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Messages - David Dubbeldam

#61
You do a: grep HYDRATED_ION_WATER *.c
in the source code and get the files back where this is used.
In the file 'potentials.c' you can check whether it is read okay, or printed out wrongly, or whether it is something with the mixing rule.
#62
Yes, that is the standard way of simulation desorption. Note that is best to start from an equilibrated restart-file at the highest pressure (usually obtained from the adsorption branch).
#63
That can not really be done without implementing that. The system must stay charge-neutral, so you cannot individually swap na and cl in and out. You will need to do that in pairs.
#64
The positions of the atoms of the framework are 'input'. There might be tools available (builders) that create these initial structures for you.
#65
See the tips in section 5.5 of the manual on debugging to find the cause of this.
Basically, compile with the flag '-g' and run the executable via a debugger.
#66
1) Methane is often modeled as a united-atom (a single bead).
2) The VTK output that can be read by iRASPA is a VTK density-file (see 'ComputeDensityProfile3DVTKGrid').
#67
Pictures and movies / Re: creating movies in iRASPA
December 02, 2021, 10:58:18 AM
Select both files when loading them into iRASPA. The first tab in the project-pane shows the project. The second tab shows the two "movies" that you have loaded: the cif file with 1 frame, and the pdb with many frames. The third tab shows the frames of the movie.

Note: there is help in iRASPA (see menu item 'Help').
#68
I would say > 0.1%. Lower then that and you will really have to simulate a long time. With biasing you can increases the acceptance at the cost of computing more.
#69
General / Re: NPT Simulations
December 02, 2021, 10:48:39 AM
I have never used it, not sure if it works. You will have to check the VolumeChange move and modify to only change in the z-direction leaving the framework intact.
#70
Output files / Re: Reg H2 adsorption in zeolites
November 13, 2021, 02:18:24 PM
At low temperatures, the isotherm are usually suddenly increasing a lot and sharply peaked. The pressure where that happens is very sensitive to forcefields and simulations setup etc. I would compute the isotherm from 1e-8 to 1e5 Pa for example to have a better idea of the full shape of the isotherm. One of two orders off in pressure where it shoots up is not too bad.
Also note, that this type of system is sensitive to the correct positioning of the cations, which is another topic in itself. This is especially important at low temperature. Equilibration of these types of systems is long and difficult.
#71
Currently, you can not change it. In a future version we will add that to the command-line utility.
#72
Note sure I fully understand. There is no such thing as "adsorbed liquid phase", there is only an adsorbed phase. So, do you mean a Vapor-liquid simulation or a binary mixture adsorption simulation?

1) Note sure what Aspen does, but in VLE simulation pressure is an output property, and an input property for adsorption simulations. In the latter, you input the total pressure and the mol-fraction.

2) In adsorption simulations in the grand-canonical ensemble you input the pressure and the mol-fraction of the fluid phase. The imaginary reservoir and the adsorbed phase are in equilibrium and for these conditions you compute the loading of each component in the framework.

3) Moves like "SwapProbability" are already biased. You would use "CBMCProbability" (which is also "PartialReinsertionProbability") to specify partial-reinsertion moves.

4) Look at the binary mixture adsorption in the examples and adapt it for you system.
#73
General / Re: Number of molecules in GEMC box
November 03, 2021, 08:47:05 AM
The length of the boxes is important to reduce finite-size effects.

But more fundamentally, it is quite hard with a simple set of LJ parameters to get both the liquid and the vapor branch accurate. This is btw one the main reason to fit parameters on VLE-data. But the united-atom approach has its limits. More complicated models like full-atom models have more parameters and are harder to optimize.
So... having a good liquid phase and 20% off for the vapor phase is not that bad.
#74
It would require reading the code and understanding the flow of the code.
In general "monte_carlo.c" is the start-point for Monte Carlo. It setups the systems and selection of moves etc.
The MC-moves themselves are in "mc_moves.c" which makes use of the routines to compute the energies in the various files like "framework_energy.c", "inter_energy.c", and "internal_energy.c".
#75
Using a Restart-file will save you the equilibration phase. Usually it is best to check your simulation after submitting to make sure the options are set.
In the output, it lists the input-settings so you can check whether options are on or off.
Also, most files are periodically updated so you can see the current results.