News:

SMF - Just Installed!

Main Menu
Menu

Show posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Show posts Menu

Messages - kokojiang

#1
Dear all,
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
#2
General / Re: Inquiry regarding reconvening a run
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.
#3
General / radial distribution function
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!
#4
Output files / Re: ENERGY DRIFT
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