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Messages - David Dubbeldam

General / Re: GCMC vs MCNPT
June 13, 2023, 12:45:10 PM
It 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.
It 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.
General / Re: Very beginner question
June 13, 2023, 12:40:19 PM
For 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'.
You 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.
In 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.
General / Re: RxMC ensemble
June 13, 2023, 12:27:05 PM
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.
General / Re: error message on restart after crash
January 11, 2023, 08:08:05 PM
Note sure,  but could be that the crash damage the restart-file. This could happen when the crash happens at the exact time the binary-restart-file is written to disk.
For running multiple simulations, you would use/create scripts that generate the needed input.
MOF simulations time depend on the size of the system, and how accurate you need the results.
Small systems, about a day. Larger system, a week or longer.
For a detailed explanation see:
Page 262 and following, and see Table  A5.
Visualization / Re: Vector image export
November 24, 2022, 10:55:40 AM
No, the data is inherently pixel-based. Exporting to pdf would just put a picture in a pdf.
This workshop/school focused on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we were also considering the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online. Due to privacy reasons, there will be no video recordings. Registration is free but compulsory. Certificates of attendance will be made available after the workshop.
We are also planning offline workshops in 2023 (November, Abu Dhabi) and 2024 (September, The Netherlands).
These value come from:
and to reduce under/overflow you input them as the log of these numbers in Table S3.
Visualization / Re: Transparent background?
November 22, 2022, 10:14:22 AM
Yes, for that very reason it saves in the tiff-file format. iRASPA uses RGBA-colors. You will need to change the background color and set the opacity to zero.

Yes, the atom colors can be changed, see the help/manual.
Input files and parameters / Re: mol file
November 22, 2022, 10:12:01 AM
You can use for example 'openbabel' to convert between formats.
Visualization / Re: RASPA visualization (Density Plot)
September 25, 2022, 06:01:19 PM
That depends on the VTK-version. But VTK-file plotting is now included in iRASPA, provided you have written the VTK with the latest version of RASPA.