the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 28 May 2026
PecubeGUI: a user interface for the Pecube thermal-kinematic model and advanced low-temperature thermochronometer predictions
Abstract. Thermochronology offers critical constraints on rock cooling and exhumation histories, enabling quantitative assessments of landscape evolution and its interactions with tectonic and climatic forcings. These interpretations increasingly rely on numerical models capable of linking measured thermochronometric data to realistic thermal and kinematic scenarios. Among such tools, the Pecube code provides a unique 3D thermal‑kinematic framework that explicitly couples tectonic and geomorphic processes with predicted thermochronometric observables, which has been widely used for reconstructing the tectonic and topographic evolution of mountain belts as well as crustal thermal structure. In this contribution, we introduce PecubeGUI, a new open‑access graphical user interface (GUI) that modernises and greatly enhances the accessibility of Pecube. Alongside the interface, we present substantial updates to Pecube, including the implementation of contemporary radiation‑damage models for apatite and zircon (U–Th)/He thermochronometers, multi-kinetic models for fission-track annealing, and the integration of ultra-low temperature thermochronometers such as the apatite 4He/3He and trapped‑charge methods, the latter being in active development. These additions expand the ability of Pecube to resolve low‑temperature cooling signals, particularly at Quaternary timescales, where increased temporal resolution is essential for understanding landscape evolution.
By lowering the technical barrier to Pecube modelling and broadening the toolkit available to users, PecubeGUI aims to foster wider adoption and stimulate new applications across the thermochronology, geomorphology, and tectonics communities.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Geochronology.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.- Preprint
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Status: open (until 31 Jul 2026)
- RC1: 'Comment on egusphere-2026-2286', Pierre Valla, 13 Jul 2026 reply
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RC2: 'Comment on egusphere-2026-2286', Maria-Laura Balestrieri, 14 Jul 2026
reply
This manuscript presents PecubeGUI, a graphical user interface for the well-known thermo-kinematic modelling code Pecube, together with substantial updates to the thermochronometric prediction capabilities of the underlying code. The authors introduce a modern and user-friendly interface, improved visualization tools, updated AHe and ZHe radiation-damage models, implementation of 4He/3He modelling, updated fission-track kinetics, and ongoing development of trapped-charge thermochronometry.
I consider this manuscript to be a highly valuable contribution to the thermochronology and landscape-evolution communities. Pecube has been a powerful thermo-kinematic modelling tool for more than two decades, however its accessibility has remained limited due to the absence of an integrated graphical interface. The new GUI substantially lowers the entry barrier for new users while preserving and even enhancing the sophistication of the original code. The manuscript is generally well written, the examples are appropriate, and the software developments are significant.
The possibility to directly enter sample coordinates, visualise them on the DEM, and associate grain-specific kinetic parameters through interactive tables represents a substantial improvement in usability compared to the previous workflow based on external input files. This feature reduce setup errors and facilitate the handling of large multi-thermochronometer datasets.
Overall, I highly appreciate that the authors do not limit themselves to presenting a graphical wrapper but also provide significant scientific updates to the thermochronometer prediction modules. The inclusion of modern radiation-damage models and 4He/3He modelling considerably enhances the applicability of Pecube for Quaternary landscape evolution studies.
Minor Comments:
The "Increased Resolution Power" (IRP) metric introduced in Eq. (9) appears to me to be a new quantity proposed by the authors. I am not aware of previous applications of this metric in the thermochronology literature. If IRP is indeed being introduced here for the first time, it would be helpful to state this explicitly and spend some more words on it.
Line 410: I would not define the cooling path of the valley bottom-sample as “distinct” respect to that one of the summit sample, it is just shifted as temperatures
I noticed some typo or formatting issues.
line 64: "rock-uplift filed" rock-uplift field
line 87: "foreland foreland fold-and-thrust belts" remove duplicate foreland
Page 6: "PyQT5" and "PyQt5" are both used. Use one convention consistently (preferably PyQt5).
Page 9: the second subsection labelled 2.4.2 (Apatite fission-track annealing) should be 2.4.3.
