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Messages - David Dubbeldam

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Simulation algorithms and theory / Re: MC and adsorption capacity
« on: October 13, 2021, 08:08:23 PM »
Search for books and literature on grand-canonical ensembles. There are also many books, reviews, articles on the topic of simulation of adsorption.

General / Re: Number of molecules in GEMC box
« on: October 13, 2021, 08:06:24 PM »
What do you mean wiith "not accurate"? Compared to what? experiment or the result of the TraPPE force field?
Force TraPPE, make sure you use an unshifted potential and tailcorrections.

General / Re: How to run the Gibbs ensemble MC simulation of 3 boxes
« on: October 13, 2021, 08:01:22 PM »
You will need to some code modifcations to make this work. Create 3 systems and specify the moves between the boxes of choice.

Input files and parameters / Re: The usage of block_file
« 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'.

General / Re: RASPA Simulations Directory not Found
« on: September 27, 2021, 07:27:24 PM »
That is done in the run-file. See manual "1.3.5 Running RASPA".

Input files and parameters / Re: RandomAlSubstitution_13X
« 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.

Visualization / Re: iRASPA unable to visualize 13X zeolite file
« 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.

Input files and parameters / Re: The usage of block_file
« 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?

Announcements / RASPA workshop announced (online) 20 January 2022
« on: September 22, 2021, 03:01:20 PM »
This workshop/school focuses on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we will also consider the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online.

General / Re: Grid potentials for mobile cations in MC/GCMC simulations
« on: September 22, 2021, 02:58:55 PM »
The grids are tested by random insertion. So there is no mechanism that avoids overlap of the ions.
You can get: large negative Coulombic energy + large repulsive energy, that nearly cancels out.
So, this is more a problem of the test then of the grid itself.
You can run a simulation with and without the grid and see if you get the same answers.

General / Re: RASPA Simulations Directory not Found
« on: September 22, 2021, 02:52:10 PM »
You should not install it on /lib, which is indeed a read-only systems directory.
Better just install it in your home account.

In the raspa-directory do:
rm -rf autom4te.cache 
mkdir m4 
autoreconf -i 
automake --add-missing 
make install

Input files and parameters / Re: The usage of block_file
« on: August 31, 2021, 08:36:53 PM »
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.

Like you say, if simulation-time was not an issue, then starting from a previous point helps with equilibration. But the computational cost is large, especially for higher pressures. So by submitting them all in parallel, you can compute the full isotherm at the costs of the time of the largest loading. For sequential running, you will need to wait for the result of the previous pressure. So, especially for isotherm with say 10-20 points, running them in parallel really helps.

General / Re: RASPA2 Run File
« on: August 31, 2021, 08:31:21 PM »
You can use:

Input files and parameters / Re: The usage of block_file
« on: August 16, 2021, 09:22:15 AM »
Probably best to ask the creators of zeo++.

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