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Messages - David Dubbeldam

Pages: 1 ... 13 14 [15] 16
211
Output files / Re: ENERGY DRIFT
« on: April 07, 2018, 04:28:20 PM »
For any error, always retry with the latest version (which is RASPA 2.0.30).

212
Input files and parameters / Re: Minimization
« on: 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.

213
Output files / Re: atom-pairs with no VDW interaction(s)
« on: April 03, 2018, 08:55:57 AM »
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

215
Visualization / Re: Mult. Val. Adsorption Surfaces
« on: 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.

216
Simulation algorithms and theory / Re: Heat Capacity (MC-NPT)
« on: March 30, 2018, 05:25:45 PM »
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.

217
Announcements / iRASPA in the news
« on: 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

218
Output files / Re: atom-pairs with no VDW interaction(s)
« on: March 29, 2018, 11:22:39 AM »
The force fields provided with RASPA are examples. If you are doing simulations for your own systems, then construct your own force fields (you can put them in your local directory). Of course you can use the provided examples as a start. If you want to get rid of the warnings you can define these VDW potentials explicitly in the forcefield files (by listing them as 'none' if they do not need any VDW interaction).

219
Output files / Re: atom-pairs with no VDW interaction(s)
« on: March 28, 2018, 09:20:23 PM »
Warnings are produced for undefined VDW pairs. If you want to get rid of the warnings you can define these VDW potentials explicitly (by listing them as 'none' if they do not need any VDW interaction).

220
Input files and parameters / Re: turning on polarizability
« on: March 28, 2018, 09:18:16 PM »
RASPA does not contain fully working polarization. For that you need extensive modifications of the source code.

221
Announcements / iRASPA 1.1.4
« on: March 27, 2018, 10:08:59 AM »
What's new in this version:
• Mouse editing of atoms (translate selected atoms with option-command-drag).
• Set precision of space-group detection.
• Dragging of pdb-, xyz-, and POSCAR-files into the project pane from the Finder.
• Bug-fixes.

222
I am not aware of such a program. Most papers that publish forcefields list all the potentials and parameters in tables, and you need to input them into the file and check it carefully.

223
Input files and parameters / Re: The usage of block_file
« on: March 21, 2018, 06:46:01 PM »
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

224
Input files and parameters / Re: The usage of block_file
« on: March 19, 2018, 02:08:45 PM »
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.

225
Checkout the example: examples/Advanced/Adsorption_of_CO2_in_Flexible_IRMOF-1_Fixed_Volume.
For a flexible framework  you need to specify:
(1) FlexibleFramework yes
(2) FrameworkDefinitions Dubbeldam2007FlexibleIRMOF-1
The first says that you treat the framework as flexible, the second specifies the force field file used.
For this example it is listed in 'framework/Dubbeldam2007FlexibleIRMOF-1/framework.def' and on 'make install' copied to '~/RASPA/simulations/share/raspa/framework/Dubbeldam2007FlexibleIRMOF-1/'
To use your own force-field you can
(1) copy this file in your current directory, so it will be read first.
(2) modify the force field for your specific case.

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