physics.chem-phOct 12, 2026
SaveTorchSpin: Differentiable Electron Paramagnetic Resonance Simulation in PyTorch
Organizations: Department of Chemistry, University of California, Davis, Davis, California 95616, United States · Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
Abstract
Interpreting electron paramagnetic resonance (EPR) spectra commonly requires repeated forward simulation and optimization of spin Hamiltonian parameters. Established software provides mature simulation and fitting methods, but these calculations are not generally available as differentiable components within machine-learning workflows. We present TorchSpin, an open-source PyTorch framework that ports the organization and numerical conventions of EasySpin into a tensor-based computational environment. Representative calculations spanning continuous-wave EPR, ENDOR, pulse EPR, spin dynamics, trajectory simulation, and magnetometry closely reproduced corresponding EasySpin results. In matched benchmarks, TorchSpin CPU execution was faster than EasySpin for six of nine workloads although performance depended strongly on the calculation. We therefore focused on the capabilities enabled by automatic differentiation in PyTorch. In a Cu(II) powder-spectrum demonstration, feedback propagated through TorchSpin improved the quality of a supervised convolutional neural network (CNN) without using parameter labels during refinement. Models trained from randomly initialized CNNs using only noisy spectra and TorchSpin reconstruction loss achieved median similarities of 0.99. CNNs trained on TorchSpin-generated libraries also transferred without adaptation to independently generated EasySpin spectra with performance comparable to EasySpin-trained controls. Once trained, the CNN produced initial parameter estimates in approximately 1 ms per spectrum while a batch of 512 was processed in approximately 1.3 ms with GPU acceleration. TorchSpin therefore provides both a tested Python implementation of established EPR calculations and a differentiable physical layer for rapid learned inference, spectral refinement, and parameter-label-free training.
Figures & tables
Figure 1: Numerical agreement between TorchSpin and EasySpin across representative EPR and ENDOR simulations. TorchSpin (red) and independently generated EasySpin (black) spectra are compared for ( A ) isotropic fast-motion cw EPR using garlic , ( B ) slow-motion cw EPR using chili , ( C ) solid-state cw EPR using pepper , and ( D ) solid-state ENDOR using salt. Blue traces show the residuals (TorchSpin EasySpin). Each EasySpin spectrum was normalized to its maximum absolute amplitude.
Figure 2: Performance of representative EasySpin and TorchSpin simulation workloads on a common computing platform. ( A ) Median wall time for EasySpin on the CPU, TorchSpin using the selected CPU thread count, and TorchSpin in CUDA mode. TorchSpin CPU calculations were evaluated using 1, 8, and 32 threads; red labels identify the selected configuration, defined as the smallest thread count whose timing interquartile range (IQR) overlapped that of the configuration with the lowest median time. Hatched blue bars denote hybrid CUDA execution, in which verified GPU kernels are combined with CPU-side operations. N/A indicates that the corresponding chili or cardamom implementation does not currently provide a CUDA execution path. ( B ) Speedup relative to EasySpin, calculated as the EasySpin wall time divided by the corresponding TorchSpin wall time. Values above unity indicate faster TorchSpin execution, and the dashed line marks equal performance. Points show ratios of median times; error bars are conservative IQR-propagated bounds calculated from the EasySpin and TorchSpin measurements. Each condition comprised one untimed warm-up followed by five timed replicates on a local workstation; bars and points report medians, and error bars span the IQR.
Figure 3: Overview of the CNN training and evaluation workflows used to test TorchSpin. ( A ) A CNN was first trained by supervised regression against the seven generating parameters of an EasySpin spectral library. During subsequent differentiable refinement, the CNN mapped noisy EasySpin spectra to the principal values of the g and 63 Cu hyperfine tensors and a Gaussian linewidth. TorchSpin reconstructed the predicted spectrum, and a spectral loss against the corresponding clean EasySpin target was backpropagated through the simulator to update the CNN. ( B ) In the parameter-label-free experiment, independently initialized CNNs were trained without supervised pretraining, parameter labels, or clean spectral targets. The same fixed noisy EasySpin spectrum served as both the CNN input and the reconstruction target, and TorchSpin supplied the spectral gradients used to update the network. ( C ) For the cross-engine library comparison, supervised CNNs were trained on independent labeled libraries generated with EasySpin or TorchSpin. The two conditions used the same architecture and training protocol, with identical initial weights within each paired initialization seed. The resulting checkpoints were frozen before prospective evaluation. ( D,E ) CNNs trained on the TorchSpin ( D ) or EasySpin ( E ) library were evaluated on the same held-out noisy EasySpin spectra. Predictions from both conditions were reconstructed using the same TorchSpin forward model and compared with the corresponding clean EasySpin spectra. Black arrows denote input and forward-computation paths; red arrows denote spectral-error propagation or comparison.
