Messages

Hi,

I am studying the adsorption of small molecules (carbon dioxide, propane, methane) in zeolite 13X using GCMC in RASPA. I am using the forcefield of Calero et al. (2004) and Garcia-Sanchez et al. (2009) for the same. Is there a general rule of thumb for the acceptance rate (For ex. >= 50%) of swap moves (insertion and deletion) in GCMC simulations for adsorption in porous materials?
Can this rate be increased by increasing the number of initialization (plus equilibration) cycles in GCMC simulations ?

Regards,
Rajasi

Hello,

I am studying the adsorption of carbon dioxide in zeolite 13X. I have the .cif file of framework and the coordinates of carbon dioxide and sodium ions in the .pdb file for every frame that is generated. How do I visualize every frame of the movie file, along with the framework .cif file in iRASPA ? I want to visually inspect adsorption sites in 13X zeolite.

Thanks,
Rajasi

Hello Dr. Dubbeldam,

I have been running adsorption simulations in RASPA 2.0 using the High Performance Computing Center (HPCC) of my University. I recently installed RASPA 2.0.45 on HPCC and some of my current simulations crashed due to wall time limit on the cluster. I always use ContinueAfterCrash option in the simulation.input file, so that the simulation continues after the point it was crashed. However, it looks like RASPA 2.0.45 does not recognize crash file of RASPA 2.0 and the simulation starts again from the beginning. Is this to expected when running files from an older version on the latest version ?

Regards,
Rajasi

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.

Thank you for the response Dr. Dubbeldam. You are right, with blocking,  the He void fraction is 0.43, as opposed to 0.49 without blocking. The way I obtained this was installing the latest version of RASPA (2.0.45), as opposed to the earlier version that I was using (RASPA 2.0). In RASPA 2.0, there is no difference in He void fraction computed with and without blocking as can be seen below from the output files.  RASPA 2.0 does not read the block file, as opposed to RASPA 2.0.45.

RASPA 2.0 :
Number of pockets blocked in a unitcell: 0
   Pockets are blocked for this component
   Block-pockets Filename: FAU.block

RASPA 2.0.45 :