Line 270: Equation numbering appears duplicated: Eq. (8) is used both for heat-production conversion and for exponential depth dependence of heat production (renumber in 8.1).
Line 402: “Fig. 7” it has to be Fig. 9
Page 12: Check equation 7b, I guess thermal diffusivity () has to appear.
Figure 11: The presentation of the two 4He/3He spectra could be improved. I suggest: i) placing the higher-elevation sample above the valley-bottom sample; 2) plotting the spectra with the conventional orientation commonly used in HeFTy and QTQt-style visualizations. This would facilitate comparison with previously published studies and improve readability.
I enjoyed reading the manuscript and believe that PecubeGUI will significantly enhance the accessibility and usability of Pecube for both new and experienced users.I confess that I am already an enthusiastic PecubeGUI user. I look forward to seeing this contribution published and I believe it will be of high interest to the GChron readers.
Regards,
Maria Laura Balestrieri
Citation: https://doi.org/10.5194/egusphere-2026-2286-RC2
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- 1
Dear Authors, dear Editors,
Please find below my evaluation concerning the revised manuscript by Bernard and co-authors entitled "PecubeGUI: a user interface for the Pecube thermal-kinematic model and advanced low-temperature thermochronometer predictions" (manuscript 2026-2286).
This manuscript provides a new graphical user interface for Pecube software, a 3D thermo-kinematic model that has been developed by Braun (2003) and has been widely used to derive exhumation histories from low-temperature thermochronometric data. The Pecube software has then been progressively updated and developed for topographic evolution and fault kinematics, among others, and latest developments where reported more than a decade ago in Braun et al. (2012). Pecube software is very efficient for solving the crustal thermal field evolution in 3D, allowing to test and quantify potential tectono-geomorphic scenarios in predicting low-temperature thermochronometric systems. However, one main limitation was the format and relative complexity to use the Pecube software, limiting its applicability compared to other thermal models. In this contribution, Bernard et al. presents a new and nice update of the Pecube software, with the development of PecubeGUI that provides a graphical and user-friendly way to use and explore Pecube software. This is a very useful contribution and will surely allow access to this approach for a large community of low-temperature thermochronometry users. In addition, this contribution also provides new developments, such as a new way to model topographic changes, easy tools for output visualizations, but also the incorporation of up-to-date kinetic models for He diffusion and FT annealing and the addition and test of novel low-temperature systems (4He/3He, trapped-charge). They provide some guidelines for the use of the new interface (together with a detailed manual and coming github repository), and expose illustrate examples of the key developments of the Pecube v4.3 that they present.
The manuscript is well written and nicely illustrated, allowing the reader to follow the PecubeGUI organization, new and ongoing developments, and potential for future directions. The interface is well introduced and some key examples allow to easily picture the potential and user-friendly idea behind this contribution. I have some comments to further illustrate these developments and illustrate their benefits, which I have detailed below. I think this is a great contribution for the interpretation of low-temperature thermochronometric data, and will be of great interest for the readership of G-Chron and beyond.
I have further detailed below my questions and suggestions in a set of general comments and more specific comments.
General comments:
- Topographic data and evolution: I would suggest to provide some further information in section 3.1 about the downscaling of topographic input data, as well as on some parameters for offset or step interpolation (former tau parameter in Pecube v4.2). Since the main motivation in this contribution is oriented towards topographic evolution, such information appears important.
- Inverse modelling: Pecube inverse modelling is only briefly presented in this contribution, since there is (to my knowledge) another manuscript under review (Bernard et al.) that specifically deals with the NA approach and Pecube inverse mode. I would thus suggest to make the link between the two manuscripts clearer (e.g. companion papers?) and to remove text/figures on inverse modelling from the present contribution (only one synthetic sentence pointing to the other manuscript would be good I guess).