Figure 4: Differentiable spectral feedback and simulation-trained CNN inversion of Cu(II) powder EPR spectra. ( A ) Representative held-out spectrum showing the noisy input, clean EasySpin target, and TorchSpin reconstructions obtained from the supervised CNN before and after differentiable spectral refinement. Residuals are shown relative to the clean target. ( B ) Paired comparison across all 512 test spectra. Refinement improved 373 spectra (72.9%), increasing the median cosine similarity from 0.977 to 0.985. The dashed diagonal denotes equal performance before and after refinement. ( C ) Empirical cumulative distributions of spectral agreement for the supervised control and three independently initialized, parameter-label-free CNNs trained from random initialization using TorchSpin spectral feedback. All models were evaluated on the same 512-spectrum EasySpin test library. The fraction exceeding the 0.950 threshold marked by the dashed line was 65.2% for the supervised control and 98.6% for each label-free model. ( D ) Mean absolute error (MAE) in the predicted g x , g y , g z , A x , A y , A z , and Gaussian linewidth ( lw ), expressed as a percentage of the full prespecified sampling span for each parameter. Label-free bars report the mean across three independently initialized models, and error bars indicate the sample standard deviation. ( E ) Cross-engine comparison of supervised CNNs trained on independent labeled EasySpin or TorchSpin spectral libraries using paired initial weights and identical training protocols. The frozen models were evaluated on the same held-out EasySpin spectra, and all predicted parameters were reconstructed using TorchSpin. Color identifies the training-library simulator, line style distinguishes the three paired initialization seeds, and the gray curve shows TorchSpin reconstructions generated from the true sampled parameters. The dashed vertical line marks a cosine similarity of 0.950. Spectral agreement in all panels was evaluated against the corresponding noise-free EasySpin spectrum.
Figure 5: Interactive Jupyter interface for conventional cw EPR fitting with TorchSpin. Parameter sliders and fixed-parameter controls allow adjustment of the spin system parameters. Additional controls select the optimization method and fitting limits. The plots display the input spectrum, starting simulation, best fit, residual, and best RMSD as a function of model evaluations. The interface supports repeated adjustment and refitting within the notebook.
Figure S1: Comparison of trajectory-based cw EPR simulations generated by TorchSpin and EasySpin. TorchSpin (red) and EasySpin (black) spectra were calculated using cardamom with the same spin-system and experimental parameters. Blue shows the residual (TorchSpin EasySpin). Because the calculations use independently sampled rotational trajectories, the residual includes finite-sampling variation. Each TorchSpin spectrum was multiplied by a single amplitude factor to account for differences in absolute-intensity convention.
Figure S2: Comparison of time-domain two-pulse ESEEM simulations generated by TorchSpin and EasySpin. The real components of the TorchSpin (red) and EasySpin (black) echo signals were calculated using saffron with equivalent spin-system, pulse-sequence, and orientation-grid parameters. Blue shows the residuals (TorchSpin EasySpin). A single amplitude factor was applied to the complete TorchSpin trace to account for different absolute-intensity conventions.
Figure S3: Comparison of pulse-driven spin dynamics calculated by TorchSpin and EasySpin. The real-valued electron z -magnetization trajectories generated by TorchSpin (red) and EasySpin (black) are shown during a frequency-swept pulse and the subsequent free-evolution period. Blue shows the pointwise residual (TorchSpin EasySpin). A single amplitude factor was applied to the complete TorchSpin trajectory to account for differences in signal convention.
Figure S4: Comparison of temperature-dependent effective magnetic moments calculated by TorchSpin and EasySpin. The normalized effective magnetic moments obtained with TorchSpin (red) and EasySpin (black) are shown as a function of temperature for an exchange-coupled Gd(III)–Cu(II) spin system. Blue shows the pointwise residual (TorchSpin EasySpin), magnified by 10 6 for visibility. A single amplitude factor was applied to the complete TorchSpin trace before normalization.
