Recent posts

#71

Input files and parameters / using grids for energy biased ...

Last post by wei123 - March 10, 2023, 11:31:49 AM

Hello RASPA community,

I have attempted to use grids for energy-biased monte carlo as in the auxillary examples. I managed to make and use the grid, but my adsorption is way too high for my system of LTA4A and water. Since LTA4A is charged-balanced with mobile Na ions, the framework cif file has a net charge (due to exclusion of the Na ions). I am wondering if this net charge of the framework is causing the incorrect calculation of my adsorption, and whether I can make grid for not only my adsorbates, but also my cations in the framework.

How can I correcly implement MakeGrid on a framework with mobile cations, if that is even possible?

Thanks!

Regards,
Wei

#72

Simulation algorithms and theory / Initialization phase of CFCMC

Last post by wei123 - March 10, 2023, 10:12:16 AM

Hello RASPA community,

I tried using the CFCMC method in RASPA according to the example which specified an initialization, equilibration and production phase. As far as I know, the equilibration phase is used to calculate the biasing factor for a flat distribution of lambda. Based on the simulation resutls that I have obtained (attachment), it seems like there is not much going on during the initialization phase (input file also attached).

Can someone tell me what happens in the initialization phase of CFCMC and if the initialization phase is even necessary, when the equilibration phase is defined?

Thank you!

Regards,
Wei

#73

General / Can the cavity of a MOF be ind...

Last post by Lingxiao Qin - February 25, 2023, 04:12:12 AM

Dear Prof. Dubbeldam,

In some literatures the cavity of a MOF is indicated by a sphere, can such an image be created by iRASPA? If not, could you please suggest me a suitable way to create such an image?

Thanks for your help.

#74

General / Is measuring distance function...

Last post by Lingxiao Qin - February 25, 2023, 04:06:22 AM

Dear Prof. Dubbeldam,

In the manual via the help menu of iRASPA, I found that the distance between two atoms coule be measured by "alt + left mouse clicking on atoms 1 and 2". However, I could not use this function on my Windows desktop. Since the manual seems to be written for Macs, I wonder whether the measuring distance function is available on Windows.

Thans for your help.

#75

Simulation algorithms and theory / Re: MSD of MD

Last post by Yu_Zhuochen - February 24, 2023, 01:47:10 PM

I met the same problem. How to solve it?

#76

General / Re: About the relation between...

Last post by w_wonder - February 22, 2023, 05:43:11 PM

These value come from: https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00092/suppl_file/ct7b00092_si_001.pdf
and to reduce under/overflow you input them as the log of these numbers in Table S3.

One more question. Does RASPA have two conventions in the partition function, that previously, the exp(D0/kT) term was not included
as in https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.5b00160/suppl_file/ct5b00160_si_001.pdf
later the exp(D0/kT) was included, as in
https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf

Thanks.

#77

General / radial distribution function

Last post by kokojiang - February 20, 2023, 09:57:47 AM

Dear Prof. Dubbeldam and RASPA community,

I am now comparing the RDF of the same molecule towards different atoms in MOF. In the output RDF files, like "RDF_H2_Ow.dat", I want to switch the positions of H2 and Ow,so I can get "RDF_Ow_H2.dat"  to avoid the influence of the radius of the center atom. I don't know whether RASPA can do this or not, but if it's possible, could you please tell me how?

Thank you!

#78

Bug reports / Re: Draw isotherms using a per...

Last post by Zihan Zhou - February 16, 2023, 08:58:30 AM

This problem has been solved.

#79

Bug reports / Draw isotherms using a perl sc...

Last post by Zihan Zhou - February 15, 2023, 12:17:33 PM

usage: simulate [ -h] [-v] [-s] [-C CRYSTAL] input simulate: error: the following arguments are required: input. After a lot of attemptance, I still can not figure it out.

#80

Output files / Re: ENERGY DRIFT

Last post by kokojiang - February 15, 2023, 08:10:07 AM

Dear Dr. Dubbeldam,

    I am getting the same error too. Like what you explained, the error happened as the number of adsorbates increased. When the number of adsorbates is low, it works well. But when the number of adsorbates is large, like 2500, the error appeared. In the forcefield I use, hydrogens did have no lennard-jones potential. How can I solve this warning? Should I change the forcefield or just run a larger simulation cycle?

Thank you!.
Jiang