- Topographic application (section 4.1.1) and kinetic models: I think this is a nice illustration of Pecube and sensitivity analysis provided by this new version, but I am not sure about the taken strategy for illustrating the topographic effect on apparent exhumation rate. I would encourage the authors to first show an example with steady-state topography (similar to Braun, 2002), and then to present the scenarios with evolving topographies. This section can also be used to a posteriori recalculate the AHe ages using different kinetic models and to illustrate this effect, as I think this is a great development but a bit hidden in the text (CalcAge routine).
- Trapped charge systems: I understand that their incorporation in Pecube is still an ongoing task, but some were already implemented (partly) in v4.2 and I think the present contribution is a good opportunity to put some emphasis on this. I would suggest, as for the 4He/3He, to show a quick and simple example of trapped-charge systems, potentially using the nice dataset and thermal histories of Wen et al. (2024) on the same study site as their Figure 11. This may be a great addition to the current manuscript, of broad interest for the community given the ongoing developments in these systems.
Specific comments, by line number:
- Line 1. Maybe add “graphical” in the title for clarity.
- Line 17. “quantitative assessments of landscape evolution”. I would suggest to also specify the possible quantification of long term erosion histories and fault activity there, so that it illustrates the versatility of the Pecube approach. Same remark for lines 32-34 (beginning of introduction)
- Line 21. “as crustal thermal structure”. Unclear how to do this (evolution of geothermal gradient? Not easy to perform this…), maybe remove or rephrase.
- Line 38. Concerning the Tc, there is also a complexity when going to low closure temperature near subsurface, and/or for saturating thermochronometers (see Guralnik et al., 2013). May worth precising this point?
- Line 50. “three main softwares”, maybe precise “main” or “largely-used”.
- Line 56. “cannot be directly translated into exhumation histories”. Not entirely correct, if geotherm is known/constrained then exhumation rates can be derived. I think the main addition of Pecube is that it allows to consider thermal advection and the influence of (evolving or not) topography on thermal field. And in addition it allows spatially distributed datasets. Maybe rephrase this sentence for clarity.
- Line 58. “explicitly address the geomorphic or tectonic processes…”. Same remark there, Pecube is also not treating the geomorphic processes but potentially landscape evolution, please rephrase.
- Line 60. “model specific parameters”. Specify these.
- Line 64. Correct “filed” by “field”.
- Lines 73-74. Maybe cite there the current paper in review by Bernard et al. on NA approach, that would be interesting for readers no?
- Line 86. “Quaternary-scale landscape evolution”. I agree this can allow going to Quaternary scales, but more importantly the low-Tc thermochronometers allow to quantify the late-stage cooling/exhumation histories, not necessarily to the Quaternary only. Maybe rephrase to specify this point.
- Line 88-89. “However, the kinetic models…”. This sentence reads a bit odd there after the low-Tc thermochronometers, maybe rephrase or move this above.
- Line 94. “…to ongoing development”. Is there an online repository or even better a github repository that could be indicated there? Same remark for lines 123 and 152.
- Line 97. Maybe change by “Python-based graphical user interface (GUI)”.
- Line 99. “in Fortran90”. I would suggest to specify that the new released version will be compiled to work on different environments (windows, linux, mac) so that readers will not be blocked by that step.
- Line 106. “to modify kinetic parameters”. Unclear, is it really modifying the parameters or to select different models? Please clarify.
- Line 124. “Pecube v4.2 are outdated”. Not totally agreeing with this statement, the available models are valid but not complete and the new version allow more flexibility in kinetic models. Please rephrase.
- Line 126-130. These lines read a bit like a repetition of the introduction, maybe remove?
- Line 132. “PyQt5”. Please provide a link or reference for this application.
- Line 135. “PyQt5”, please correct the “t” (no capital).
- Line 142. Are these files aimed to be modified by the users, or are they structuring the graphical interface? I think this is important to precise this point.
- Line 159. “associated kinetic values”. Unclear what this means, are they really sample-specific kinetic values and/or proxy (eU etc.). Please clarify, and same remark for line 192.
- Line 163. “Radiation damages”. Maybe rephrase as “Radiation-damage effects…”.
