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In case of a segmentation fault, run it under a debugger (like gdb, or lldb) to figure out at which line in the code it crashes. That can help to pinpoint what the problem might be.

About modeling flexibility, different types of flexibility requires different treatments. So it depends on the situation. For flexibility around equilibrium positions simple atom-displacements might suffice. For large scale movements you will need to use MC/MD-hybride moves since it is collective motion on longer time scales.

Yes, add the cation as 'Adsorbates' but just do not use these in defined reactions.

What is a 'fluctuating state'?

TranslationProbability, RotationProbability, ReinsertionProbability are input parameters, not output parameters. So, you decide these.

Note sure,  but could be that the crash damage the restart-file. This could happen when the crash happens at the exact time the binary-restart-file is written to disk.

For running multiple simulations, you would use/create scripts that generate the needed input.
MOF simulations time depend on the size of the system, and how accurate you need the results.
Small systems, about a day. Larger system, a week or longer.

For a detailed explanation see:
https://homepage.tudelft.nl/v9k6y/thesis-Rahbari.pdf
Page 262 and following, and see Table  A5.

No, the data is inherently pixel-based. Exporting to pdf would just put a picture in a pdf.

This workshop/school focused on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we were also considering the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online. Due to privacy reasons, there will be no video recordings. Registration is free but compulsory. Certificates of attendance will be made available after the workshop.
We are also planning offline workshops in 2023 (November, Abu Dhabi) and 2024 (September, The Netherlands).

https://iraspa.org/workshops/iraspa-raspa-online-workshop-2023/

These value come from: https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00092/suppl_file/ct7b00092_si_001.pdf
and to reduce under/overflow you input them as the log of these numbers in Table S3.

Yes, for that very reason it saves in the tiff-file format. iRASPA uses RGBA-colors. You will need to change the background color and set the opacity to zero.

Yes, the atom colors can be changed, see the help/manual.

That depends on the VTK-version. But VTK-file plotting is now included in iRASPA, provided you have written the VTK with the latest version of RASPA.

Based on a Peng-Robinson equation of state it calculates the phase and density of the pure fluid (without framework). This density is used to calculate the excess adsorption.

You can select whether an atom is visible or not (checkbox).

The bond-distance criteria is a standard one. This is not yet easily changeable.

I would suggest to talk to experimental people and ask why their data goes up.
I expect this is due to adsorption at the external surface. You would expect that the results for adsorption should level off to a saturation value.

There are no standard methods. By making choices you need to create a structure with no symmetry (P1) so that all atom positions are defined.

Instead of a Box use a Framework.