasySpin: https://ajerschow.github.io/spynach/easyspin.html
+
+Attribution: EPReasy is a translation of EasySpin and keeps its notice; see `LICENSE`.

easyspyn-0.2.0/easyspyn.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+easyspyn.egg-info/PKG-INFO
+easyspyn.egg-info/SOURCES.txt
+easyspyn.egg-info/dependency_links.txt
+easyspyn.egg-info/requires.txt
+easyspyn.egg-info/top_level.txt
+epreasy/__init__.py
+epreasy/components.py
+epreasy/constants.py
+epreasy/endor.py
+epreasy/fitting.py
+epreasy/garlic.py
+epreasy/grids.py
+epreasy/hamiltonian.py
+epreasy/interp.py
+epreasy/kernels.py
+epreasy/lineshapes.py
+epreasy/magnetometry.py
+epreasy/nucdata.py
+epreasy/oracle.py
+epreasy/pepper.py
+epreasy/perturb.py
+epreasy/processing.py
+epreasy/pulsed.py
+epreasy/resfields.py
+epreasy/rotations.py
+epreasy/slowmotion.py
+epreasy/spinops.py
+epreasy/spinsystem.py
+epreasy/symmetry.py
+epreasy/units.py
+epreasy/data/isotopedata.txt

easyspyn-0.2.0/easyspyn.egg-info/dependency_links.txt

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+

easyspyn-0.2.0/easyspyn.egg-info/requires.txt

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+numpy>=1.26
+scipy>=1.11
+
+[fast]
+numba>=0.60
+
+[test]
+pytest>=8
+spynach
+h5py>=3.10

easyspyn-0.2.0/easyspyn.egg-info/top_level.txt

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+epreasy

easyspyn-0.2.0/epreasy/__init__.py

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+"""epreasy: EasySpin's EPR simulation functions in Python, beside Spynach.
+
+Spin systems are dicts with EasySpin's field names; units are EasySpin's
+(mT, MHz); spin numbers are 1-based as in EasySpin. See ``docs/epreasy.md``
+and ``docs/coming-from-easyspin.md``.
+"""
+
+from .constants import amu, avogadro, bmagn, boltzm, clight, echarge, evolt, gfree, hbar, mu0, nmagn, planck
+from .endor import EndorResonances, anisosubsys, endorfrq, endorfrq_perturb, orisel, salt
+from .fitting import (
+    FitResult,
+    addnoise,
+    basecorr,
+    deriv,
+    esfit,
+    esfit_genetic,
+    esfit_grid,
+    esfit_levmar,
+    esfit_montecarlo,
+    esfit_simplex,
+    esfit_swarm,
+    hccm,
+    jacobianest,
+    rescaledata,
+)
+from .garlic import Spectrum, equivcouple, fastmotion, garlic
+from .grids import SphGrid, gridparam, sphgrid
+from .hamiltonian import ham, ham_ee, ham_ez, ham_hf, ham_nn, ham_nq, ham_nz, ham_zf, levels
+from .interp import esspline1d, esspline2d, gridinterp
+from .kernels import lisum1i, projecttriangles, projectzones
+from .lineshapes import convspec, gaussian, lorentzian, lshape, voigtian
+from .magnetometry import curry
+from .nucdata import isotopes, nucabund, nucdata, nucgval, nucqmom, nucspin, nucstring2list
+from .pepper import pepper
+from .perturb import resfields_perturb
+from .processing import fieldmod
+from .pulsed import apowin, exponfit, fdaxis, larmorfrq, saffron, sf_pathways
+from .resfields import Resonances, cubicsolve, nucspinrmv, photoselect, resfields, resfields_eig
+from .rotations import ang2vec, erot, eulang, letter2vec, vec2ang
+from .slowmotion import chili, tensor_cart2sph, tensor_sph2cart, wigner3j, wigner6j, wignerd
+from .spinops import sop, stev
+from .spinsystem import hsdim, spinvec, validatespinsys
+from .symmetry import hamsymm
+from .units import mhz2mt, mt2mhz, unitconvert
+
+__version__ = "0.2.0"
+
+__all__ = [
+    "amu", "avogadro", "bmagn", "boltzm", "clight", "echarge", "evolt", "gfree", "hbar", "mu0", "nmagn", "planck",
+    "ham", "ham_ee", "ham_ez", "ham_hf", "ham_nn", "ham_nq", "ham_nz", "ham_zf", "levels",
+    "Spectrum", "equivcouple", "fastmotion", "garlic",
+    "EndorResonances", "anisosubsys", "endorfrq", "endorfrq_perturb", "orisel", "salt", "curry",
+    "chili", "tensor_cart2sph", "tensor_sph2cart", "wigner3j", "wigner6j", "wignerd",
+    "apowin", "exponfit", "fdaxis", "larmorfrq", "saffron", "sf_pathways",
+    "FitResult", "addnoise", "basecorr", "deriv", "esfit", "esfit_genetic", "esfit_grid", "esfit_levmar",
+    "esfit_montecarlo", "esfit_simplex", "esfit_swarm", "hccm", "jacobianest", "rescaledata",
+    "SphGrid", "gridparam", "sphgrid",
+    "esspline1d", "esspline2d", "gridinterp",
+    "lisum1i", "projecttriangles", "projectzones",
+    "fieldmod", "hamsymm", "pepper", "resfields_perturb",
+    "convspec", "gaussian", "lorentzian", "lshape", "voigtian",
+    "Resonances", "cubicsolve", "nucspinrmv", "photoselect", "resfields", "resfields_eig",
+    "isotopes", "nucabund", "nucdata", "nucgval", "nucqmom", "nucspin", "nucstring2list",
+    "ang2vec", "erot", "eulang", "letter2vec", "vec2ang",
+    "sop", "stev",
+    "hsdim", "spinvec", "validatespinsys",
+    "mhz2mt", "mt2mhz", "unitconvert",
+]  # fmt: skip

