Recent posts

#21

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.

#22

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.

#23

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.

#24

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

#25

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?

#26

General / Error with RASPA2 with 5185 at...

Last post by sree.h - April 22, 2025, 11:50:05 AM

Dear all,

I have been stuck with a problem for over a month and a half now, and I am still unable to reach the end of it.

NDPC_1_completed/cont/cont/bond_analysis$ simulate simulation.input
_cell_length_a: 82.675664
_cell_length_b: 71.671734
_cell_length_c: 69.479348
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
_symmetry_space_group_name_Hall: P 1 found space group: 1
_symmetry_space_group_name_H-M: P 1 found space group: 1
_symmetry_Int_Tables_number: 1
space group found from symmetry elements: 1 (nr elements: 1)
End reading cif-file
Shift all potentials
free(): invalid next size (normal)
Aborted (core dumped)

I have defined pseudo atoms for 5185 atoms and force field mixing for 5185 atoms. I have the atom site label the same as the pseudo atoms, and the force field mixing and consistency in label are maintained. Yet I am getting this error!
This is my input file. If anyone is interested in resolving the error please ping into this thread. Thank you!

#27

General / Difficulty installing iraspa

Last post by kareems - April 20, 2025, 06:05:34 PM

If you face any difficulty installing iraspa, the following additional steps helped me successfully installing and I thought I would share them with you:

Steps as mentioned in the section 1.3 of the raspa2 manual:
Open terminal in macOS

1. git clone https://github.com/iraspa/RASPA2
2. export RASPA DIR=${HOME}/RASPA/simulations/
3. rm -rf autom4te.cache
4. mkdir m4
5. (new step) /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
6. (new step) brew install automake (This is to install aclocal)
7. (New step) brew install libtool (This is to run autoreconf and make)
8. aclocal
9. autoreconf -i
10. automake --add-missing
11. autoconf
12. ./configure --prefix=${RASPA_DIR}
13. make

#28

General / Re: Help with GCMC Simulation ...

Last post by Elnaz Jangodaz - April 15, 2025, 09:01:03 AM

Hi, I'm experiencing the same issue with water uptake — the calculated uptake is zero at partial pressures corresponding to certain relative humidity values. I noticed something unusual: when I set the external pressure to 101325 Pa at 298 K, the simulation gives an uptake value which is similar to paper results at the saturation point. I put a range of 0-101325 pa for external pressure, the resulting isotherm shows the same uptake trend and point, but now with p₀ = 101325 Pa instead of 31.7 kPa, which is the correct saturation pressure. I'm not sure why the uptake appears at such a high pressure, especially since water should already be in liquid form at 101325 Pa. Let me know if you've figured out what the issue might be.

#29

Input files and parameters / CB/CFC Monte Carlo Input File

Last post by hooman - April 11, 2025, 06:47:04 PM

Dear Prof. Dubbeldam, all,

I want to simulate adsorption in MOFs using CB/CFCMC ensemble, but I'm not sure if I'm doing it the right way.
I have done it with the following settings, but although the number of cycles are relatively large and I've done a similar simulation with GCMC, I still see points in the isotherm where the uptake is not consistently increasing with partial pressure and it's at points lower than CBGCMC uptake.

Thank you very much.
You cannot view this attachment.

#30

Input files and parameters / Gibbs Ensemble Monte Carlo (GE...

Last post by hooman - April 11, 2025, 06:17:51 PM

Dear Prof. Dubbeldam, all,

I'm simulating adsorption in a MOF model system using the GEMC ensemble in RASPA. I have several questions regarding the methodology and input file;

1- Should the properties of the reservoir box (size, number of molecules) change in accordance to the pressure point (P as in P/Psat) in the isotherm?
2- How do I fix the volume of the MOF simulation box and how would that translate in thermodynamic terms?
3- How should I choose the proper volume move probability?

Thank you very much.