Recent posts

#21

Input files and parameters / No VDW interaction

Last post by CharleneZ - 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!

#22

Output files / Re: Enthalpy of adsorption "na...

Last post by dddD - 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.

#23

Visualization / Density Plot

Last post by saif - 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

#24

General / Density Histogram from GCMC si...

Last post by Cigdem - 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,

#25

Input files and parameters / RDF for adsorption

Last post by mhaeri - 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

#26

General / Re: Can the cavity of a MOF be...

Last post by Lingxiao Qin - 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.

#27

General / How does Unitcell size affect ...

Last post by Z.GAO - June 25, 2023, 04:30:37 AM

When we calculate the enthalpy of adsorption under infinite dilution conditions, we find that the enthalpy of adsorption varies greatly with different unit cells. So what is the basis of unit cell setup? When I set the unit cell to less than 2 times the truncation radius, the results file prompts a warning. But according to the manual, there is no cut-off radius setting, which is why?

#28

General / Re: Inquiry regarding reconven...

Last post by kokojiang - June 24, 2023, 08:46:18 AM

Hi, actually I met with the same problem. I still dont know how to solve this yet. I tried this to make it continue, but I DONT know if it is correct:

1.Copy the whole simulation files, including input,output...
2.Rename  "Restart" folder to "RestartInitial"
3.Add "RestartFile  yes" to the simulation.input file and run

This will start new simulation cycles after the last results.

In the Raspa manual, it says "ContinueAfterCrash yes" will work, however, I tried it many times and it won't. My senior said he used to run it successfully, but now he can't either. Maybe this is becuase we uploaded Raspa to the latest version?

I also tried to interrupt some still running simulations, change the input file, increase the number of cycles, add "ContinueAfterCrash yes", and continue. After this, I checked the output file, it still continue after the original inputfile, not the one I changed. For example, the origin inputfile:"NumberOfCycles   100000", changed to "NumberOfCycles   200000", it still finished at 100000 sycles.

I am still finding a way that can continue the simulation in the same outputfile directory.

#29

Input files and parameters / Re: using grids for energy bia...

Last post by wei123 - June 22, 2023, 09:05:35 AM

Yes, the adsorption using the grid was much higher than without using the grid (about 10 times more already within a few thousand MC steps until I stopped the simulation, and the adsorption increases continuously as the simulation runs). I assume it is because the framework was charged, because the energy grid was created for the framework without the presence of cations.

#30

General / Re: RxMC ensemble

Last post by Mohammad Ahmadi - June 18, 2023, 08:47:52 AM

I mean the sentence "how can the values of TranslationProbability, RotationProbability, ReinsertionProbability be calculated?"
  That is, is there a formula to calculate these values or do they have to be guessed؟