Documentation - pdf manual

[MichalTra]

Dear Raspa developers,

thank you very much for the great work you are doing! I have a few questions and suggestions related to the documentation of your project.

1) I was not able to find the raspa.pdf manual in the current github repository. The newest version I was able to find is from numat / RASPA2 and it is from 27th January 2020. All my notes will be with respect to that version. It would be nice if the raspa.pdf file is added to the Docs directory.

2) In section 1.2 Units and conventions would be desirable to briefly mention the minimum image convention, as it has a consequences for the size of simulation cell. (Example 6 is dealing with minimum image convention, but prior to that example, there is no sign of cell-size limitations)

3) In section 2.1 a zframework.def file is mentioned. However, I was not able to find any example of such file. It is evident that it would be similar to the molecule.def file, but some differences must be present (e.g., no critical constants).

4) During the study of Examples, I have found some settings not mentioned in the 2.2 Simulation input section: ComputeNumberOfMoleculesHistogram WriteNumberOfMoleculesHistogramEvery NumberOfMoleculesHistogramSize NumberOfMoleculesRange ProbabilityCFCRXMCLambdaChangeMove (and the related setting for Components)

5) In Non-basic example 1 I believe I found an error. Component 1 should have IdentityChangesList 1 0 instead of 0 1

6) In Non-basic example 3, I was confused how the box was filled with water molecules, even though the CreateNumberOfMolecules is 0. Some explanation may be desirable (at least for users like me).

7) Is Raspa using IdealGasRosenbluthWeight and IdealRosenbluthValue (Basic Example 7)? Is there any difference between these two?

I do apologize for this long list of comments and questions. I am sending it in hope that such notes may help make the manual more clear for users.

Thank you and have a nice day! Michal T.

[ltalirz]

Hi @MichalTra , thanks for reporting these issues.

You can always compile a pdf of the most recent documentation using pdflatex on this file https://github.com/iRASPA/RASPA2/blob/master/Docs/raspa.tex

However, I notice that a recent pdf is also available from https://iraspa.org/raspa/ This should really be documented in this github repository - I will make a pull request

Would you mind checking whether the points you raised still apply?

[MichalTra]

Hello Italirz,

thank you very much for your kind response.

I have checked the pdf on https://iraspa.org/raspa/ from 11th January 2021 and it seems that points 2, 4, 5 (also affects the related example file) and 7 still apply.

[ltalirz]

Thanks! Perhaps @dubbelda will find the time to go through those when the next updates to the docs are due

[dubbelda]

@MichalTra Thanks for the comments! 1) pdf added. 2) Minimum-image convention is a simulation aspect, which is discussed in many classical simulation books. RASPA is not a replacement for users knowing about these details. 3) In Advanced example, Example 2: Benzene diffusion in flexible IRMOF-10, the framework.def is explained. Other examples can be found in the 'framework'-directory in RASPA. 4) These are now added to the manual. 5) NumberOfIdentityChanges lists the number of changes, IdentityChangesList lists the ids of the component. So with 2 changes, 0 1 for component 0 means that it can change its identity to 0 (a molecule of the current type) or 1. There is no harm in changing a molecule into its own type, which is also more or less a partial-reinsertion. 6) It uses "RestartFile yes" to to read from a restart-file containing the positions. 7) 'IdealRosenbluthValue' is wrong (fixed in the new docs), it should be 'IdealGasRosenbluthWeight'