reflectorch 1.1.0__tar.gz → 1.2.1__tar.gz

{reflectorch-1.1.0 → reflectorch-1.2.1}/.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 
 *.pt
 *.h5
+*.safetensors
 
 # Distribution / packaging
 .Python

{reflectorch-1.1.0 → reflectorch-1.2.1}/MANIFEST.in

@@ -9,5 +9,7 @@ exclude .github/*
 
 include exp_data/data_C60.pt
 include exp_data/data_PTCDI-C3.pt
+include exp_data/data_C60.txt
+include exp_data/data_PTCDI-C3.txt
 include exp_data/33a.dat
 include exp_data/DIP-nSi_34a.dat

{reflectorch-1.1.0 → reflectorch-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.1.0
+Version: 1.2.1
 Summary: A Pytorch-based package for the analysis of reflectometry data
 Author-email: Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>
 Maintainer-email: Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>, Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Alexander Hinderhofer <alexander.hinderhofer@uni-tuebingen.de>
@@ -27,6 +27,7 @@ Requires-Dist: click
 Requires-Dist: matplotlib
 Requires-Dist: ipywidgets
 Requires-Dist: huggingface_hub
+Requires-Dist: safetensors
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"

reflectorch-1.2.1/exp_data/data_C60.txt

@@ -0,0 +1,92 @@
+# q	R(q)
+1.42368058e-02	9.99013913e-01
+1.56604844e-02	9.97201582e-01
+1.70841625e-02	1.00000000e+00
+1.85078401e-02	9.98838316e-01
+1.99315182e-02	9.96319110e-01
+2.13551957e-02	9.92375339e-01
+2.27788704e-02	9.89743023e-01
+2.42025465e-02	9.86378958e-01
+2.56262219e-02	9.75717850e-01
+2.70498944e-02	9.60515827e-01
+2.84735682e-02	9.30343836e-01
+2.98972390e-02	8.36874918e-01
+3.13209110e-02	5.06307942e-01
+3.27445821e-02	9.57114507e-02
+3.41682500e-02	1.72501680e-02
+3.55919191e-02	2.19172468e-02
+3.70155849e-02	3.02606295e-02
+3.84392538e-02	3.46351062e-02
+3.98629173e-02	3.63926902e-02
+4.12865797e-02	3.56133498e-02
+4.27102449e-02	3.31841454e-02
+4.41339047e-02	3.00055263e-02
+4.55575631e-02	2.62583437e-02
+4.69812244e-02	2.23786456e-02
+4.84048799e-02	1.86479132e-02
+4.98285341e-02	1.48919751e-02
+5.12521909e-02	1.15645186e-02
+5.26046603e-02	8.81495735e-03
+5.41706729e-02	6.16748023e-03
+5.54519576e-02	4.41031274e-03
+5.69467895e-02	2.85552699e-03
+5.83704338e-02	1.82277111e-03
+5.97940764e-02	1.09309472e-03
+6.12177214e-02	6.45209121e-04
+6.26413603e-02	4.51815994e-04
+6.40649973e-02	4.05545553e-04
+6.54886365e-02	4.71986389e-04
+6.69122696e-02	6.33676016e-04
+6.83359006e-02	8.24721598e-04
+6.97595337e-02	1.02122815e-03
+7.11831605e-02	1.19991309e-03
+7.26067851e-02	1.37747504e-03
+7.40304075e-02	1.45628994e-03
+7.54540277e-02	1.56260066e-03
+7.68776540e-02	1.56385635e-03
+7.83012696e-02	1.55499805e-03
+7.97248827e-02	1.48071534e-03
+8.11484934e-02	1.37202330e-03
+8.25721016e-02	1.25561119e-03
+8.39957073e-02	1.12940707e-03
+8.54193190e-02	9.70388349e-04
+8.68429195e-02	8.14503931e-04
+8.82665174e-02	6.66042995e-04
+8.96901126e-02	5.22589578e-04
+9.11137051e-02	3.97105516e-04
+9.24661205e-02	2.92556151e-04
+9.40320644e-02	2.05435132e-04
+9.53844743e-02	1.37877745e-04
+9.68080554e-02	8.99905383e-05
+9.82316336e-02	6.01704429e-05
+9.96552087e-02	4.57869602e-05
+1.01078781e-01	4.57521348e-05
+1.02502358e-01	5.87806384e-05
+1.03925924e-01	7.33169291e-05
+1.05349487e-01	9.99188747e-05
+1.06773047e-01	1.24738986e-04
+1.08196603e-01	1.53505862e-04
+1.09620156e-01	1.75739919e-04
+1.11043706e-01	1.95222433e-04
+1.12467261e-01	2.04343119e-04
+1.13890803e-01	2.12539731e-04
+1.15314343e-01	2.14384693e-04
+1.16737879e-01	2.07431638e-04
+1.18161411e-01	2.05379924e-04
+1.19584940e-01	1.91959662e-04
+1.21008473e-01	1.68736759e-04
+1.22431995e-01	1.48284283e-04
+1.23855512e-01	1.36160797e-04
+1.25279026e-01	1.13203424e-04
+1.26702536e-01	9.44118517e-05
+1.28126043e-01	7.29784509e-05
+1.29549554e-01	5.48038635e-05
+1.30973052e-01	4.14296076e-05
+1.32396546e-01	2.71453572e-05
+1.33820037e-01	1.79044017e-05
+1.35243523e-01	1.12678662e-05
+1.36667005e-01	6.18756266e-06
+1.38090492e-01	6.12377904e-06
+1.39513965e-01	5.68246646e-06
+1.40937435e-01	8.06260534e-06
+1.42432068e-01	9.64781290e-06

