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Messages - David Dubbeldam

Pages: [1] 2 3 ... 6
1
Output files / Re: Visualization of adsorption
« on: December 09, 2019, 08:54:35 AM »
You just import all the pdb- and cif-files you would like to visualize (so select multiple files during import).
Then you can set individual visualization properties, like origin, drawing-method, etc.

2
Either use a model that puts the charge-centers on the atomic centers (OPLS) or if the molecule is small you can also make the whole molecule rigid.

3
General / Re: Flexible-MOFs forcefield Issue
« on: November 08, 2019, 04:13:47 PM »
For a force field for a flexible MOF you need to define all the interactions similar to the flexible IRMOF-1 example.
The GenericMOFs defines only the interactions of molecules with the framework.

4
Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites
« on: October 04, 2019, 01:18:16 PM »
You could do some basic debugging, like setting the PrintEvery to 1 and see if it is just slow or that you are really stuck at step 0.
The latter can happen if you try to put in more molecules than fit in the simulation volume.

5
Visualization / Re: Making the grid finer for adsorption surfaces
« on: October 03, 2019, 11:56:24 AM »
Currently it is using a grid of 128x128x128. Several opties are considered in future releases:
1) an option for 256x256x256
2) Use tessellation on newer videocards to create smoother surfaces.

6
Announcements / New review on force fields
« on: September 30, 2019, 06:41:57 PM »
An open access review that potentially could be of interest to some members on the forum, especially those that are interested in force fields, force field types and design, implementation (gradients, second derivatives, strain derivatives), Ewald summation, polarization, optimization, parameterization, Machine Learning, and General-Purpose GPU computing:
https://onlinelibrary.wiley.com/doi/10.1002/adts.201900135

7
Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites
« on: September 29, 2019, 11:45:36 AM »
In open ensembles (Gibbs, grand-canonical ensemble) the number of molecules fluctuates. So if more memory is needed the code needs to realloc the memory to make it larger.

8
General / Re: Superimposing pdb files using iRASPA
« on: September 19, 2019, 07:00:13 PM »
Yes, just select both files when you import the structures.

9
General / Re: Status of iRASPA-QT
« on: September 18, 2019, 08:07:20 PM »
The windows/linux QT-versions has some basic functionality implemented (but still way less than the mac-version).
Windows QT version is available from the Windows store, and the linux version is available from the snap-store.

For both: good OpenGL >3.3 drivers are needed, and OpenCL drivers, which is a problem on both linux and windows.

10
Input files and parameters / Re: Raspa taking more time
« on: September 12, 2019, 07:15:15 PM »
For a comparison between some MC codes (Cassandra, DL Monte, Music, Raspa and Towhee) see:
https://www.tandfonline.com/doi/full/10.1080/08927022.2017.1375492

There is a wide difference in the statistical value of a single MC step, however their computational performance is quite comparable.

RASPA is not optimized for speed, and meant for relatively small system-sizes. The most expensive part is usually the Ewald-summation.

11
Output files / Re: Histograms produced by raspa
« on: August 31, 2019, 06:42:21 PM »
Histograms do not really have units on the y-axis. The x-axis, for energy, would be Kelvin.
You can easily figure these things out by checking the source, and check what is exactly counted and how it is written out.
See source file: sample.c, and the function 'void SampleEnergyHistogram(int Switch)'.

12
Input files and parameters / Re: Average configuration as restart-file
« on: August 31, 2019, 06:37:30 PM »
Saving of snapshots is more easily done by adding them to a movie. But you could run short simulations and copy the restart-file saved at the end to another directory if the goal is to create many restart-files.

13
That is not possible. The atoms for the molecule file needs to be defined and the charge is taken from the pseudo_atoms.def file.
So, currently, the same type of atom of a molecule must have the same properties.

14
You could add your way of computing the pressure in the source code, or modify the implemented calculation of the pressure.

15
To reliably model adsorption/diffusion, the mobility of the cations needs to be taken into account. For example, in FAU there are many different cation-sites with certain "occupancy" ratios. Your cation model needs to be able to reproduce that.
That is why it is hard to reach an equilibrated system and it is a good idea to, when you have generated that, to store these positions in a restart-file.
Since cations are charged, the usual CBMC biasing can lead to numerical issues, but for single-atom cations you can achieve the same with a random-translation that tries to place the cation randomly in the box.
Look in the literature for papers on modeling of zeolites with cations for more pointers.

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