Potku, version history with update notes
Major previous updates and milestones
20.12.2022 News
No public release version for the next update yet. There will be major restrucuturing of the configuration files, hence, old and new versions will not be compatible (eg. if old project is opened with new version, old version cannot open it anymore). We will push i) energy detector, ii) MCERD simulations of SCT and ERD elements in the same process and iii) restructurign of the configuraion file-updates to same release (which all would brake the old-new usability otherwise). Also speed enhancements and modification+copying+changing of the cut/selection files, simulated energy output data for the MCERD.. etc.. During 2023. One can also ask experimental version earlier if required.
31.3.2022 Mac and windows versions
New release of both Mac and Windows versions dated 2022-03-31 can be found from here.
Note: Window 10 and new MacOs warns about these programs (without the authentication "stamp"), as "do you want to still Run this program (Potku.exe)".
This update has made lot of internal upgrades but now also offers
- plotting and storing the sum of the individual energy spectra in the slab analysis as well as sin the MCERD
- faster automated (linear) optimization available in the MCERD. This is test version, but can already be used. The previous, still existing NSGA-II (evolutionary multiparameter code) was way too slow for the purpose.
- Usability features for the MCERD side, including:
** Target composition is now directly exported to the recoil atom distribution and modifications of target atom composition are now taken into account
** Yellow indicators for individual recoils/scatter atoms if non-default values are activated by the user
** User can delete all recoil atom distributions at the same time
Something coming soon, work already in progress:
- Improved speed for the slab analysis cut files saving and while doing the selection
- Possibility to import single cut file to the ToF-E historgram
- Possibility to modify the selections, by dragging the points of the cut
- Important one: automated calculation of the "Reference density", for the MCERD, side (this value affects the depth scale, together with the density and composition of the target),
- Python version upgrade from 3.6 to 3.10(or 11)
7.9.2021 Mac and windows versions
New release of both Mac and Windows versions dated 2021-09-07 can be found from here.
Also the "ToDo" list is updated in the same folder (partially it's for internal usage, but if there's interes one can look it through).
11.8.2021 quick fix
Quick bug fix for MCERD side where software crashed when recoil atom distribution was changed while the energy spectra window was open (now it again auto-updates the plot when moving the circles). Here.
27.7.2021 Lots of minor improvements, bug correction and user friendliness improvements
During the spring and summer 2021, two MSc workers from physics and IT departments have been updating the code. Short list of update notes can be found from here. These include: Sum spectra for different ion energies, automated export of sample concentration to recoil atom distribution, warnings if multiple same element cut files is selected while plotting depth distribution, ToF calibration can be updated afterwards, working loading of detector settings (so room of improvement still exist however), possibility to use zero foil thicknesses (eg for timing foil 2 and E detector) to speed up the MCERD calculation and possibility to plot the efficiency files.
15.2.2021 Correction to the tools tab in the depth profiles -window
13.12.2020 Update for slab analysis side: sample specific settings now work
25.8.2020 Update for slab analysis side where RBS elements didnt work well in cut files
3.7.2020: New, most stable and reliable version released after 6 month dedication to debugging only.
(yet, mac version still has startup issues, and there were nasty refactoring related bug reported 25.8.2020)
- Efficiency file handling: The biggest change to slab analysis side will be that the isotope cut files need to have isotope specific efficiency files eg. 1H, 2H, 16O cut files need to have 1H.eff, 2H.eff and 16O.eff files and the elemental cut files H, O, need to have elemental efficiency files in the future like H.eff and O.eff. No other filename -types are anymore accepted. (Note: in previous versions there were troubles for example in 16O.eff handling and other heavier than H efficiency files.)
- Efficiency file handling: When plotting energy spectra on the slab analysis side (also in the MCERD), experimental data can be selected to be corrected with efficiency files. This was not the case in reality before.
- Many additions to the general parameters.
- Many changes to the MCERD side, so that features which were seemingly present before, now actually works. Also many user friendly features are now more user friendly than never before (like showing the simulation progresses).
- Plenty of more info printed on the console window, helping for debugging/reporting and following the process.
- MCERD uses the Jibal library (https://github.com/JYU-IBA/jibal). The library provides stopping forces, straggling models, cross sections and various atomic data e.g. atomic masses and abundances. This replaces hard coded ZBL stopping model from MCERD and will also replace the GSTO (Generic STOpping) library used by the slab analysis side soon.
- Multiple pieces of code refactored "under the hood" to support upcoming browser-based Potku with open access ans sharing features.
- In request settings, saving of the settings is possible (with "arbitrary" naming unfortunately). Will be developed more in future. However, In the 01072020 versions, the save in the "profile" tab crashes the Potku, this is corrected in later versions already.
