Recent Posts

Pages: [1] 2 3 ... 10
1
Input files and parameters / Re: The usage of block_file
« Last post by David Dubbeldam on September 27, 2021, 07:38:58 PM »
Without blocking you should get around 0.49. With blocking it should be around 0.4-0.43 depending on the details of FAU.
Check that you use the same definition of the structure in zeo++ so that the pockets really match the structure in the CIF-file.
The centers should be close to the ones in 'structures/zeolites/block/FAU.block'.
2
General / Re: RASPA Simulations Directory not Found
« Last post by David Dubbeldam on September 27, 2021, 07:27:24 PM »
That is done in the run-file. See manual "1.3.5 Running RASPA".
3
Input files and parameters / Re: RandomAlSubstitution_13X
« Last post by David Dubbeldam on September 27, 2021, 07:22:09 PM »
Usually, the experimental structure is an average over all unit cells, and that is then described by a space group.
In simulation, you need to define all atoms, so it is unlikely that the space group is the same (for structures with partial occupancies).
So, just convert to P1 and do the substitution.
4
Visualization / Re: iRASPA unable to visualize 13X zeolite file
« Last post by David Dubbeldam 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.
5
Visualization / Re: iRASPA unable to visualize 13X zeolite file
« Last post by rshukre on September 26, 2021, 01:00:51 AM »
Please see the attachment for the Movie file generated.
6
Input files and parameters / RandomAlSubstitution_13X
« Last post by rshukre on September 26, 2021, 12:58:13 AM »
Hello,

I have a question regarding RandomAlSubstitution to modify the Si/Al ratio in zeolite 13X. In the manual, it is written that the 'Substitute' command is useful to have the same structure, whereas the 'RandomlySubstitute' command may not keep the same space group. I want to substitute 10 Al atoms by 10 Si atoms in the framework. How many 'Substitute' commands do I need to consider in the input file, so as to keep the space group in the fd-3, with 96 elements ? How do I check if the same space group is followed at the end of simulation.

Regards,
Rajasi

7
Visualization / iRASPA unable to visualize 13X zeolite file
« Last post by rshukre 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


8
Input files and parameters / Re: The usage of block_file
« Last post by rshukre on September 25, 2021, 06:27:31 PM »
Hello Dr. Dubbeldam,

Please see attached the simulation input file and the block file. I obtained the block file for the 13X structure ( Si = 86, Al = 106) using Zeo++ and the format is the same as that required in RASPA. The block file has 8 pockets, which should be for the sodalite units in the 13X structure.
I have also defined the input for switching on the block using the format followed in the RASPA examples. 

INPUT FILE :

SimulationType        MonteCarlo
NumberOfCycles        100000
PrintEvery            1000
PrintPropertiesEvery  1000

Forcefield             local
UseChargesFromCIFFile  yes

Framework 0
FrameworkName NaX
UnitCells 1 1 1
ExternalTemperature 298.0

Component 0 MoleculeName             helium
            MoleculeDefinition       local
            BlockPockets             yes
            BlockPocketsFileName     zeoNaX
            WidomProbability         1.0
            CreateNumberOfMolecules  0

BLOCK FILE :

8
0.920026 0.868617 0.846936 3.49194
0.126382 0.106569 0.0971705 3.71214
0.350113 0.356273 0.881404 3.84527
0.61603 0.611122 0.13383 3.75885
0.418688 0.884354 0.342678 3.14328
0.882809 0.374691 0.426361 3.61778
0.65533 0.130399 0.617683 3.96516
0.155449 0.630486 0.585976 3.53465


9
General / Re: RASPA Simulations Directory not Found
« Last post by amogh on September 24, 2021, 08:48:44 PM »
For setting the RASPA_DIR variable, what is the ideal path to do so? After cloning from Github and running the install commands in the RASPA2 main directory, I just want to make sure I set RASPA_DIR correctly as it often looks for files that don't exist when I have done it before.
10
Input files and parameters / Re: The usage of block_file
« Last post by David Dubbeldam on September 22, 2021, 03:06:43 PM »
Just checked the code: the Widom move _does_ check for blocking.
How did you define the blocking-pockets and what is your input-file to switch on blocking for that component?
Pages: [1] 2 3 ... 10