reflectorch-1.2.1/exp_data/data_PTCDI-C3.txt

@@ -0,0 +1,142 @@
+# q	R(q)
+1.42368058e-02	9.82044589e-01
+1.56604844e-02	9.83464915e-01
+1.70841625e-02	9.96593967e-01
+1.85078401e-02	9.91586687e-01
+1.99315182e-02	1.00000000e+00
+2.13551957e-02	9.92022512e-01
+2.27788704e-02	9.98568937e-01
+2.42025465e-02	9.87853497e-01
+2.56262219e-02	9.89907742e-01
+2.70498944e-02	9.70983733e-01
+2.84735682e-02	9.46983437e-01
+2.98972390e-02	8.80801224e-01
+3.13209110e-02	7.19476528e-01
+3.27445821e-02	3.67459239e-01
+3.41682500e-02	1.15510963e-01
+3.55919191e-02	8.06758266e-02
+3.70155849e-02	7.01391188e-02
+3.84392538e-02	6.14631441e-02
+3.98629173e-02	5.12756187e-02
+4.12865797e-02	4.27515249e-02
+4.27102449e-02	3.34815932e-02
+4.41339047e-02	2.54358846e-02
+4.55575631e-02	1.83058769e-02
+4.69812244e-02	1.27533556e-02
+4.84048799e-02	8.09708921e-03
+4.98285341e-02	5.06697636e-03
+5.11810049e-02	2.72937432e-03
+5.26758419e-02	1.41903158e-03
+5.40994914e-02	6.12297600e-04
+5.55231391e-02	3.28475560e-04
+5.69467895e-02	3.61580064e-04
+5.83704338e-02	5.49662522e-04
+5.97940764e-02	7.89839220e-04
+6.12177214e-02	1.06217044e-03
+6.26413603e-02	1.31711525e-03
+6.40649973e-02	1.45729095e-03
+6.54886365e-02	1.51852702e-03
+6.69122696e-02	1.56528192e-03
+6.83359006e-02	1.46318592e-03
+6.97595337e-02	1.40552582e-03
+7.11119801e-02	1.17709374e-03
+7.26067851e-02	1.06406540e-03
+7.40304075e-02	8.80648522e-04
+7.54540277e-02	7.17192736e-04
+7.68776540e-02	5.30855152e-04
+7.83012696e-02	4.35611063e-04
+7.97248827e-02	3.24093883e-04
+8.11484934e-02	2.50403810e-04
+8.25721016e-02	1.85126238e-04
+8.39957073e-02	1.61616756e-04
+8.54193190e-02	1.45902206e-04
+8.68429195e-02	1.33658480e-04
+8.82665174e-02	1.38611041e-04
+8.96901126e-02	1.43406388e-04
+9.11137051e-02	1.68397288e-04
+9.25372948e-02	1.61492000e-04
+9.39608902e-02	1.76953011e-04
+9.53844743e-02	1.60857424e-04
+9.68080554e-02	1.75578481e-04
+9.82316336e-02	1.75937243e-04
+9.96552087e-02	1.63121564e-04
+1.01078781e-01	1.62799229e-04
+1.02502358e-01	1.58590629e-04
+1.03925924e-01	1.23488110e-04
+1.05349487e-01	1.19383055e-04
+1.06773047e-01	1.02566636e-04
+1.08196603e-01	9.46274959e-05
+1.09620156e-01	8.68945574e-05
+1.11043706e-01	7.31960151e-05
+1.12467261e-01	6.31407527e-05
+1.13890803e-01	5.88458351e-05
+1.15314343e-01	5.66354921e-05
+1.16737879e-01	6.22966808e-05
+1.18161411e-01	4.75474338e-05
+1.19584940e-01	5.43744507e-05
+1.21008473e-01	5.23207207e-05
+1.22431995e-01	4.75194895e-05
+1.23855512e-01	4.21378404e-05
+1.25279026e-01	4.34801989e-05
+1.26773715e-01	4.97443190e-05
+1.28126043e-01	4.65206097e-05
+1.29549554e-01	4.24871806e-05
+1.30973052e-01	3.74526907e-05
+1.32396546e-01	3.54344561e-05
+1.33820037e-01	3.11148876e-05