- Line 174. “Ft factor values are set to one.”. Please specify something like “(i.e. no ejection)” for clarity.
- Line 175. “a sphere…”. I would suggest to point out that only this diffusion geometry is currently available in Pecube, different to QTQt that allows other geometries.
- Line 191. Figure 3. I don’t entirely understand this figure and the different symbols (some are not defined in caption. What is the first line, unclear what is NHe and 4He? And for fourth line (Nnew), isn’t there missing “+” between the different terms? Or maybe I missed something, but I would suggest the authors to expand the explanation in caption/main text.
- Line 194. “(e.g., rm0).” Please provide a reference for this and some explanation, this only comes afterwards on line 210.
- Line 197. Please cite there Shuster and Farley (2004) and Schildgen et al. (2010) for the 4He/3He approach.
- Lines 200-206. I found this strange to detail the misfit computation only there for the 4He/3He method, and only report a line for the other thermochronometers. I would suggest to move this before and illustrate the different misfits that are possible (maybe a simple figure?). And the structuration of section 2.4 is not easy to follow, I think there is no real need for subsections there no?
- Line 227. “90-m Shuttle Radar Topography…”. I would suggest to stress there that the users are then encourage to degrade the resolution of the input DEM to 0.5-1 km (by changing model points nx and ny), to ensure low computation time while keeping predictions on the thermal field evolution (as shown in Valla et al., 2012 – EPSL).
- Line 230. Please cite Braun et al., 2012 there.
- Lines 238-241. There was a smoothing option in version 4.2 that was also in the same line, but less explicit as the new version. Maybe specify this earlier possibility?
- Line 249. The section 3.1.1 is nice and very interesting to read, however I still have some questions: what is the effect and motivation for using the Dz parameter? And how are interpolated the different topographic configurations in Pecube v4.3? Linearly or still with t parameter? See also my general comment on this
- Line 257. “erosion” or exhumation?
- Lines 259-261. Please provide references for the two equations.
- Line 262. “Ts surface temperature”. Maybe precise that this is user defined (also lapse rate) as illustrated in figure 5.
- Line 265. How is the surface heat flux calculated? Please clarify.
- Lines 270-273. What is the aim/motivation of allowing Hp to vary with depth? I agree this is a nice development but I think this needs to be better explained and linked to practical cases or questions from the literature.
- Line 279, Figure 6. “with three nodes”. Would it be possible to indicate the three nodes on the figure (right zoom panel)?
- Line 289. “dedicated tables”. Where are these tables, in specific files (Figure 2) or directly accessible in the graphical unit? Please clarify.
- Line 291. “grain-specific kinetic information”. Maybe replace “information” by “proxies” there?
- Line 293. “additional inofrmation”. Please specify which ones.
- Line 299. “to input kinetic parameter values”. Are these really kinetic parameters (i.e. D0 and Ea) or models/proxies? Please clarify. Also, is it possible to use different models for different grains, and what would be the motivation there?
- Line 306. “observed ages and uncertainties”. Are these Ft corrected or non-corrected data? Please clarify.
- Line 309. Maybe specify for readers that this example is taking literature data and DEM from Valla et al., 2012 – JGR (and DEM is zoom of figure 3).
- Line 316. “is to down-sample the input topography…”
- Line 318. “can affect the comparison between observed and modelled…”. Elevation comparison or also age comparison? Please clarify.
- Line 322, Figure 8. Panel c is interesting and shows that misfit can be individually calculated and illustrated for the different systems. I would suggest the authors to put one sentence on this in the main text.
Panels d-e-f are referring to the inverse modeling mode of Pecube, is it needed there or can this be only shown in the other paper on the NA approach (Bernard et al. in review)? See my general comment on this. If kept, panel e needs precision that the pdf is derived after the exploration stage, so different from the appraisal stage outputs…
- Lines 323-327. See my general comment on the inverse Pecube modeling, not sure this is relevant/needed in the present contribution knowing that another manuscript is specifically dedicated to this approach.
