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#41
General / Re: How the partition function...
Last post by David Dubbeldam - June 13, 2023, 12:50:29 PMPartition functions are not part of RASPA but are input. So you will need to compute them. There are many different ways of doing that, and they do differ in results.
For some pointers:
https://homepage.tudelft.nl/v9k6y/thesis-Rahbari.pdf
Page 262 and following, and see Table A5.
For some pointers:
https://homepage.tudelft.nl/v9k6y/thesis-Rahbari.pdf
Page 262 and following, and see Table A5.
#42
General / Re: Problem with pressure calc...
Last post by David Dubbeldam - June 13, 2023, 12:47:02 PMPressure is not well-defined if you use a fixed framework. Even for a flexible framework, keep in mind that for solids pressures are in the orders of Gpa for a small structural difference and hence pressure for solids fluctuate a lot more than liquids, which fluctuate more than gases.
#43
General / Re: GCMC vs MCNPT
Last post by David Dubbeldam - June 13, 2023, 12:45:10 PMIt is always a good idea to check you solution for consistency and whether the result is correct.
So yes, in general you would take at least two different approaches to confirm you get the correct values.
So yes, in general you would take at least two different approaches to confirm you get the correct values.
#44
Input files and parameters / Re: Generating framework.def a...
Last post by David Dubbeldam - June 13, 2023, 12:41:55 PMIt is very customary to write scripts precisely for the reason you mention. Different software use different input, and you often need to convert.
It pays off to write scripts to take care of that.
It pays off to write scripts to take care of that.
#45
General / Re: Very beginner question
Last post by David Dubbeldam - June 13, 2023, 12:40:19 PMFor classical simulations and classical simulations software, you always need to define the same things:
1) the positions of all the atoms that are present at the start of the simulation, like the framework.
2) the types of atoms
3) the force field, including charges, VDW, and all the bond, bend, torsions for flexible adsorbates and flexible frameworks.
4) the simulation input parameters, like pressure, temperatures, and MC moves etc.
......
There is no way around that issue and is the nature of classical simulations. Most people working with RASPA, Towhee, GULP, DLPOLY, LAMMPS struggle with this simulation-theory side. But there are many good books on this topic.
RASPA is not the most difficult input, for example, you can just list the amount of molecules, and the code generates the positions atomically. In LAMMPS, DLPOLY etc you first need to create all the initial positions 'by hand'.
1) the positions of all the atoms that are present at the start of the simulation, like the framework.
2) the types of atoms
3) the force field, including charges, VDW, and all the bond, bend, torsions for flexible adsorbates and flexible frameworks.
4) the simulation input parameters, like pressure, temperatures, and MC moves etc.
......
There is no way around that issue and is the nature of classical simulations. Most people working with RASPA, Towhee, GULP, DLPOLY, LAMMPS struggle with this simulation-theory side. But there are many good books on this topic.
RASPA is not the most difficult input, for example, you can just list the amount of molecules, and the code generates the positions atomically. In LAMMPS, DLPOLY etc you first need to create all the initial positions 'by hand'.
#46
General / Re: Warning messages during en...
Last post by David Dubbeldam - June 13, 2023, 12:34:28 PMYou have interactions pairs that are undefined. To get rid of this warning, define the interactions (if you really meant no interactions, then use type 'none').
Also, apparently there is a net charge, which might be small but non-zero. Check whether the value is small enough.
Also, apparently there is a net charge, which might be small but non-zero. Check whether the value is small enough.
#47
Bug reports / Re: Segmentation fault related...
Last post by David Dubbeldam - June 13, 2023, 12:32:39 PMIn 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.
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.
#48
General / Re: RxMC ensemble
Last post by David Dubbeldam - June 13, 2023, 12:27:05 PMYes, 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.
What is a 'fluctuating state'?
TranslationProbability, RotationProbability, ReinsertionProbability are input parameters, not output parameters. So, you decide these.
#49
General / RxMC ensemble
Last post by Mohammad Ahmadi - June 13, 2023, 08:15:32 AMWe 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. 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?
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. 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?
#50
General / RxMC ensemble
Last post by Mohammad Ahmadi - June 13, 2023, 08:02:51 AMWe 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?
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?