+1.35243523e-01	3.28961178e-05
+1.36667005e-01	2.42064352e-05
+1.38090492e-01	2.68482573e-05
+1.39513965e-01	2.75823412e-05
+1.40937435e-01	2.54965082e-05
+1.42360900e-01	2.66438782e-05
+1.43784361e-01	1.94379718e-05
+1.45207818e-01	2.19970554e-05
+1.46631270e-01	2.00330537e-05
+1.48125901e-01	2.11888292e-05
+1.49478160e-01	2.49936726e-05
+1.50901599e-01	1.32294175e-05
+1.52325050e-01	1.49780468e-05
+1.53748479e-01	1.52103619e-05
+1.55171904e-01	1.64492640e-05
+1.56595324e-01	1.20199226e-05
+1.58018739e-01	1.47993208e-05
+1.59442149e-01	1.50182341e-05
+1.60865555e-01	1.34737057e-05
+1.62288956e-01	1.17739547e-05
+1.63712351e-01	1.25426001e-05
+1.65135742e-01	1.13982815e-05
+1.66559127e-01	9.07494407e-06
+1.67982508e-01	9.84692108e-06
+1.69405900e-01	1.17843608e-05
+1.70829271e-01	8.43073844e-06
+1.72252636e-01	9.27168515e-06
+1.73675996e-01	7.55361002e-06
+1.75099350e-01	1.02610674e-05
+1.76522699e-01	1.03398905e-05
+1.77946043e-01	8.49423083e-06
+1.79369382e-01	7.31384994e-06
+1.80792715e-01	7.88724994e-06
+1.82216042e-01	7.19958971e-06
+1.83639364e-01	5.59079085e-06
+1.85062680e-01	8.16758282e-06
+1.86485991e-01	6.11950164e-06
+1.87909313e-01	5.76729036e-06
+1.89332612e-01	4.51889607e-06
+1.90684729e-01	4.93369698e-06
+1.92179193e-01	7.56833479e-06
+1.93602475e-01	4.56654050e-06
+1.95025751e-01	5.55684346e-06
+1.96449021e-01	4.93589114e-06
+1.97872285e-01	5.62103336e-06
+1.99295543e-01	4.86539221e-06
+2.00718795e-01	4.26255248e-06
+2.02142041e-01	4.51470999e-06
+2.03565280e-01	3.64255540e-06
+2.04988531e-01	4.03464158e-06
+2.06411758e-01	4.42284629e-06
+2.07834979e-01	3.84216415e-06
+2.09258193e-01	3.27088515e-06
+2.10681401e-01	3.31647258e-06
+2.12104603e-01	4.03373799e-06
+2.13456644e-01	3.13870114e-06

{reflectorch-1.1.0 → reflectorch-1.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "reflectorch"
-version = "1.1.0"
+version = "1.2.1"
 authors = [
     {name = "Vladimir Starostin", email="vladimir.starostin@uni-tuebingen.de"},
     {name = "Valentin Munteanu", email="valentin.munteanu@uni-tuebingen.de"}
@@ -38,6 +38,7 @@ dependencies = [
     "matplotlib",
     "ipywidgets",
     "huggingface_hub",
+    "safetensors",
 ]
 
 [project.optional-dependencies]

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/__init__.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from reflectorch.data_generation import *
 from reflectorch.ml import *
 from reflectorch.models import *

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/__init__.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from reflectorch.data_generation.dataset import BasicDataset, BATCH_DATA_TYPE
 from reflectorch.data_generation.priors import (
     Params,

