Recent posts

#11

Input files and parameters / Error: Unknown input 'WriteBin...

Last post by Kimchen - May 29, 2025, 10:23:12 AM

Hi Guys, i want to create a input file which contains WriteBinaryRestartFileEvery, but when i try to run the simulation, this error comes out. i read the manual, it should have this function in the simulation, does anyone knows what is the reason for that?
Here is my input file:
{
    "SimulationType": "MonteCarlo",
    "NumberOfCycles": 4000,
    "NumberOfInitializationCycles": 1000,
    "PrintEvery": 100,
    "Forcefield": ".",
    "WriteBinaryRestartFileEvery": 100,
    "Systems": [
        {
            "Type": "Framework",

#12

General / Segmentation Fault When Creati...

Last post by had-sham - May 28, 2025, 11:52:20 PM

Hi everyone,

I'm encountering a "Segmentation fault (core dumped)" error every time I try to generate grids. Has anyone faced a similar issue, or does anyone know how I can resolve this?

Thanks in advance for your help!

#13

General / Status of Flexibility

Last post by petersbk - May 28, 2025, 07:20:04 PM

The README says that flexible molecules (and frameworks) are on the ToDo list, but I noticed several ...flexible...cpp files. What is the status and/or expected timeline or prioritization for inclusion of flexibility? Of course, I'm not expecting promises! I have a project that requires flexibility (molecules most important) and RASPA3 just looks so promising, I'd love to use it. Thanks.

#14

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)

[The preprocessor macro `STDC_HEADERS' is obsolete.configure.ac:23: Except in unusual embedded environments, you can safely include allconfigure.ac:23: ISO C90 headers unconditionally]

#15

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

#16

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,

#17

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

#18

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

#19

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.

#20

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.