However, user can still do wrong if for example the efficiency file is not named correctly, meaning file name has spaces or other features than element of isotope characters (H1.eff, H2.eff, 16O.eff or H.eff or O.eff), or for example user tries to do depth profiles from "H" + "1H" + "2H" isotopes _at the same time_. Here, result would be that H and H1 concentration would be summed up as to 1H, with correct efficiency's, and 2H would be ok with correct efficiency -> this is due to 'user' error, but we'll work to prevent these also. Automated fitting tool in MCERD-side is still to be developed more user friendly and still has some bugs.
As for today Windows, Mac and Linux versions are provided here, but the development is still fast. Further updates/versions will come at least for 5 more years. MacOS app-version has currently no console window unfortunately, but starts "easier" from icon.
Spring and summer 2021: Lot's of minor improvements and corrected bugs. Improvement of user friendliness on many parts. Biggest contributors Aleksi Kauppi together with Joonas Koponen.
Summer 2020: Version with most of the bugs corrected, in both MCERD and slab analysis side. Biggest contributor and bug fixer Juhani Sundell.
Summer 2019: Automated fitting algorithm to MCERD side. Biggest contributor Heta Rekilä
End of the year 2018: First stable MCERD release with work also on isotope issues at efficiency at slab analysis side. Biggest contributor Heta Rekilä.
Summer 2018: First MCERD version after the student software project "Monisiro".
2013-2018: Different minor bug fixes here and there.
Autumn 2013: First version of Potku publicly released after student software project "Potku". Biggest contributors Timo Konu and Jaakko Julin.
More detailed info about updates
3.7.2020: New, most stable and reliable version released after 6 month dedication to debugging only.
- Efficiency file handling: The biggest change to slab analysis side will be that the isotope cut files need to have isotope specific efficiency files eg. 1H, 2H, 16O cut files need to have 1H.eff, 2H.eff and 16O.eff files and the elemental cut files H, O, need to have elemental efficiency files in the future like H.eff and O.eff. No other filename -types are anymore accepted. (Note: in previous versions there were troubles for example in 16O.eff handling and other heavier than H efficiency files.)
- Efficiency file handling: When plotting energy spectra on the slab analysis side (also in the MCERD), experimental data can be selected to be corrected with efficiency files. This was not the case in reality before.
- Many additions to the general parameters.
- Many changes to the MCERD side, so that features which were seemingly present before, now actually works. Also many user friendly features are now more user friendly than never before (like showing the simulation progresses).
- Plenty of more info printed on the console window, helping for debugging/reporting and following the process.
- MCERD uses the Jibal library (https://github.com/JYU-IBA/jibal). The library provides stopping forces, straggling models, cross sections and various atomic data e.g. atomic masses and abundances. This replaces hard coded ZBL stopping model from MCERD and will also replace the GSTO (Generic STOpping) library used by the slab analysis side soon.
- Multiple pieces of code refactored "under the hood" to support upcoming browser-based Potku with open access ans sharing features.
2020 April (10.4.2020) update! From the beginning of 2020 we have had a IT student Juhani Sundell hunting for the multiple bugs and making more permanent fixes to the code. Now the isotope efficiency related bug(s) is corrected and the MCERD side seems to work quite fluently. Also, the simulated energy spectra are now updating instantly when one changes the recoil distribution and the foil-related mismatch between slab-analysis and MCERD side is one of the corrected issues.
However, user can still do wrong if for example the efficiency file is not named correctly, meaning file name has spaces or special characters (H1.eff, H2.eff are default names but H1_Jan_2017.eff -type format works also), or for example user tries to do depth profiles from "H" + "1H" + "2H" isotopes _at the same time_. Here, result would be that H and H1 concentration would be summed up as to 1H, with correct efficiency's, and 2H would be ok with correct efficiency -> this is due to user error, but we'll work to prevent these also. Automated fitting tool in MCERD-side is still to be developed more user friendly and still has some bugs.
As for today Windows and Mac versions are provided here, but the development is still progressing fast. So please be patient to wait for further updates/versions.
ALSO: After the summer 2020, one can expect new ePotku, the www-browser/server based version of the desktop Potku, where your analysis stay on the the secure server, and you can continue your analysis from anywhere, including continue your offline analysis, after uploading the date to your own secure folder. One can also share the data and analysis to your own research group, and beyond if needed. In addition to normal private sharing ePotku will in the future provide Open Access platform to your Open Data. So this update is also currently developed, on the parallel track with the desktop version.
2019 Summer update (Masters thesis by Heta Rekilä): in a new Potku version is included automatic fitting option for the MCERD. This is preliminary code for testing. This option enables simulated composition curve to be matched automatically with the experimentally measured data. Here are still some limitations, like the sample profile cannot be arbitrary, but the fitting will search two possible outcomes, which might represent tow possibilities, e.g. "thicker film with lower concentration" or "thinner film with higher concentration" - from which the user can decide/continue if necessary (see image). Also multiple bugs have been corrected during the recent update process.