- Line 333. “spatial distribution of temperature at ta given depth”. Figure 9 is showing the end of the run right? Is it possible to also derive Temperature/Age maps for intermediate run steps?
- Line 334. “erosion rates” might be replaced by “exhumation rates” to be consistent with Figure 9.
- Line 334, Figure 9. What are the input parameters for the rock uplift and topographic changes during this run. Since the final exhumation rate and the output (AHe) ages will be the consequence of these inputs, I think this is important to report them in the caption.
- Line 343-344. “teaching”. Why teaching application? This can be also used as sensitivity analysis or else no?
- Line 354. AER can also be used for “age-elevation relationship”, maybe precise there for clarity.
- Line 353. “Dz = 1 km”. Please explain what is the motivation of this parameter and what this will model in the present application?
- Line 365. I agree with the results, but I am not sure about the modelling strategy there. There is an input topographic evolution, so the apparent exhumation rate (combining both rock uplift and topographic change) will of course be different from the input rock uplift, no? See my general comment on this point.
- Line 384. “at least 2-3 times higher than…”. Is this result depending on the AHe/AFT kinetic model? What if ages are re-run with different models, as this is a possibility in the new version? See also my general comment on this.
- Line 385. “Valla et al., 2010).”. Not in the current reference list, please check thanks .
- Line 390. Maybe add Shuster and Farley (2004) as reference there.
- Line 396. “while HeFTy modeling…”. Not thermal modelling was performed using the approach of Schildgen et al., 2010. Please correct.
- Line 402. “updated version of Pecube for the region of Sion”. Maybe add “v4.3” for clarity, and rephrase the study sites as I am not sure readers are all aware of the location of Sion in the Rhone valley nor in Switzerland.
- Line 418. This approach shown in figure 11c is really interesting, as this can (also for other thermochronometers) be used to a priori define sampling strategies (in line with first-order results from Valla et al., 2012 – EPSL). I would encourage the authors to further develop this point as would be of interest for readers I guess.
- Line 423, figure 11. What are the green boxes in panels a-b, is observed uncertainties why are they not centered with black circles and errors? Please clarify and correct if needed (green boxes need to be defined in caption or legend).
- Lines 426-428. Not sure this sentence about the use of trapped charge methods in paleodosimetry is relevant there. Maybe remove?
- Line 432. “ultra-low-temperature thermochronometers”. I am not sure about this definition, if below 100°C the AHe system is also part of these. Why not keeping low-Tc thermochrometers?
- Line 433. Maybe provide some references there for each system?
- Line 437. “beyond which additional signal accumulation cannot be recorded”. Please cite there Guralnik et al. (2013) – EPSL.
- Line 438. “to rapidly exhuming regions (>1 km.Myr-1)”. Please provide a reference there.
- Lines 443-447. I think it would be interesting to precise there that for trapped-charge methods there is potential to derive (from lab measurements) sample-specific kinetic parameters, which can then be input in Pecube.
Moreover, how about showing an example there as for the 4He/3He method? Based on the Wen et al., 2024’s study, there are available quartz ESR and feldspar IRSL data for the same samples as figure 11, would it be possible to run a forward model and show the expected outcomes/ age maps for these two systems (based on Wen et al., 2024)? I think this would be great for readers to see this ongoing development and possibility, no?
- Line 451. “modern radiation-damage models”. Maybe replace “modern” by “updated”.
- Line 453. “improvements to the implementation of thermal parameters”. I think this sentence is restrictive and not giving credit to all the developments in this new version (topographic changes, fault definition and visualization, etc.). Please provide more details on the different changes.
- Line 455. “for which previous diffusion models often proved inadequate”. Unclear sentence, and not specific to Pecube so I would encourage to remove or rephrase this sentence for clarity.
- Line 458. “cooling events”, maybe rephrase by “exhumation steps”?
- Line 471. No available link already for readers?
I hope these comments and suggestions may be useful for revising this manuscript, and I look forward to seeing this nice contribution published and available for the community.
Sincerely,
Pierre Valla
(Grenoble, 13 July 2026)