Figure S5: CPU thread scaling of representative TorchSpin simulation workloads. Median wall times were measured using 1, 8, and 32 CPU threads on a local workstation. Each cell reports the median execution time with its IQR in brackets and the speedup relative to the corresponding one-thread calculation. Cell color encodes the speedup on a log 2 scale: blue indicates faster execution, red indicates slower execution, and white indicates little or no change. The black outline and bold text identify the selected CPU configuration, defined as the smallest thread count whose timing interquartile range overlapped that of the configuration with the lowest median wall time. Each condition comprised one untimed warm-up followed by five timed replicates; quartiles were calculated as the linearly interpolated 25th and 75th percentiles.
| Workload | EasySpin (s) | TorchSpin CPU (s) | ES/TS CPU | TorchSpin CUDA mode (s) | ES/TS CUDA |
|---|---|---|---|---|---|
| pepper: Cu + 2 N, matrix | 0.292 [0.229–0.351] | 0.847 (32 t) | 0.344 | 0.674 (hybrid) | 0.433 |
| pepper: Mn(II), matrix | 3.03 [3.03–3.14] | 1.07 (32 t) | 2.83 | 0.954 (hybrid) | 3.18 |
| pepper: perturbative grid | 0.0818 [0.072–0.0825] | 0.0616 (1 t) | 1.33 | 0.162 (hybrid) | 0.506 |
| pepper: strain summation | 0.814 [0.808–0.816] | 0.994 (8 t) | 0.82 | 1.23 (hybrid) | 0.661 |
| pepper: 20-call fit pattern | 2.5 [2.5–2.5] | 1.29 (8 t) | 1.93 | 1.77 (hybrid) | 1.41 |
| chili: nitroxide + proton | 1.15 [1.14–1.16] | 0.157 (1 t) | 7.32 | N/A | N/A |
Table S1: Matched-host performance measurements used in the manuscript comparison.
| Model coordinate | Sampled interval | Physical transformation |
|---|---|---|
| g center | 2.040–2.080 | g x = g g/2; g y = g + g/2 |
| g rhombicity, g | 0–0.030 | g y g x |
| g z | 2.18–2.30 | – |
| A center | 35–85 MHz | A x = A A/2; A y = A + A/2 |
| A rhombicity, A | 0–40 MHz | A y A x |
| A z | 450–650 MHz | – |
Table S2: Bounded coordinates used to generate the Cu(II) spectral libraries.
Figure S6: Analysis of differentiable spectral refinement after supervised initialization. ( A ) Cumulative distribution of cosine similarity to the clean EasySpin test spectrum for the supervised and physics-refined CNNs. ( B ) Median cosine similarity within six predefined noise intervals; error bars show the interquartile range. The bin counts from lowest to highest noise were 82, 97, 84, 83, 79, and 87 spectra. ( C ) Training and validation histories for supervised parameter regression ( left ) and parameter-label-free spectral refinement ( right ); dotted lines mark the selected checkpoints. ( D ) Predicted and generating g and hyperfine components for the refined model.
| Metric | Supervised CNN | Physics-refined CNN |
|---|---|---|
| Median clean-spectrum cosine | 0.9768 | 0.9849 |
| Minimum cosine | 0.5934 | 0.8178 |
| Fraction with cosine 0.950 | 76.6% | 90.2% |
| Spectra improved | — | 373/512 (72.9%) |
Table S3: Test-set effects of parameter-label-free spectral refinement after supervised initialization.
| Parameter | Supervised MAE | Refined MAE |
|---|---|---|
| g x | 0.00125 | 0.00116 |
| g y | 0.00111 | 0.00099 |
| g z | 0.00369 | 0.00396 |
| A x (MHz) | 5.72 | 5.89 |
| A y (MHz) | 4.25 | 4.44 |
| A z (MHz) | 8.26 | 8.42 |
Table S4: Component-wise parameter MAE before and after parameter-label-free spectral refinement.
Figure S7: Optimization histories for the three parameter-label-free CNNs. Validation spectral loss and training spectral loss across the 24-epoch schedules. Line styles distinguish the three initialization seeds.
Figure S8: Parameter recovery and predicted-parameter correlations for training without labels. Top : generating versus predicted physical parameters for the supervised control (black) and all three label-free seeds (red); the dashed line denotes equality. Bottom : correlation matrices of the seven predicted parameters for each label-free seed.
