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#11
Breakthrough / Breakthrough curve time overes...
Last post by AntonioDouglas - May 27, 2025, 05:18:42 AM
Hi, everyone.
I am trying to get the breakthrough curve for CO2/H2 mixture in a MOF.
I read and followed the instructions present in "S. Sharma, S. Balestra, R. Baur, U. Agarwal, E. Zuidema, M. Rigutto, S. Calero, T.J.H. Vlugt, and D. Dubbeldam, Molecular Simulation Journal, 49(9), 2023". And everything seems right, however, the breakthrough curve time appears to be overestimated. I saw in different papers (theoretical studies GCMC) that CO2 usually start under 50 (Time, t/[min.]) or under 600 (Dimensionless time)(experimental studies), but my results (with isotherms obtained with GCMC/RASPA and fitted with RUPTURA) start around 400 (Time, t/[min.]) or close to 1700 (Dimensionless time). 
I already used several approaches combined: SIAST, IAST, EI, Langmuir, Langmuir-Freundlich, the number of isotherm sites, changes in column entrance velocity, and more. But the results that I get are weird. Curiously, when I tried repeating the examples provided in GitHub, I was able to get the same good results.
I am new in the RUPTURA use, so if someone has some tips, I would appreciate it.
(Attached is one between 21 tries done until now)
#12
General / The preprocessor macro `STDC_H...
Last post by cicci - May 23, 2025, 03:27:54 PM
Hi everyone,
I am trying to install Raspa2.0 on my PC (SO. Windows) and utilizing Ubuntu 24.01.1 for windows. COnsidering the procedure reported in manual, after the installation I obtained the following error message:

The preprocessor macro `STDC_HEADERS' is obsolete.
configure.ac:23:   Except in unusual embedded environments, you can safely include all
configure.ac:23:   ISO C90 headers unconditionally


What can I do to fix this problem? Thanks
#13
General / Generating Adsorbate Density P...
Last post by had-sham - May 11, 2025, 12:48:17 PM
Hi all,

I understand that grids are used to speed up GCMC simulations and for visualization purposes. I have already run some GCMC simulations without energy grids, and I have the snapshots.
Is it possible to use the Restart file (final configuration) to perform a new GCMC run with grids enabled, in order to obtain adsorbate density plots?
Alternatively, is there a way to generate density plots from the final configuration of a GCMC run that was performed without grids?

Best regards,
#14
General / MOF structure atoms not shown ...
Last post by had-sham - May 11, 2025, 12:39:53 PM
Hi all,
I have trouble working with the final pdb file named "allcomponents" in the Movies folder. I run the simulations and save movies in the "Movies" folder. when I open the "allcomponents" pdb file, the visualization softwares just show the adsorbed molecules and the MOF structure is not shown. could you please help me to solve the problem?

Thank you
#15
Visualization / Density Profile Visualiztion
Last post by aimipa - April 29, 2025, 02:55:21 PM
Hello,

I would like to visualise the density profile of a gas adsorbed in a framework.

From the simulation, i get two VTK files: 1) COMDensityProfile_CF4.vtk , 2) DensityProfile_CF4.vtk.

Which one is the file to plot? And what is the difference between them?

Best regards
#16
General / Re: Limit on the number of ato...
Last post by David Dubbeldam - April 28, 2025, 08:50:42 PM
Make sure the box is large enough so that the molecules can be placed in the box without overlap.
If your chosen amount of molecules cannot be placed in the chosen box, then it hangs for ever.
#17
General / Re: What is the source of Gene...
Last post by David Dubbeldam - April 28, 2025, 08:48:48 PM
Yes, it is a UFF/Dreiding combination, to just have a generic force field to use for the examples.
For any realistic simulations you would probably use your own chosen force field.
#18
Isotherm fitting / Re: multiple temperatures
Last post by David Dubbeldam - April 28, 2025, 08:44:26 PM
You can fit them in any way that you want, the models are just a description of the isotherm.
RUPTURA fits a single isotherm with a chosen model. For dual-site Langmuir you get 4 parameters back that give a functional form of the isotherm. You could also fit the isotherm with your own software and put in the obtained parameters in RUPTURA to then compute the breakthrough using that isotherm model and parameters.
#19
Input files and parameters / Re: No VDW interaction
Last post by justyna - April 25, 2025, 03:30:36 PM
Hi,

there is an empty line between the last atom and #general mixing rules. This is very often causing errors. To avoid it remove the empty line like so:

...
C              lennard-jones     0.8      6.38     
# general mixing rule for Lennard-Jones
#20
Isotherm fitting / multiple temperatures
Last post by evZENy - April 24, 2025, 05:28:02 AM
We usually collect isotherms at different temperatures and fit them all to the same model.
Most of my experience has been with Dual-Site Langmiur, the output providing some thermodynamic parameters.
And also help plug-in the parameters for mixed isotherms (e.g., IAST).

I am still new to RUPTURA - seems to be much more powerful, but with power comes too many options.
Are there examples where the data isotherms collected at different temperatures is fit?
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