2018 December UPDATE: New versions have been released with multiple bugs corrected. Now the original measured data analysis side works better, with isotope efficiencies included. Also a bug related to carbon foil handling is corrected, and the setup/running the Potku should work better.
2018 September UPDATE: Potku 2.0 with integrated MCERD is now launched. Currently windows, mac and linux users have versions where no installation is needed. The overview for the Potku 2.0 properties and how to do the analysis can be found from the slides originally presented in the CAARI 2018 conference by Mikko Laitinen
Other Comments of the versions:
Potku 2.0 - 10th of April 2020
- Downloads for Windows (7-10), Mac (High Sierra) are here.
- No installation is needed
- Mac version need to be started from the command line, not from the icon.
Tcl/Tk-software is needed on Mac (should be installed as default). Mac version runs through the terminal by running a command "./potku" in potku folder.. - Linux and other users can found the Potku from the github, but take the "external files" from the win/mac packages.
- Corrected bugs - and need to know 'bugs" or "features":
- Efficiency files for multiple isotopes should now work from now on (the issue earlier was related to so called "external files" which were not updated at the summer 2019 version vs December 2018).
- User can still do wrong if for example the efficiency file is not named correctly (has spaces or special characters -> H1.eff, H2.eff as default but H1_Jan_2017.eff -type format works also), or for example user tries to do depth profiles from "H" , "1H" and "2H" isotopes _at the same time_. Here result would be H and H1 concentration would be summed up as to 1H, with correct efficiency's, and 2H would be ok with correct efficiency -> this is due to user error, but we'll work to prevent these also.
- Earlier if user changed the efficiency files multiple times during the analysis, the new additions did not register properly without restart. Now they do work and user can change, test, multiple efficiency corrections fast in a single analysis.
- If one used zoom in the depth profiles to draw selection limits (blue vertical lines), the window unzoomed. Now this is fixed for depth profiles, will be fixed elsewhere also.
- Might be still an issue: Long filenames/long chain of folders might cause troubles to 'gsto' and 'stopping' C-codes still. (possible if total folder path of the working files is longer than 256 or so characters..)
- "Open Recent requests" - option is now in the file-tab, which can be used when starting potku and looking for previously opened requests.
- MCERD: there were a critical mismatch of the first timing foil handling when using the MCERD wand compared the data with slab analysis energy. For the energy spectra, the slab-analysis side _adds_ by default the energy loss to the energy which is actually detected between timing gates(ToF) -> this output then matches to the original energy from the sample. However, before the fix, MCERD used this slab-analysis output energy for it's own comparisons, resulting that front edge of scattered ion energy with thick T1 foil resulted: slab analysis got very high original energy from the sample, MCERD (as detector energy) resulted very low energy. Now the slab analysis energy, the measured-one, is brought to the MCERD-side without the energy loss-addition in the T1. Now both programs compare the ToF(energy) that is seen (eg. recorded vs simulated) by the difference of timing signals of two timing gates.
- MCERD: when one adds processing units, the MCERD now divides the original "number of events" to be simulated with this number, to each of the core. Eg simulated ions + presimulation = 1 000 000 + 100 000 and if one uses 4 cores, each core currently calculates 250 000 + 25 000. (previously this was 4x 1 000 000 + 4x 100 00, which wasn't speeding up anything.) HOWEVER: presimulation minimum number should not be much smaller than 10 000 at least, this is now user to be seen (in the console) but we'll work automation for this too.
- MCERD: one can now select some of the elements "OFF" from the "calculate percentages", to reject uncertainty tests or so ending to the total concentration.
- MCERD: No new graph is needed if the recoil distribution is changed, the energy graph updates in about 0.3 seconds after the spheres/dots are changed in the recoil distribution.
- MCERD: there's a bug that crashes the potku, in the recoil
atom distribution, if opening the menu from where element's name or color can be changed, and in one presses "OK" potku will crash (see pic). (is already fixed at the github source code).
- Optimization results can now be transferred to recoil distribution, but this is work in progress as, one needs to restart that those _really_ appear there. Also the optimization starts the MCERD still even if there's correct amount of MCERD events.. will be fixed too..
- In the sample data-folder, example_efficiency_files.zip, the 2H.eff file "X-column" had turned to date-format for energies above 1 MeV. This is now corrected for sample data. NOTE it needs to be checked that windows tab-delimited MeV, efficiency - columns work on the mac, where space delimited columns are often used.. this applies to unix users also. Tab ad space delimited versions are provided for test.
Potku 2.0 - 28th of May 2019
- Downloads for Windows (7-10), Mac (High Sierra), Linux (Ubuntu, at least) are here.
