Hi, everyone, I have been using the RASPA code to study the N2 adsorption in Zeolites, it is known that some of cages in zeolites need to be blocked, however, if there not exist a corresponding *.block file, can I use the *.block file as a attachment to the simulation.input to calculate the N2 adsorption? and if ok, what should I do?
For each specific case (i.e. framework), you need to define your own blocking pockets.
See for example: structures/zeolites/block/LTA_SI.block
You can put this file in your current directory, and then you can set:
BlockPockets yes
BlockPocketsFilename LTA_SI
(see for example: examples/Non-Basic/MC_Adsorption_of_CO2_in_LTA4A_Sodium).
The blocking file looks something like:
32
0.0 0.0 0.0 4.0
0.5 0.0 0.0 4.0
0.0 0.5 0.0 4.0
0.5 0.5 0.0 4.0
.......
So first the number of pockets in the unit cell, then for each pocket the fractional position and the radius in Angstrom.
Everything within that radius from the given point will be blocked.
Also check the output-file to confirm your pockets have been properly read.
Hi, David Professor:
Thanks for your reply.
It is mandatory to put the block files in the dictionary: structures/zeolites/block/?
For example, the OFF zeolite, the corresponding "OFF.block" file was generated by the zeo++ code, and I set the option in "simulation.input" file:
BlockPockets yes
BlockPocketsFilename OFF
I put the "OFF.block" and "simulation.input" files in the same dictionary; then, I run the simulation.input file, however, in the output-file, I found the "OFF.block" file could not be read.
Is there any solutions to solve the above problem if I put the *.block and simulation.input in the same dictionary?
Looking forward to your reply!
Yes, you can put the block file in the current directory (where the run-file and the simulation.input file is) and it is then properly read.
If your file is called: LTA12345.block
then use:
BlockPockets yes
BlockPocketsFilename LTA12345
If it does not work, then make sure you use the latest version (2.0.29). The output-file should start with:
Compiler and run-time data
===========================================================================
RASPA 2.0.29
Thanks for your reply. I will check and download the latest version of RASPA.
Dear Professor Dubbeldam,
I have installed zeo++ and have been trying to generate blockfile from a cif file for a mof but apparently it only accepts cssr format. Am I right?
How can I obtain the cssr file for a mof?
Best regards,
Masoud
You can use a tool like "openbabel" to convert between different file formats.
Dear Professor Dubbeldam,
I have installed zeo++, and I have the cssr file from openbabel, when I run the command "./network -ha -block probe_radius num_samples input_structure.cssr" this error is shown: "voro++: periodic cell computation failed". What should I do? please guide me.
Thanks a lot
best regards
Probably best to ask the creators of zeo++.
Dear Professor Dubbeldam,
I have solved the problem. I want to block inaccessible pores for different zeolites when they adsorb propane or propene. In zeo++ website, the related command is " ./network -ha -block probe_radius num_samples input_structure.cssr ". I set a value instead of term "probe_radius" for example 0.5,1,1.5, but the output file is just zero. I will be very grateful if you can guide me.
Thanks a lot
best regards
Probably best to ask the creators of zeo++.
Use a structure that you know is porous so you can interpret the values that zeo++ gives.
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
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?
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
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'.
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