Author Topic: iRASPA unable to visualize 13X zeolite file  (Read 85 times)

rshukre

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iRASPA unable to visualize 13X zeolite file
« on: September 26, 2021, 12:42:38 AM »
Hello,

I have modified the base file of NaX, available in RASPA to suit the Si/Al ratio, which I want. The base file in RASPA has Si/Al = 1 (96 Si, 96 Al). For my simulations, I need Si/Al = 1.23 (106 Si, 86 Al), differentiating the oxygen atoms based on connectivity to Si or Al. I have changed the base file using RASPA simulations, whose input file is given below.  RASPA generates an output file in the Movie folder, titled 'Framework_0_final_1_1_1.cif',  which I have attached in this post. This file has 86 Al and 106 Si, meaning that random substitution has worked. My question is as follows :

Why is iRASPA unable to visualize this file? There are total 576 atoms/ unit cell. When I upload the modified file, it only reads 232 atoms and the structure generated is not right. However, VESTA is able to generate the correct structure. I would really appreciate it if you could help me with this.

Thanks,
Rajasi

INPUT :

SimulationType                MC
NumberOfCycles                0
NumberOfInitializationCycles  0
PrintEvery                    10
     
Forcefield                      local
UseChargesFromCIFFile           yes

RandomlySubstitute 10 Al1 Si1

ModifyFrameworkAtomConnectedTo O1 Oa1 Al1
ModifyFrameworkAtomConnectedTo O2 Oa2 Al1
ModifyFrameworkAtomConnectedTo O3 Oa3 Al1
ModifyFrameworkAtomConnectedTo O4 Oa4 Al1
     
Framework 0
FrameworkName NaX
UnitCells 1 1 1
ExternalTemperature 293



rshukre

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Re: iRASPA unable to visualize 13X zeolite file
« Reply #1 on: September 26, 2021, 01:00:51 AM »
Please see the attachment for the Movie file generated.

David Dubbeldam

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Re: iRASPA unable to visualize 13X zeolite file
« Reply #2 on: September 27, 2021, 07:20:06 PM »
I have no problems reading this file in iRASPA (Mac/windows, version 2.1.6).
Could you retry using the latest version?

Also, the difference between unix and windows end-of-line codes can potentially lead to issue.

rshukre

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Re: iRASPA unable to visualize 13X zeolite file
« Reply #3 on: September 28, 2021, 06:58:10 PM »
Thank you Dr. Dubbeldam for the response. There was an error on my end in the pseudo_atoms.def file which I gave as an input for the RandomAlSubstitutions. I incorrectly specified the number of pseudo_atoms as 1 instead of 11. This lead to the molecular weight being almost 5937 g/mol as opposed to 11430 g/mol in (Si/Al = 1). I could not find this mistake using VESTA. However, iRASPA made me check the output file. I have now corrected the pseudo_atoms.def file and the molecular weight is around 11441 g/mol in both RASPA and iRASPA, with 576 atoms.