Recent Posts

1

General / Inquiry regarding RASPA calculations -Chemical potential and Number of molecules

« Last post by Temoor on Today at 06:26:45 PM »

Hi all,

I have a 3 questions to discuss regarding GCMC by RASPA.

1) I believe that the default calculation of adsorption in RASPA is through GCMC. Is it correct?

2) If yes (refer to question 1), how does the RASPA calculating the chemical potential during the adsorption calculation (as I am not inputting any chemical potential in the input file) and I cannot see the chemical potential printed in the output file. For example, please see this tutorial example from RASPA github: https://github.com/iRASPA/RASPA2/tree/master/examples/Basic/7_Adsorption_of_Methane_in_MFI/Output/System_0

3) The GCMC is calculating the total number of molecules in porous system. If the pores are small let's say 1A, we could say that the number of molecules is equal to the adsorbed phase in that confined pore. However, if the pores are larger (let's say 3nm ~ 30A), there is a significant free gas in the system in the middle region and I believe that the total number of molecules will not correspond to the adsorbed molecules. However, RASPA is considering number of molecules = adsorbed molecules in the calculation and provide final results based on this assumption. Do you think I need to subtract the free gas molecules from the calculation to get an actual adsorption value.

I believe these are some basic  questions, but I need the clarity for generating accurate results.

Thanks,
Temoor

2

Input files and parameters / Crash restart

« Last post by mhaeri on September 16, 2023, 03:50:30 AM »

Hi,
I am running an isotherm set point on cluster and therefore need to restart it every few days.
recently the simulations have been crashing with Out Of Memory error.
I am trying to start with a higher memory request but it won't restart or start from scratch.
Right now I am getting the following error:

read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
Input error in 'Component'-command: the number of the component 0 is already taken

where lies the problem?
Thanks
Mas Haer

3

General / Quantitative density profile in a small pore.

« Last post by Temoor on September 14, 2023, 07:34:10 PM »

Hi,

I wanted to create a density profile while running my GCMC.  My system has two slabs separated by vacant pore and I wanted to see the fluid density in the middle pore. A picture of how exactly I wanted the profile is attached.  Can you please help me with that.

Thanks

4

Output files / Re: Enthalpy of adsorption "nan"

« Last post by chenyaxin on August 31, 2023, 09:34:41 AM »

I also encountered the same problem in the process of carbon dioxide adsorption by LTA4A molecular sieve containing Na ions. I checked the force field file and input file which taken from raspa's user manual ,but I did not solve the problem. So I would like to ask you how to solve it. I would appreciate it very much if you could reply to my questions.

5

Input files and parameters / No VDW interaction

« Last post by CharleneZ on August 29, 2023, 09:53:57 PM »

I am getting an error regarding no VDW interaction for some molecules. I have defined the appropriate molecules to the force_field_mixing_rules to the file, but I still get the error. Is there anything immediately wrong with the file below? I am not sure how to erase this issue. When running the simulation I get the error below:

WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION CH4-C1 CH4-C2 CH4-C3 CH4-C4 C1-CH4 C1-C2 C1-C3 C1-C4 C2-CH4 C2-C1 C2-C3 C2-C4 C3-CH4 C3-C1 C3-C2 C3-C4 C4-CH4 C4-C1 C4-C2 C4-C3  (maximum 50 interactions shown)



My force_field_mixing_rules.def file is below:

# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
9
# type interaction, parameters.    IMPORTANT: define shortest matches first, so that more specific ones overwrites these
C1             lennard-jones    47.0      3.74
C2             lennard-jones    47.86     3.47
C3             lennard-jones    47.86     3.47
C4             lennard-jones    47.86     3.47
CH4            lennard-jones    158.5     3.72       
CH3            lennard-jones    108.0     3.76       
CH2            lennard-jones    56.0      3.96       
CH             lennard-jones    17.0      4.67       
C              lennard-jones     0.8      6.38     

# general mixing rule for Lennard-Jones
Lorentz-Berthelot

Any help is appreciated!

6

Output files / Re: Enthalpy of adsorption "nan"

« Last post by dddD on August 27, 2023, 02:41:40 PM »

i meet the same question. I want to know how to calculate enthalpy of adsorption in this simulation.

7

Visualization / Density Plot

« Last post by saif on August 21, 2023, 06:49:01 PM »

Hi,

I'm seeking advice.

I'm attempting to plot the DensityProfile.vtk file that I obtained from my simulation run. However, I'm encountering an issue where the plot appears completely white without any visible content.
All the data inside the file consists of very small values.

-----------------------------------------------------------
Part of my file:

# vtk DataFile Version 1.0
CELL_PARAMETERS 19.152000 19.152000 19.152000 90.000000 90.000000 90.000000
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 150 150 150
ORIGIN 0.000000 0.000000 0.000000
SPACING 0.127680 0.127680 0.127680
POINT_DATA 3375000
SCALARS scalars double
LOOKUP_TABLE default
0
0.000584217
0.00084387
0.00183199
0.00266144
0.00421935
0.00569792
0.00809249
0.00786169
0.0121387

-----------------------------------------------------------
Thank you

8

General / Density Histogram from GCMC simulation for four-component gasmixture adsorption

« Last post by Cigdem on August 16, 2023, 08:32:36 AM »

Dear Prof. Dubbeldam and dear RASPA Community,

With adding these lines to the simulation input, we can obtain density profiles as a result of the GCMC simulation:

ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints 150 150 150
AverageDensityOverUnitCellsVTK yes
DensityAveragingTypeVTK FullBox
FreeEnergyAveragingTypeVTK FullCell


However, we encounter a problem when we want to run GCMC simulations to obtain density profiles from four-component gas mixture adsorption in a MOF.
The error message is long but starts and ends as given below:

" *** Error in `simulate': free(): invalid next size (normal): 0x000056087ce427e0 ***

......
....
..
.

/var/spool/slurm/d/job5763373/slurm_script: line 67: 14511 Aborted                 $COMMAND $INPUT

RASPA finished. Return code is 134".

I tried with different cif files and different gas definitions, but, as far as I note, it only happens when I run the simulation for a mixture of more than three components.
I would be glad to learn if there is something that I am missing and avoids the production of density profiles for a mixture of more than three components.

Thank you,

9

Input files and parameters / RDF for adsorption

« Last post by mhaeri on July 22, 2023, 06:31:25 PM »

Hi Professor Dubeldam,
I have a question about the implementation of rdf:
The RASPA documents contain a clear description of rdf calculation for pure fluids.
How can I get rdf for systems involving the adsorbent-adsorbate?
I know that rdf for adsorbate-adsorbent, as well as adsorbate-adsorbate, are routinely reported in the literature using RASPA.
But I am not sure how it is implemented. It looks like it is more than just replacing the box with the framework. Could you kindly provide me with a sample simulation.input script ?
Best regards,
Mas

10

General / Re: Can the cavity of a MOF be indicated by a sphere in iRASPA?

« Last post by Lingxiao Qin on June 27, 2023, 01:40:37 PM »

In the gallery, then primitives, then IRMOF-1, you can see such an example.

Thank you for your reply. I do find the example. However, I am struggling to reproduce such a picture. The illustrations in the gallery are very compelling, but I think it may be difficult for a beginner like me to figure out how to draw those pictures without a tutorial. I was wondering if it would be possible for you to write a tutorial about how to draw the pictures in the gallery in the future. I understand that creating tutorials requires time and effort, but I believe this tutorial would be invaluable to the community.