RxMC ensemble

[Mohammad Ahmadi]

Dear Dr. Dubbeldam
I want to simulate a reaction in bulk phase and pore phase with Raspa software
To perform the reaction in the form of bulk phase, I have used the reaction simulation code available in the tutorial in the Raspa examples folder.
How can I change this code to simulate the reaction as a pore phase?

[David Dubbeldam]

Instead of a Box use a Framework.

[Mohammad Ahmadi]

Thank you for your answer;
But when I use this method, the software does not create output folders

[LeoAdams]

Dear Dr. Dubbeldam
I want to simulate a reaction in bulk phase and pore phase with Raspa software
To perform the reaction in the form of bulk phase, I have used the reaction simulation code available in the tutorial in the Raspa examples folder.
How can I change this code to simulate the reaction as a pore phase?

To simulate a reaction in a pore phase using Raspa, you need to modify the input file to specify the pore geometry, adsorbate and host material properties, and reaction conditions. Specifically, you need to define the pore geometry in the "framework" section, specify the adsorbate molecule and initial positions in the "molecule" section, set the "framework" and "frameworktype" keywords in the "simulation" section, and specify the pore volume in the "reaction" section. Once you have defined the input file, you can run the simulation using the Raspa executable.

[Mohammad Ahmadi]

We want to simulate a reaction on LTA4A zeolite with sodium as extra cation with RxMC ensemble in Raspa code.
When we add sodium as an extra cation to the simulation code, Raspa shows an error saying that extra cation cannot be used in this ensemble.
To solve this problem, we introduce 96 sodium atoms into the framework along with other reactants including 120 carbon dioxide atoms and 30 hydrogen sulfide atoms, and we have set the sodium stoichiometric coefficient to zero.
At the end, the results were obtained which have a fluctuating state, for example. Is it correct to enter sodium as mentioned? And can the reason for fluctuating results be related to this issue?
Since we are going to investigate the reaction in different ratios of carbon dioxide to hydrogen sulfide, how should we determine the number of atoms we want to enter into the framework? And can the number of atoms or the size of the unit cell cause the results to fluctuate?
And as the last question, how can the values of TranslationProbability, RotationProbability, ReinsertionProbability be calculated?

[David Dubbeldam]

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.

[Mohammad Ahmadi]

The meaning of fluctuating behavior is that, for example, in a temperature range, the results obtained from the conversion behave like a sine function and do not have a specific trend, sometimes they increase and sometimes decrease.

[Mohammad Ahmadi]

I mean the sentence "how can the values of TranslationProbability, RotationProbability, ReinsertionProbability be calculated?"
  That is, is there a formula to calculate these values or do they have to be guessed؟

[dubbelda]

They are input, you set these. These probabilities are relative to each other, and they do not influence the accuracy of the computation, just the efficiency.