Number of pockets blocked in a unitcell: 56
   Pockets are blocked for this component
   Block-pockets Filename: FAU.block
      Block center: 9.412125 21.961625 9.412125  distance: 3.000000
      Block center: 21.961625 21.961625 21.961625  distance: 3.000000
      Block center: 9.412125 9.412125 21.961625  distance: 3.000000
      Block center: 21.961625 9.412125 9.412125  distance: 3.000000
      Block center: 15.686875 3.137375 15.686875  distance: 3.000000
      Block center: 3.137375 3.137375 3.137375  distance: 3.000000
      Block center: 15.686875 15.686875 3.137375  distance: 3.000000
      Block center: 3.137375 15.686875 15.686875  distance: 3.000000
      Block center: 0.000000 0.000000 0.000000  distance: 1.000000
      Block center: 6.274750 6.274750 0.000000  distance: 1.000000
      Block center: 12.549500 12.549500 0.000000  distance: 1.000000
      Block center: 18.824250 18.824250 0.000000  distance: 1.000000
      Block center: 6.274750 0.000000 6.274750  distance: 1.000000
      Block center: 12.549500 0.000000 12.549500  distance: 1.000000
      Block center: 18.824250 0.000000 18.824250  distance: 1.000000
      Block center: 0.000000 6.274750 6.274750  distance: 1.000000
      Block center: 0.000000 12.549500 12.549500  distance: 1.000000
      Block center: 0.000000 18.824250 18.824250  distance: 1.000000
      Block center: 12.549500 6.274750 18.824250  distance: 1.000000
      Block center: 12.549500 18.824250 6.274750  distance: 1.000000
      Block center: 18.824250 12.549500 6.274750  distance: 1.000000
      Block center: 6.274750 12.549500 18.824250  distance: 1.000000
      Block center: 6.274750 18.824250 12.549500  distance: 1.000000
      Block center: 18.824250 6.274750 12.549500  distance: 1.000000
      Block center: 23.791760 23.791760 20.131489  distance: 0.500000
      Block center: 20.131489 20.131489 20.131489  distance: 0.500000
      Block center: 20.131489 23.791760 23.791760  distance: 0.500000
      Block center: 23.791760 20.131489 23.791760  distance: 0.500000
      Block center: 11.242260 11.242260 20.131489  distance: 0.500000
      Block center: 7.581989 7.581989 20.131489  distance: 0.500000
      Block center: 7.581989 11.242260 23.791760  distance: 0.500000
      Block center: 11.242260 7.581989 23.791760  distance: 0.500000
      Block center: 4.967510 1.307239 1.307239  distance: 0.500000
      Block center: 4.967510 4.967510 4.967510  distance: 0.500000
      Block center: 1.307239 1.307239 4.967510  distance: 0.500000
      Block center: 1.307239 4.967510 1.307239  distance: 0.500000
      Block center: 4.967510 13.856739 13.856739  distance: 0.500000
      Block center: 4.967510 17.517010 17.517010  distance: 0.500000
      Block center: 1.307239 13.856739 17.517010  distance: 0.500000
      Block center: 1.307239 17.517010 13.856739  distance: 0.500000
      Block center: 20.131489 7.581989 7.581989  distance: 0.500000
      Block center: 20.131489 11.242260 11.242260  distance: 0.500000
      Block center: 23.791760 7.581989 11.242260  distance: 0.500000
      Block center: 23.791760 11.242260 7.581989  distance: 0.500000
      Block center: 13.856739 13.856739 4.967510  distance: 0.500000
      Block center: 17.517010 17.517010 4.967510  distance: 0.500000
      Block center: 13.856739 17.517010 1.307239  distance: 0.500000
      Block center: 17.517010 13.856739 1.307239  distance: 0.500000
      Block center: 17.517010 4.967510 17.517010  distance: 0.500000
      Block center: 13.856739 4.967510 13.856739  distance: 0.500000
      Block center: 13.856739 1.307239 17.517010  distance: 0.500000
      Block center: 17.517010 1.307239 13.856739  distance: 0.500000
      Block center: 7.581989 20.131489 7.581989  distance: 0.500000
      Block center: 11.242260 20.131489 11.242260  distance: 0.500000
      Block center: 7.581989 23.791760 11.242260  distance: 0.500000
      Block center: 11.242260 23.791760 7.581989  distance: 0.500000

Thank you.

Please see the attachment for the Movie file generated.

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

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

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

Hello Dr. Dubbledam,

I have a question regarding block pockets. I am working on adsorption of propane and carbon dioxide in zeolite NaX. I determined the helium void fraction using RASPA, which comes out to be around 0.49 for NaX with a Si/Al ratio of 1.23. I have also considered two cases for void fraction computation. Case I : with no block file and Case 2 : with a block file FAU.block. In both cases, the void fraction is the same.
I have three questions :
1. Is Widom insertion code in RASPA unable to consider blocked pockets, when the user has specified the .block file ?
2. Can Helium not access the sodalite cages of FAU, which is why the answer is same in both the cases ?
3. Since the He void fraction is same for both Case 1 and Case 2, it may lead to inaccurate excess loadings for both propane and carbon dioxide because the void fraction may contain volume of the inaccessible sodalite cage as well. How do I then know the correct void fraction ?

Thanks,
Rajasi

Does RASPA have the capability to do simulated Annealing? If so, how to specify the temperature range for annealing?

Dear all,

The pseudo_atom radii for N_N2 and NCOM_N2  are 0.7 in the pseudo_atoms.def file. The model for N2 molecule is taken from Potoff and Siepmann as the charge values for N and NCOM match with the partial charges given to these sites of N2 molecule of Potoff and Siepmann. How is the pseudo atom radius of 0.7 defined? What is the basis for the same. The experimental bond length of N2 molecule is 1.1 A.
The reason I am asking this question is because I want to define the pseudo_atoms for two CO models developed by Calero et al  (2012) and Piper et al (1984). For these models, I have the LJ parameters, charges and the distance of the sites from the COM of the molecule. What should be the basis to define the pseudo_atom radii for each site of these models?

Thanks,
Rajasi