- No installation is needed
- Mac version might need to be started from the command line, not from the icon.
- Corrected bugs - and need to know 'bugs" or "features":
- Many December 2018 minor bugs -corrected, some most likely still exists...
- the MCERD automatic fitting tool does not use old MCERD generated files but currently generates it's own versions. Also multicore option seems not to be working so well when doing the automatic fitting (but manual version seems working ok).
- Might be still an issue: Long filenames/long chain of folders might cause troubles to 'gsto' and 'stopping' C-codes still. (possible if longer than 256 or so characters..)
Potku 2.0 - 21st of December 2018
- Bug corrected downloads for Windows (7-10), Mac (High Sierra ++), Linux (Ubuntu, at least) are here.
- No installation is needed, old Potku versions are not affected. (was due to same named .ini file, previously)
- Mac version might need to be started from the command line, not from the icon.
- Example efficiency files are also provided, mac versions filename extension might need to be changed a bit.
- Corrected bugs - and need to know 'bugs' and features:
- potku.ini file is now potku2.ini file - previous users of 2013 version of potku had difficulties starting the new potku previously.
- Carbon foil handling was messed in the previous Potku 2 release (nm was given but ug/cm2 was used in the old code). Now only nm and g/cm3 units are requested from the user.
- Timing foil can only deal single foil layer, and it is dealt as carbon (by erd_depth.exe). this apply to the measurement side of the Potku. For MCERD side, multiple layers in timing foil(s) should be handeld ok. This affected to the ToF-calibration as well as depth profile calculations
- Isotopes can now have independent efficiencies corrected. eg. 1H.eff for Hydrogen and 2H.eff for Deuterium.
- Multiple minor bugs
Potku 2.0 - 1st of September 2018
- Downloads for Windows (7-10), Mac (High Sierra), Linux (Ubuntu, at least) are here.
- No installation is needed, old Potku versions are not affected.
- NOTE (10.10.2018) at least for some mac + windows 7-8 (10 seems to work) users, there exists some file / folder problems, and potku will not either start or crashes if pressing new/load request.
- Example data -folder for Potku 2.0: a sample Request is here.
- Guide / presentation for the usage of MCERD and Potku 2.0 is here.
2016 December:
- 64 bit Windows (Win 7, Win 10, most likely also Win 8) installation of Python libraries working with potku are provided. Also 32 bit (python) windows version(s) are provided. Downloads and installation guides from here.
- 64 bit Potku 1.1 for Windows
- 32 bit Potku 1.0 for Windows
Install notes for Potku version 2014-2015
- Mac OS X 10.6 or later (tested on 10.6 and 10.7), Relatively modern Linux (tested on Arch), Windows XP or later (testing platforms are Windows 7 and 8)
- Python 3.3
- Numpy 1.7
- SciPy 0.12
- MatplotLib 1.2
- PyQt 4.8 (or later)
- "awk.exe" for data import (gawk-3.1.6-1-setup.exe) (needs PATH for windows)
- Plenty of memory and hard drive space
Many of the Python packages for Windows are available here.
For development
- C compiler (gcc), make and other essential C development tools, provided by MinGW on Windows
Reported and / or corrected Bugs:
Version 2.0 (1st of September 2018)
- In MCERD-simulation side, there are few places in the request settings, if changes are made, the current simulation parameters are zeroed (user is notified) even when there's no need for re-simulations.
- Binning has a bug in a MCERD side when simulated and experimental spectra are compared.
- Other bugs and limitations are listed in the "TODO" file at the file downloads.
Version 1.1 (December 2016)
- PyQT related issues fixed for the tool icons, labels
- AWK.exe file included from the gawk package to potku files directly (no need to instal gawk separalety)
- Currently known bugs and TODO and "need to check" -list here
version 0.8.2
- ....
version 0.8.1
- Depth profiling uses previous settings, i.e. has to be run always twice. (Fixed 2013-09-26)
- Stopping in carbon foil is neglected in depth profiling code. (Fixed 2013-11-15)
- Choice of stopping model in general settings has no effect (Removed option 2013-11-19, use stoppings.txt instead)
- Number of depth steps fixed to 100. (User option added 2013-11-21)
version 0.8
- SRIM stopping generator in gsto doesn't work (Fixed 2013-09-13)
- Efficiencies only work on Windows platform (Fixed 2013-09-16)
Old Version history
2019-05-28
Automatic fitting tool added to MCERD.
2018-12-21
Multiple bugs corrected for Potku 2.0
2018-09-01
Potku 2.0, first public release of the new potku with integrated MCERD
2016-11-29
Potku 1.1 - Windows installers provided, minor bugfixes relating to PyQT
2013-12-03
Bugfix release, v.0.8.2
2013-09-11
First public release, v0.8