easyspyn-0.2.0/epreasy/components.py

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+"""EasySpin's loop over component spin systems (``compisoloop`` without the isotopologue expansion).
+
+``pepper({Sys1, Sys2}, Exp)`` sums the spectra of the components, each
+weighted by ``Sys.weight`` (default 1); ``Opt.separate = 'components'``
+stacks them. Isotope mixtures (``isotopologues``) are not ported, so each
+component is one spin system.
+"""
+
+from __future__ import annotations
+
+from collections.abc import Callable
+
+import numpy as np
+
+_RANGE_FIELDS = ("Range", "CenterSweep", "mwRange", "mwCenterSweep")
+
+
+def compisoloop(simfcn: Callable, systems: list | tuple, exp: dict, opt: dict | None, *, needs_range: bool = True):
+    """Sum (or stack) the spectra of the component systems ``systems`` simulated by ``simfcn``; ``needs_range``
+    is the cw simulators' demand for an explicit sweep range (pulse experiments carry their own axes)."""
+    from .garlic import Spectrum
+
+    opt = dict(opt or {})
+    separate = opt.get("separate", "") == "components"
+    if separate:
+        opt["separate"] = ""
+    if needs_range and len(systems) > 1 and not any(exp.get(k) is not None for k in _RANGE_FIELDS):
+        raise ValueError(
+            "For multiple components, EasySpin cannot automatically determine a sweep range. "
+            "Please specify sweep range manually using Exp.Range or Exp.CenterSweep "
+            "(Exp.mwRange or Exp.mwCenterSweep for frequency sweeps)."
+        )
+    spectra = []
+    inverse = []  # the other domain of pulse experiments (info["fd"]), summed with the same weights
+    info: dict = {"Component": [], "Transitions": [], "nTransitions": []}
+    x = None
+    for k, system in enumerate(systems, start=1):
+        sys_k = dict(system)
+        weight = float(np.asarray(sys_k.pop("weight", 1.0)).ravel()[0])
+        res = simfcn(sys_k, exp, opt)
+        x = res.x
+        spec_k = np.asarray(res.spec)
+        spectra.append((spec_k if np.iscomplexobj(spec_k) else spec_k.astype(float)) * weight)
+        info["Component"].append(k)
+        if res.info.get("fd") is not None:
+            inverse.append(np.asarray(res.info["fd"]) * weight)
+            for key in ("f", "f1", "f2"):
+                if key in res.info:
+                    info[key] = res.info[key]
+            info["td"] = None if res.info.get("td") is None else True
+        for key in ("Transitions", "nOrientations", "nSites", "resfields"):
+            if key in res.info:
+                info.setdefault(key, []).append(res.info[key])
+        if "Transitions" in res.info:
+            info["nTransitions"].append(np.asarray(res.info["Transitions"]).shape[0])
+    if not info["Transitions"]:
+        info.pop("Transitions")
+        info.pop("nTransitions")
+    elif len(info["Transitions"]) == 1:
+        info["Transitions"] = info["Transitions"][0]
+    if "resfields" in info and len(info["resfields"]) == 1:
+        info["resfields"] = info["resfields"][0]
+    if separate:
+        spec = np.stack([np.atleast_2d(s) for s in spectra]).reshape(-1, spectra[0].shape[-1])
+    else:
+        spec = sum(spectra)
+    if inverse:
+        info["fd"] = np.stack(inverse) if separate else sum(inverse)
+        if info["td"] is not None:
+            info["td"] = spec
+    return Spectrum(x, spec, info)

easyspyn-0.2.0/epreasy/constants.py

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+"""Physical constants with EasySpin's names and values.
+
+EasySpin exposes each constant as a function (``bmagn()``); here they are
+module attributes (``epreasy.bmagn``). Values are those of EasySpin 6.0.15
+(CODATA 2022 where not exact by the 2019 SI redefinition).
+"""
+
+from math import pi
+
+bmagn = 9.2740100657e-24  # Bohr magneton, J/T
+nmagn = 5.0507837393e-27  # nuclear magneton, J/T
+planck = 6.62607015e-34  # Planck constant, J s (exact)
+hbar = planck / (2 * pi)  # reduced Planck constant, J s
+gfree = 2.00231930436092  # free-electron g factor
+clight = 299792458.0  # speed of light in vacuum, m/s (exact)
+mu0 = 1.25663706127e-6  # vacuum permeability, N/A^2
+boltzm = 1.380649e-23  # Boltzmann constant, J/K (exact)
+echarge = 1.602176634e-19  # elementary charge, C (exact)
+evolt = echarge  # electron volt, J (exact)
+amu = 1.66053906892e-27  # atomic mass unit, kg
+avogadro = 6.02214076e23  # Avogadro constant, 1/mol (exact)