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11
Simulation algorithms and theory / MC and adsorption capacity
« Last post by YadiJiang on October 02, 2021, 03:47:37 PM »
Hi Prof. Dubbeldam,

When using Monte Carlo method to carry out a simulation, i can gaint 'average loading absolute' and 'average loading excess' of absorbate. However i don't know the theory of obtaining the adsorption capacity by Monte Carlo method. What is the theory of this process, or what can I learn to understand the theory?

Thank you,
Jiang
12
General / RASPA 2.0 vs RASPA 2.0.45
« Last post by rshukre on September 29, 2021, 08:46:07 PM »
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
13
General / Re: RASPA Simulations Directory not Found
« Last post by amogh on September 28, 2021, 07:31:24 PM »
I have figured out how to properly name the RASPA_DIR variable to my home directory and so my home directory structure looks like this:

amogh (home)
- RASPA
- RASPA_2
   -  RASPA2 (github repo)
   -  venv

Despite this, I tried running some of the sample simulations that come with the Github repo and hit a segfault when executing the run file. I used BookChapter/6-GrandCanonicalAdsorption/Methane example simulation which has all of the required files in its folder locally and modified the run file to this:

#! /bin/sh -f
export RASPA_DIR=$/RASPA/simulations
export DYLD_LIBRARY_PATH=${RASPA_DIR}/lib
export LD_LIBRARY_PATH=${RASPA_DIR}/lib
/Users/amogh/RASPA/simulations/bin/simulate -simulation.input

And this is the produced error when I try to run the "run" file from the home directory. I also tried to run this without the   
"-simulation.input" parameter and it claimed that it is unable to open the input file. All of the ".def" that are mentioned to not be found are in that local folder, which is visible in the RASPA2 repo as well.

(venv) (base) amogh@Amoghs-MBP ~ % ./RASPA_2/RASPA2/examples/BookChapter/6-GrandCanonicalAdsorption/Methane/run
     
'pseudo_atoms.def' file not found and therefore not used
'force_field_mixing_rules.def' file not found and therefore not used
'force_field.def' file not found and therefore not used

./RASPA_2/RASPA2/examples/BookChapter/6-GrandCanonicalAdsorption/Methane/run: line 5:  1436 Segmentation fault: 11  /Users/amogh/RASPA/simulations/bin/simulate -simulation.input

Any guidance would be greatly appreciated!
14
Visualization / Re: iRASPA unable to visualize 13X zeolite file
« Last post by rshukre 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.
15
Input files and parameters / Re: The usage of block_file
« Last post by rshukre on September 28, 2021, 06:52:03 PM »
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




16
Input files and parameters / Re: RandomAlSubstitution_13X
« Last post by rshukre on September 28, 2021, 06:45:14 PM »
Thank you.
17
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'.
18
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".
19
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.
20
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.
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