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Messages - David Dubbeldam

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136
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

137
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.

138
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.

139
Announcements / iRASPA 1.1.3
« on: March 15, 2018, 07:00:51 PM »
What's new in this version:
• VASP POSCAR/CONTCAR importing/exporting.
• Bug-fixes.

140
RASPA Workshops: Molecular simulations for adsorption and diffusion in nanoporous materials, modeling of ionic liquids, and other applications

The workshops focus on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials, and applying the RASPA software. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon. The content of the Europe and US workshops is identical. Participants will learn the theoretical foundations of Molecular Dynamics (MD) and Monte Carlo (MC), as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. We will use our publicly available code RASPA, but the gained knowledge and understanding are also directly applicable to other software. Participants will need to bring their own laptop (Mac, Linux, Windows).

Topics: (1) introduction to MD, MC; (2) studying adsorption and diffusion in porous materials (e.g. zeolites, MOFs); (3) Fluid and ionic liquid properties; (4) vapor-liquid equilibrium; (5) advanced simulation methods; (6) applying RASPA to industrial relevant systems.

Registration link:
RASPA USA workshop at Northwestern University, Evanston, IL, USA

More info:
Preliminary course schedule

141
RASPA Workshops: Molecular simulations for adsorption and diffusion in nanoporous materials, modeling of ionic liquids, and other applications

The workshops focus on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials, and applying the RASPA software. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon. The content of the Europe and US workshops is identical. Participants will learn the theoretical foundations of Molecular Dynamics (MD) and Monte Carlo (MC), as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. We will use our publicly available code RASPA, but the gained knowledge and understanding are also directly applicable to other software. Participants will need to bring their own laptop (Mac, Linux, Windows).

Topics: (1) introduction to MD, MC; (2) studying adsorption and diffusion in porous materials (e.g. zeolites, MOFs); (3) Fluid and ionic liquid properties; (4) vapor-liquid equilibrium; (5) advanced simulation methods; (6) applying RASPA to industrial relevant systems.

Registration link:
RASPA EUROPE workshop at Delft University of Technology, Delft, The Netherlands

More info:
Preliminary course schedule

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