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Messages - David Dubbeldam

#151
General / Re: Mg and K cations .def file
May 26, 2020, 05:57:06 PM
All structure, molecule and force field files are examples. For you own use case, you need to construct these files with the exact parameters that you want.
#152
Negative excess adsorption indicates that you are in the liquid phase. That happens when you go above the vapor pressure.
#153
A common inconstancy between MC and MD is the VDW potential. Make sure you use a shifted VDW potential for MC.
#154
Depending on the value of 'f' you could probably rewrite that functional form into into another form that is supported (using cosine and sine rules). If that is not possible, another option is add the functional form in the code.
#155
The energy-bias method is not implemented in RASPA (it is implemented in the code 'MUSIC').
#156
1) if you need to convert from fugacity to pressure (or when computing excess) adsorption, that look upon the critical parameter that you want to use, and add them tot he molecule definition.
2) You input the fugacity (directly related to the pressure). So for your system you need to compute the correct fugacity to input.
#157
Output files / Re: Excess adsorption
April 24, 2020, 07:34:21 PM
Critical constants can be taken from handbooks or using google.

The parameters for potentials are taken from force fields that are also published. The functional forms that can be used are described in the manual.
#158
Input files and parameters / Re: Gibbs Ensemble MC
April 24, 2020, 07:31:05 PM
You could take the restart-file:
mv Restart RestartInitial

use:
RestartFile                   yes

and use:
CreateNumberOfMolecules   X Y
to add additional molecules X and Y to box 0 and 1 (on top of the molecules read from the restart-file).
#159
General / Re: MIL-53(Cr) flexible MOF MD problem
April 24, 2020, 07:26:57 PM
I would do this as a function of loading. Around 2 waters per unit cell many models start to collapse (the same for CO2).
So five water molecule might be so high that the unit cell starts to become larger again.
#160
Visualization / Re: create movie
April 24, 2020, 07:22:43 PM
For now, many capabilities are only available on the Mac version. The window version will be updated in the coming months.
#161
What do you mean with "Total fluid"? Self-diffusion of water inside a framework is not the same as self-diffusion of pure water.
You can not compute infinite dilution diffusion with just a single water molecule. The limit of low density is using lots of particles but using a larger volume.
#162
For space groups, see http://cci.lbl.gov/sginfo/hall_symbols.html.
Hermann-Mauguin are not unique, the Hall symbol is.

C2/c is space group 15. You have the following flavors:

15:b1     C 1 2/c 1     -C 2yc
    15:b2     A 1 2/n 1     -A 2yac
    15:b3     I 1 2/a 1     -I 2ya
    15:-b1    A 1 2/a 1     -A 2ya
    15:-b2    C 1 2/n 1     -C 2ybc
    15:-b3    I 1 2/c 1     -I 2yc
    15:c1     A 1 1 2/a     -A 2a
    15:c2     B 1 1 2/n     -B 2bc
    15:c3     I 1 1 2/b     -I 2b
    15:-c1    B 1 1 2/b     -B 2b
    15:-c2    A 1 1 2/n     -A 2ac
    15:-c3    I 1 1 2/a     -I 2a
    15:a1     B 2/b 1 1     -B 2xb
    15:a2     C 2/n 1 1     -C 2xbc
    15:a3     I 2/c 1 1     -I 2xc
    15:-a1    C 2/c 1 1     -C 2xc                        <-----
    15:-a2    B 2/n 1 1     -B 2xbc
    15:-a3    I 2/b 1 1     -I 2xb
#163
Yes, the first component is then not changing it's number of molecules, while the second component is swapped in and out.
#164
General / Re: error run simulate
March 01, 2020, 09:40:13 AM
Since I see some python stuff, so it is probably that you are using the numat-code (https://github.com/numat/RASPA2).
You could ask them about their additional python routines.
Our version is strictly C, and is at: https://github.com/iraspa/raspa2
#165
Visualization / Re: Visualisation using Para View
February 03, 2020, 09:32:40 PM
I guess you need to figure out how Paraview scales these. For the density file, it is by default 150x150x150 points, and this needs to be converted to the real unit cell.