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Probe-Particle / ppafm

Classical force field model for simulating atomic force microscopy images.
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Adding a beter description for the Zenodo database of images #260

Closed ondrejkrejci closed 7 months ago

ondrejkrejci commented 7 months ago

I will write something for FePc (IETS) and STM @mondracek, could you do something also for the KPFM. Who could write, how the Fig. 2 was obtained?

NikoOinonen commented 7 months ago

how the Fig. 2 was obtained

What exactly do we want here? The description of the parameters is already in the paper, and the script is in the examples.

ondrejkrejci commented 7 months ago

how the Fig. 2 was obtained

What exactly do we want here? The description of the parameters is already in the paper, and the script is in the examples.

Just a description, what script you should run, to get the image. Thus just in the zenodo database, to say the what is the path to that script.

mondracek commented 7 months ago

Okay, I can do it. But I am a bit overwhelmed now so please remind on Monday (2024-02-12) if I'll not have done it by then.

ondrejkrejci commented 7 months ago

Sure, I am overwhelmed as well, I just wanted to remind myself too 😊. Thank you!

From: Martin Ondráček @.> Sent: Thursday, February 8, 2024 4:40 PM To: Probe-Particle/ppafm @.> Cc: Krejci Ondrej @.>; Author @.> Subject: Re: [Probe-Particle/ppafm] Adding a beter description for the Zenodo database of images (Issue #260)

Okay, I can do it. But I am a bit overwhelmed now so please remind on Monday (2024-02-12) if I'll not have done it by then.

— Reply to this email directly, view it on GitHubhttps://github.com/Probe-Particle/ppafm/issues/260#issuecomment-1934261526, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADFZAFN2XVTPQ43NVUSVN2DYSTPU5AVCNFSM6AAAAABC7WYJDWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZUGI3DCNJSGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

mondracek commented 7 months ago

To specify, I mean I can write about the KPFM figure, not so much Fig. 2. Probably @NikoOinonen is the best person to write about Fig. 2.

ondrejkrejci commented 7 months ago

[heart] Krejci Ondrej reacted to your message:

From: Martin Ondráček @.> Sent: Thursday, February 8, 2024 4:05:38 PM To: Probe-Particle/ppafm @.> Cc: Krejci Ondrej @.>; Author @.> Subject: Re: [Probe-Particle/ppafm] Adding a beter description for the Zenodo database of images (Issue #260)

To specify, I mean I can write about the KPFM figure, not so much Fig. 2. Probably @NikoOinonenhttps://github.com/NikoOinonen is the best person to write about Fig. 2.

— Reply to this email directly, view it on GitHubhttps://github.com/Probe-Particle/ppafm/issues/260#issuecomment-1934446064, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADFZAFISNHFJDJIESFMMWA3YSTZVFAVCNFSM6AAAAABC7WYJDWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZUGQ2DMMBWGQ. You are receiving this because you authored the thread.Message ID: @.***>

NikoOinonen commented 7 months ago

Probably @NikoOinonen is the best person to write about Fig. 2.

Yes, I can do this.

ondrejkrejci commented 7 months ago

This is what I came up with fo my part:

The STM (dI/dV) maps shown at Figure 4 (b,c,) of the paper/manuscript could be obtain after download of the PPSTM code (https://github.com/Probe-Particle/PPSTM) and proper compilation. After that navigate to tests/PTCDA_mol and use the run_all.sh script. The IETS image shown at Figure 5 (b) can be obtained by downloading the PPAFM code and navigation to examples/FePc_Au-IETS and running the run_ppafm-iets.sh script. The IETS image can be found in the Q0.00K0.24 folder.

mondracek commented 7 months ago

@ondrejkrejci , how can I access the Zenodo database?

ondrejkrejci commented 7 months ago

I think that @Oinonen @.***> is taking care of that. I have sent him the description of my part.

