Author Topic: Slit pore/ visualization/adsorption  (Read 57 times)


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Slit pore/ visualization/adsorption
« on: March 17, 2021, 06:43:58 AM »
Dear Dr Dubbeldam,

I am simulating in RASPA adsorption of methane on an illite surface. I am using pyrophyllite (Al2Si4O10(OH)2) as my framework (neutral clay) and considering isomorphic substitution (one silica atom in tetrahedral layers is replaced by an aluminum atom so that the clay sheet has a negative charge). The negative charge is neutralized by potassium, therefore K ( potassium) is a cation component.
I have three questions:

1) I would like to perform my adsorption simulations on an illite slit pore. For instance, I would like to have two clay sheets separated by a fixed distance. Is it possible to make a slit pore on RASPA? If yes, are there any explanation or examples in the manual?

2) I am running the adsorption simulations but I don't see a way to visualize the final system: framework + cations + adsorbate together. In movies/System I can only see the framework without the cations. How can I  have a picture or a .pdb file of my final system (framework + cations + adsorbate  together)?

3) Is there any reason why RASPA would give zero absolute adsorption ?

Thank you.

My simulation input:
SimulationType                MonteCarlo
NumberOfCycles                25000
NumberOfInitializationCycles  100000
PrintEvery                    1000

ContinueAfterCrash            no
WriteBinaryRestartFileEvery   2000

Forcefield                    CLAYFF
CutOffVDW                     12.5
RemoveAtomNumberCodeFromLabel yes

RandomlySubstitute 1 Si1 Al

Framework 0
FrameworkName illite
UnitCells 5 3 1
HeliumVoidFraction 0.64
ExternalTemperature 300.0
ExternalPressure 1e4 1e5

ComputeNumber1fMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 5000
NumberOfMoleculesHistogramSize 1100
NumberOfMoleculesRange 80

ComputeEnergyHistogram yes
WriteEnergyHistogramEvery 5000
EnergyHistogramSize 400
EnergyHistogramLowerLimit -110000
EnergyHistogramUpperLimit -20000

Component 0 MoleculeName                 kalium
       MoleculeDefinition           Cations
       TranslationProbability       1.0
       RandomTranslationProbability 1.0
       ExtraFrameworkMolecule       yes
       CreateNumberOfMolecules      15

Component 1 MoleculeName             methane
            MoleculeDefinition       TraPPE
            TranslationProbability   0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0

Thank you.
« Last Edit: March 26, 2021, 01:02:50 AM by isaaraujo »