Figure S9: Representative parameter-label-free reconstructions across the performance distribution. Best, median-ranked, and worst examples are shown for each initialization seed. Gray traces are fixed noisy observations, black traces are clean EasySpin spectra, and red traces are TorchSpin reconstructions from the label-free CNN predictions. Test indices and cosine similarities are given above each panel.
| Model | Median cosine | Fraction 0.950 | g x MAE | g y MAE | g z MAE | A x MAE (MHz) | A y MAE (MHz) | A z MAE (MHz) | lw MAE (mT) |
|---|---|---|---|---|---|---|---|---|---|
| Supervised control | 0.9698 | 65.2% | 0.00144 | 0.00140 | 0.00432 | 6.45 | 4.41 | 10.0 | 0.0855 |
| Label-free seed 1 | 0.9923 | 98.6% | 0.00118 | 0.000821 | 0.00392 | 6.98 | 5.01 | 9.04 | 0.107 |
| Label-free seed 2 | 0.9921 | 98.6% | 0.00115 | 0.000879 | 0.00454 | 7.01 | 4.82 | 9.81 | 0.105 |
| Label-free seed 3 | 0.9913 | 98.6% | 0.00126 | 0.000945 | 0.00444 | 6.96 | 5.05 | 9.87 | 0.124 |
Table S5: Prospective test-set performance for parameter-label-free training from random initialization.
Figure S10: Cumulative distributions of reconstruction NRMSE for CNNs trained on labeled EasySpin or TorchSpin libraries and evaluated on the same prospective EasySpin test set. Line styles identify the three paired initialization seeds. All predictions were decoded with TorchSpin.
Figure S11: Ranked prospective reconstructions for paired initialization seed 1. Left : CNN trained on the TorchSpin library. Right : CNN trained on the EasySpin library. For each condition, the best, median-ranked, poor, and worst cases were selected by cosine similarity to the clean EasySpin test spectrum. Gray traces are noisy inputs, black traces are clean EasySpin references, and red traces are TorchSpin reconstructions.
Figure S12: Ranked prospective reconstructions for paired initialization seed 2. Left : CNN trained on the TorchSpin library. Right : CNN trained on the EasySpin library. For each condition, the best, median-ranked, poor, and worst cases were selected by cosine similarity to the clean EasySpin test spectrum. Gray traces are noisy inputs, black traces are clean EasySpin references, and red traces are TorchSpin reconstructions.
Figure S13: Ranked prospective reconstructions for paired initialization seed 3. Left : CNN trained on the TorchSpin library. Right : CNN trained on the EasySpin library. For each condition, the best, median-ranked, poor, and worst cases were selected by cosine similarity to the clean EasySpin test spectrum. Gray traces are noisy inputs, black traces are clean EasySpin references, and red traces are TorchSpin reconstructions.
| Training library | Median cosine | Fraction 0.950 | Mean NRMSE |
|---|---|---|---|
| TorchSpin | 0.9656 ± 0.0008 | 61.59 ± 2.07% | 0.3075 ± 0.0067 |
| EasySpin | 0.9667 ± 0.0004 | 63.93 ± 1.59% | 0.3005 ± 0.0063 |
Table S6: Prospective cross-engine comparison averaged across three paired CNN initialization seeds. Values are mean ± sample standard deviation across three paired initialization seeds evaluated on the same 512-spectrum test set; percentage uncertainties are percentage points, not confidence intervals.
| Training library | g x | g y | g z | A x (MHz) | A y (MHz) | A z (MHz) | lw (mT) |
|---|---|---|---|---|---|---|---|
| TorchSpin | 0.00142 | 0.00138 | 0.00481 | 5.65 | 4.56 | 10.9 | 0.0799 |
| EasySpin | 0.00141 | 0.00133 | 0.00490 | 5.99 | 4.55 | 10.5 | 0.0807 |
Table S7: Mean component-wise parameter MAE across three paired initialization seeds in the cross-engine training-library comparison.
| Operation | Device/configuration | Median [IQR] (ms) | Per-spectrum value (ms) |
|---|---|---|---|
| Single CNN inference, resident | CPU, 1 thread | 0.976 [0.974–0.985] | 0.976 |
| Host normalization + CNN prediction | CPU, 1 thread | 0.994 [0.992–0.998] | 0.994 |
| Single CNN inference, resident | RTX 4090 | 1.019 [1.016–1.024] | 1.019 |
| Host normalization + transfer + prediction | RTX 4090 | 1.047 [1.045–1.053] | 1.047 |
| Batch CNN inference, n = 32 | RTX 4090 | 1.029 [1.026–1.034] | 0.0321 |
| Batch CNN inference, n = 128 | RTX 4090 | 1.016 [1.014–1.021] | 0.00794 |
Table S8: CNN inference and TorchSpin reconstruction latency.