Sent from Outlook for Androidhttps://aka.ms/AAb9ysg

From: Martin Ondráček @.> Sent: Monday, February 12, 2024 7:48:03 PM To: Probe-Particle/ppafm @.> Cc: Krejci Ondrej @.>; Mention @.> Subject: Re: [Probe-Particle/ppafm] Adding a beter description for the Zenodo database of images (Issue #260)

@ondrejkrejcihttps://github.com/ondrejkrejci , how can I access the Zenodo database?

— Reply to this email directly, view it on GitHubhttps://github.com/Probe-Particle/ppafm/issues/260#issuecomment-1939232663, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADFZAFM7K6GUYXKWJAEG3RDYTJIVHAVCNFSM6AAAAABC7WYJDWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZZGIZTENRWGM. You are receiving this because you were mentioned.Message ID: @.***>

ondrejkrejci commented 7 months ago

By the way @NikoOinonen once you will be changing the description at the zenodo please temporarily change the "paper" to the manuscript. We can also put there the arXiv citation: arXiv:2401.14564. And there is also wrongly speled Angstrom, but that is a very minor issue :-) .

NikoOinonen commented 7 months ago

@mondracek If you can provide the KPFM description, then I can do the update.

mondracek commented 7 months ago

@NikoOinonen , I would follow @ondrejkrejci 's template, if you don't mind, something like this:

The LCPD and AFM maps shown at Figure 3 (a,b) of the manuscript could be obtained with the PPSTM code (https://github.com/Probe-Particle/PPSTM). After download and installation, navigate to the examples/FFPB_KPFM/ folder and download the archive file KPFM_hartree.tar.gz (https://zenodo.org/records/10563098/files/KPFM_hartree.tar.gz?download=1) to this folder. Expand it to get the LOCPOT_V0.xsf and LOCPOT_Vz.xsf files and then run the script ./run.sh After running the scipt, the LCPD map of Figure 3(a) can be found in examples/FFPB_KPFM/LCPD_atoms_cbar_018.png and the AFM map of Figure 3(b) in examples/FFPB_KPFM/Q-0.10K0.25V0.00/Amp0.50/df_atoms_cbar_018.png

NikoOinonen commented 7 months ago

So all together, I would put there something like this:

Reproducing the figures in the manuscript:

  • Fig. 2 (comparison of force-field models): Install ppafm with the [opencl] option, and run the example script in the ppafm repository at examples/paper_figure/run_simulation.py. The image is saved into the same folder with the script.
  • Fig. 3 (KPFM LCPD map): Install ppafm, navigate to examples/FFPB_KPFM, and run the script ./run.sh. After running the script, the LCPD map of Fig. 3(a) can be found in LCPD_atoms_cbar_018.png and the AFM map of Fig. 3(b) in Q-0.10K0.25V0.00/Amp0.50/df_atoms_cbar_018.png.
  • Fig. 4 (STM dI/dV map): Download and compile the PPSTM code (https://github.com/Probe-Particle/PPSTM). After that navigate to tests/PTCDA_mol and use the run_all.sh script.
  • Fig. 5 (IETS): Install ppafm, navigate to examples/FePc_Au-IETS, and run the script run_ppafm-iets.sh. The IETS image can be found in the Q0.00K0.24 folder.

The ppafm version 0.3.1 was used when producing the images for the manuscript.

Are we happy with this?

@mondracek I removed the thing about downloading the data, since the run.sh script already seems to do that automatically.

@ondrejkrejci Maybe we should add also some version/commit number for the PPSTM code, to ensure reproducibility?

ondrejkrejci commented 7 months ago

@NikoOinonen - agreed from my side.

The PPSTM version is this one: https://doi.org/10.5281/zenodo.10669867 (it is named v1.0.2), which is an ooold mistake of mine, when I did not understand naming.

NikoOinonen commented 7 months ago

I updated the Zenodo description and added a reference to the arXiv preprint there: https://zenodo.org/records/10563098

ondrejkrejci commented 7 months ago

@NikoOinonen - thank you. I think that we can close this issue, until the paper is published.

We can update the description, based on (hopefull) publishing and maybe on referees comment.

Thank you all for working on it!