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Messages - David Dubbeldam

#226
There is a new example added to the last version (v2.0.31): examples/Advanced/dcTST-LTA_SI.
See also the updated raspa.pdf in: Docs.

#227
Input files and parameters / Re: Makegrid
April 25, 2018, 06:00:05 PM
I am not sure, but you can always try it and sees if it works or not.
#228
For all force field files, use your own values. All force field files in RASPA are just meant as examples.
The important value are epsilon and sigma for the Lennard-Jones.
The radii in the 'pseudo_atoms.def' are only used to compute bonds.
#229
Output files / Re: MSD calculation
April 25, 2018, 05:55:49 PM
The files with 'self' are self-diffusion, the 'total' file is self-diffusion of the total fluid (so independent of the component type). So for a single component run the output for the component and the total is the same. For a multi-component mixture they differ. The files with 'onsager' in the name contain mixture Onsager coefficients.
Note the files contains in the columns:
1: correlation time in picoseconds.
2: MSD averaged over x,y,z (number of dimensions = 3).
3: MSD in the x-direction  (number of dimensions = 1).
4: MSD in the y-direction (number of dimensions = 1).
5: MSD in the z-direction (number of dimensions = 1).
6: number the times this point has been computed.

The source for this is `src/sample.c'.
#230
No, you do that by setting for the component:
FugacityCoefficient 1.0
Then you compute vs fugacity (see the manual).
#232
Yes, but you can look them up somewhere if you need them. These are used to convert pressure to fugacity using an equations of state.
Alternatively, if you use fugacity in your simulations (instead of pressure) then these number are not used.
#233
Announcements / iRASPA 1.1.5
April 10, 2018, 02:36:16 PM
What's new in this version:
• Greatly improved drag and drop, and copy and paste, for the project- and scene-panes (using concurrent background queues).
• Added and modified the 'New"-menu item under 'File'.
• Properly implemented the add- and remove-buttons for the project- and scene-panes.
• Many, many bug-fixes for crystal, molecular crystal, protein crystal, molecule, and protein.
• Updated for Swift 4.1.
#234
Output files / Re: ENERGY DRIFT
April 07, 2018, 04:28:20 PM
For any error, always retry with the latest version (which is RASPA 2.0.30).
#235
Input files and parameters / Re: Minimization
April 05, 2018, 11:13:39 AM
These structures are either from experiment (published in the literature) or from the IZA website.

If you want to minimize a zeolite or MOF structure, then you need a forcefield for it (and a good one).
So yes, options "FlexibleFramework and FrameworkDefinitions" need to be there and FrameworkDefinitions.def needs to contain a good force field for the framework.

If you want to minimize molecules inside the framework, the you can keep the framework fixed and "FlexibleFramework and FrameworkDefinitions" are not needed.
#236
See the manual for the format of the file. If you add an interaction you need to increase the number of interactions.
Change
# number of defined interactions
28

to
# number of defined interactions
29
#238
Visualization / Re: Mult. Val. Adsorption Surfaces
March 30, 2018, 05:31:19 PM
In the scene-navigator (https://www.iraspa.org/iRASPA/index.html#/SceneNavigator) use copy and paste to create an identical new structure (select, then command-C, command-V). Then select the second (the new one) and change the properties of the adsorption surface. If you want to avoid drawing the second set of atoms needlessly, then you can switch off the drawing of atoms and bonds for the second one, and only use the adsorption surface.
For example, see the gallery-section of the project-navigator, then "Adsorption surfaces", then "CHA_SI", it has three structures for the three surfaces, each with a different isovalue, transparency and color.
#239
If I am not mistaken (but check carefully) it is identical to e.g. the equation 10 from the paper: "Nested sampling in the canonical ensemble: Direct calculation of the partition function from NVT trajectories", S. Nielsen, The Journal of Chemical Physics 139, 124104 (2013); doi: 10.1063/1.4821761
There are however many different formulas published for the heat capacity.
#240
Announcements / iRASPA in the news
March 29, 2018, 02:53:06 PM
Folia is the medium outlet, for and by students, teachers, and employees of the University of Amsterdam (UvA):
https://www.folia.nl/wetenschap/120254/chemicus-maakt-app-om-moleculen-in-3d-te-analyseren