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/dataset.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Dict, Union
 import warnings
 

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/likelihoods.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Union, Tuple
 
 import torch

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/noise.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Union, Tuple
 from math import log10
 

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/__init__.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from reflectorch.data_generation.priors.params import Params
 from reflectorch.data_generation.priors.base import PriorSampler
 from reflectorch.data_generation.priors.no_constraints import BasicPriorSampler

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/base.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from torch import Tensor
 
 from reflectorch.data_generation.priors.params import Params

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/exp_subprior_sampler.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Tuple, Union, List
 
 import torch

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/independent_priors.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Union, Tuple
 from math import log
 

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/multilayer_structures.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Tuple, Dict
 
 import numpy as np

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/no_constraints.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 import logging
 from functools import lru_cache
 from typing import Tuple

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/parametric_subpriors.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Tuple, Dict, Type, List
 
 import torch

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/params.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import List, Tuple
 
 import torch

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/subprior_sampler.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from functools import lru_cache
 from typing import Tuple
 

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/priors/utils.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Tuple
 
 import torch

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/process_data.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Any
 
 __all__ = [

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/q_generator.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from typing import Tuple, Union
 
 import numpy as np

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/__init__.py

@@ -24,21 +24,25 @@ def reflectivity(
         log: bool = False,
         abeles_func=None,
 ):
-    """Function which computes the reflectivity from thin film parameters using the Abeles matrix formalism
+    """Function which computes the reflectivity curves from thin film parameters. 
+    By default it uses the fast implementation of the Abeles matrix formalism.
 
     Args:
-        q (Tensor): the momentum transfer (q) values
-        thickness (Tensor): the layer thicknesses
-        roughness (Tensor): the interlayer roughnesses
-        sld (Tensor): the SLDs of the layers
-        dq (Tensor, optional): the resolution for curve smearing. Defaults to None.
+        q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
+        thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
+        roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape 
+            [batch_size, n_layers + 1] (excluding ambient SLD which is assumed to be 0)  or [batch_size, n_layers + 2] (including ambient SLD; only for the default ``abeles_func='abeles'``) 
+        dq (Tensor, optional): tensor of resolutions used for curve smearing with shape [batch_size, 1].
+                            Either dq if ``constant_dq`` is ``True`` or dq/q if ``constant_dq`` is ``False``. Defaults to None.
         gauss_num (int, optional): the number of gaussians for curve smearing. Defaults to 51.
-        constant_dq (bool, optional): whether the smearing is constant. Defaults to True.
+        constant_dq (bool, optional): if ``True`` the smearing is constant (constant dq at each point in the curve) 
+                                    otherwise the smearing is linear (constant dq/q at each point in the curve). Defaults to True.
         log (bool, optional): if True the base 10 logarithm of the reflectivity curves is returned. Defaults to False.
-        abeles_func (Callable, optional): a function implementing the simulation of the reflectivity curves, if different than the default implementation. Defaults to None.
+        abeles_func (Callable, optional): a function implementing the simulation of the reflectivity curves, if different than the default Abeles matrix implementation ('abeles'). Defaults to None.
 
     Returns:
-        Tensor: the computed reflectivity curves
+        Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]
     """
     abeles_func = abeles_func or abeles
     q = torch.atleast_2d(q)

