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Messages - David Dubbeldam

In RASPA2 you input the final result: the partition-factor. In more recent RASPA versions the Log of the partition function to avoid over/underflow.
It is an user input, and up to the user to compute it.
Input files and parameters / Re: pseudo_atom radii
June 13, 2023, 02:09:19 PM
You can look these radii up in handbooks.
You could modify the RASPA code, or label the atoms differently.
Output files / Re: ENERGY DRIFT
June 13, 2023, 02:00:25 PM
I would modify the force field. One of the options is to put a hard-sphere potential around the hydrogen to shield it from overlap.
General / Re: radial distribution function
June 13, 2023, 01:58:25 PM
That is not implemented. Usually, these should be the same, since you are looping of interaction-pairs.
Simulation algorithms and theory / Re: MSD of MD
June 13, 2023, 01:52:53 PM
Are you using the official version from ?
Versions by other people (not us) via python-use reportedly can show this issue.

If so, check that it actually writes output by running MUCH shorter (10 cycles) and check all the output.
In the output-file it should say whether it computes MSD or not.
This is on the TODO list.
In the gallery, then primitives, then IRMOF-1, you can see such an example.
Note that if you do not use an initialization phase, the bias is measured while the adsorption is going up.
Also note that you are comparing CBCMC vs CFCMC. I would guess that CB/CFCMC would probably not plateau like that during initialization.
"I managed to make and use the grid, but my adsorption is way too high for my system of LTA4A and water.", way too high compared to what?
Did you compare with and without using grids?
These are old files, 'RASPA2/examples/Visualization' will be removed soon. These files you do not need to generate, you can directly use volume-rendering in iRASPA to visualize the framework.
Only for density volume-renderings do you need to regenerate the 3D VTK-densities using the latest version of RASPA.
The values are not the same. Excess is slightly smaller.

In the limit of low pressure, excess and absolute adsorption become equal. They start to deviate at high pressures.
You could email Reza Rahbari and ask him how he did it. But note there is no single convention and the results will differ depending on what assumptions and choices you make.
Partition 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:
Page 262 and following, and see Table  A5.
Pressure 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.