Comments to documentation

[jfaraudo]

Comments to the documentation

[jfaraudo]

In general, the documentation is clear and covers all relevant aspects. I have only two minor comments:

• For me, the flowchart in the section "Essential information (See before you start)" athttps://sntioudis.github.io/papreca/md_essentials.html is a bit confusing. I agree that all the information is correct. But at a first look , for an expert in MD like me, it looks pretty strange to see, in the MD part, the sequence of minimization - MD run - and minimization again, because it is pretty unusual in the MD community. I understood that flow when looking at your paper Computational Materials Science, vol. 229, 2023. The flow in Figure 1 of that paper is much clear to me. It is essentially the same, but it contains a schematic with a PES and the exploration over the PES implied by these steps. This makes it more clear to me. Also, the general organization of the flowchart is better. I suggest considering an update of this flowchart recycling elements of (or based on) that previous figure.
• I do not understand the reason of the comment about LJ units in the section "PAPRECA units". I agree that there is no simple way of converting LJ units to real time, that's clear. But imagine that we select LJ units in LAMMPS. Then, if PAPRECA is also working in LJ units (if I understand correctly, PAPRECA uses the same units as LAMMPS), why not providing the time of MC, MD and total time in LJ units (no need of conversion to seconds)?

[sntioudis]

For me, the flowchart in the section "Essential information (See before you start)" athttps://sntioudis.github.io/papreca/md_essentials.html is a bit confusing. I agree that all the information is correct. But at a first look , for an expert in MD like me, it looks pretty strange to see, in the MD part, the sequence of minimization - MD run - and minimization again, because it is pretty unusual in the MD community. I understood that flow when looking at your paper Computational Materials Science, vol. 229, 2023. The flow in Figure 1 of that paper is much clear to me. It is essentially the same, but it contains a schematic with a PES and the exploration over the PES implied by these steps. This makes it more clear to me. Also, the general organization of the flowchart is better. I suggest considering an update of this flowchart recycling elements of (or based on) that previous figure.

Fair point. I will make the flowchart a bit more detailed.

I do not understand the reason of the comment about LJ units in the section "PAPRECA units". I agree that there is no simple way of converting LJ units to real time, that's clear. But imagine that we select LJ units in LAMMPS. Then, if PAPRECA is also working in LJ units (if I understand correctly, PAPRECA uses the same units as LAMMPS), why not providing the time of MC, MD and total time in LJ units (no need of conversion to seconds)?

I should have mentioned that explicitly in the documentation and thank you for spotting that. All kMC units (i.e., length, velocity, energy, etc.) are consistent with LAMMPS, however, under the hood, PAPRECA uses seconds for the time/frequency units for the predefined events. This was done to facilitate the passing of intuitive rate values from the PAPRECA input file to PAPRECA (using the rate_arrhenius, rate_hertz, rate_manual options in the create_BondBreak, create_BondForm, create_Deposition, create_DiffusionHop, and create_MonoatomicDesorption commands). This is effectively why I mention this in the documentation:

Note that PAPRECA will always report time in seconds on the terminal and in any exported file (e.g., heightVtime.log or execTimes.log).

Ultimately, exporting time values in LJ units would require the calculation of effective LJ parameters (if the system contains more than one atom), but I am not sure that it would lead to easily-interpretable and intuitive time values.

I will rephrase the above so it becomes clearer and I could possibly create an LJ units converter in a future release of PAPRECA.

[jfaraudo]

All of this sounds good to me. I do not think that the "LJ community" (so to speak) is really working a lot on kMC these days. So I think it is not a big priority to implement a LJ units converter. But I think it is worth explaining in more detail that PAPRECA uses "real" units so all other LAMMPS units options are handled by internal conversion to "real" at PAPRECA.

[sntioudis]

1) I updated the general PAPRECA flowchart in the Essentials section. I realized that the General flowchart in the documentation with the two minimization steps (i.e., one before and one after executing the MD trajectory) was referring to the phosphates examples (and to our [previous paper]). PAPRECA is a more general software, in the sense that the user has complete freedom over the MD simulation options. For example, someone might choose to perform only one minimization (i.e., before the MD trajectory), or none (as exhibited in some of the examples). Therefore, I removed the specific steps and the flowchart now depicts a general MD stage (without further description).

2) A more detailed discussion regarding the units of PAPRECA is now in the essentials section.

[jfaraudo]

sounds perfect to me