reflectorch-1.2.1/reflectorch/data_generation/reflectivity/abeles.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+import math
+from functools import reduce
+
+import torch
+from torch import Tensor
+
+
+def abeles(
+        q: Tensor,
+        thickness: Tensor,
+        roughness: Tensor,
+        sld: Tensor,
+):
+    """Simulates reflectivity curves for SLD profiles with box model parameterization using the Abeles matrix method
+
+    Args:
+        q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
+        thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
+        roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom). The tensor shape should be one of the following:
+            - [batch_size, n_layers + 1]: in this case, the ambient SLD is not included but assumed to be 0
+            - [batch_size, n_layers + 2]: this shape includes the ambient SLD as the first element in the tensor
+
+    Returns:
+        Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]
+    """
+    c_dtype = torch.complex128 if q.dtype is torch.float64 else torch.complex64
+
+    batch_size, num_layers = thickness.shape
+
+    if sld.shape[-1] == num_layers + 1:
+        # add zero ambient sld
+        sld = torch.cat([torch.zeros(batch_size, 1).to(sld), sld], -1)
+    if sld.shape[-1] != num_layers + 2:
+        raise ValueError(
+            "Number of SLD values does not equal to num_layers + 2 (substrate + ambient)."
+        )
+
+    sld = sld[:, None]
+
+    # add zero thickness for ambient layer:
+    thickness = torch.cat([torch.zeros(batch_size, 1).to(thickness), thickness], -1)[
+        :, None
+    ]
+
+    roughness = roughness[:, None] ** 2
+
+    sld = (sld - sld[..., :1]) * 1e-6 + 1e-36j
+
+    k_z0 = (q / 2).to(c_dtype)
+
+    if k_z0.dim() == 1:
+        k_z0.unsqueeze_(0)
+
+    if k_z0.dim() == 2:
+        k_z0.unsqueeze_(-1)
+
+    k_n = torch.sqrt(k_z0**2 - 4 * math.pi * sld)
+
+    # k_n.shape - (batch, q, layers)
+
+    k_n, k_np1 = k_n[..., :-1], k_n[..., 1:]
+
+    beta = 1j * thickness * k_n
+
+    exp_beta = torch.exp(beta)
+    exp_m_beta = torch.exp(-beta)
+
+    rn = (k_n - k_np1) / (k_n + k_np1) * torch.exp(-2 * k_n * k_np1 * roughness)
+
+    c_matrices = torch.stack(
+        [
+            torch.stack([exp_beta, rn * exp_m_beta], -1),
+            torch.stack([rn * exp_beta, exp_m_beta], -1),
+        ],
+        -1,
+    )
+
+    c_matrices = [c.squeeze(-3) for c in c_matrices.split(1, -3)]
+
+    m = reduce(torch.matmul, c_matrices)
+
+    r = (m[..., 1, 0] / m[..., 0, 0]).abs() ** 2
+    r = torch.clamp_max_(r, 1.0)
+
+    return r
+
+
+# @torch.jit.script # commented so far due to complex numbers issue
+def abeles_compiled(
+        q: Tensor,
+        thickness: Tensor,
+        roughness: Tensor,
+        sld: Tensor,
+):
+    return abeles(q, thickness, roughness, sld)

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/kinematical.py

@@ -13,6 +13,20 @@ def kinematical_approximation(
         apply_fresnel: bool = True,
         log: bool = False,
 ):
+    """Simulates reflectivity curves for SLD profiles with box model parameterization using the kinematical approximation
+
+    Args:
+        q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
+        thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
+        roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
+                    It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
+        apply_fresnel (bool, optional): whether to use the Fresnel coefficient in the computation. Defaults to ``True``.
+        log (bool, optional): if True the base 10 logarithm of the reflectivity curves is returned. Defaults to ``False``.
+
+    Returns:
+        Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]
+    """
     c_dtype = torch.complex128 if q.dtype is torch.float64 else torch.complex64
 
     batch_size, num_layers = thickness.shape

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/memory_eff.py

@@ -12,6 +12,19 @@ def abeles_memory_eff(
         roughness: Tensor,
         sld: Tensor,
 ):
+    """Simulates reflectivity curves for SLD profiles with box model parameterization using a memory-efficient implementation the Abeles matrix method. 
+    It is computationally slower compared to the implementation in the 'abeles' function.
+
+    Args:
+        q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
+        thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
+        roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
+                    It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
+
+    Returns:
+        Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]
+    """
     c_dtype = torch.complex128 if q.dtype is torch.float64 else torch.complex64
 
     batch_size, num_layers = thickness.shape

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/smearing.py

@@ -68,8 +68,8 @@ def _get_q_axes_for_linear_dq(q: Tensor, resolutions: Tensor, gaussnum: int = 51
     lowq = torch.clamp_min_(q.min(1).values, 1e-6)
     highq = q.max(1).values
 
-    start = torch.log10(lowq) - 6 * resolutions / _FWHM
-    end = torch.log10(highq * (1 + 6 * resolutions / _FWHM))
+    start = torch.log10(lowq)[:, None] - 6 * resolutions / _FWHM
+    end = torch.log10(highq[:, None] * (1 + 6 * resolutions / _FWHM))
 
     interpnums = torch.abs(
         (torch.abs(end - start)) / (1.7 * resolutions / _FWHM / gaussgpoint)

{reflectorch-1.1.0 → reflectorch-1.2.1}/reflectorch/data_generation/scale_curves.py

@@ -1,9 +1,3 @@
-# -*- coding: utf-8 -*-
-#
-#
-# This source code is licensed under the GPL license found in the
-# LICENSE file in the root directory of this source tree.
-
 from pathlib import Path
 
 import torch