Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Messages - David Dubbeldam

Pages: [1] 2 3 ... 7
General / Re: Mg and K cations .def file
« on: May 26, 2020, 04:57:06 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.

Negative excess adsorption indicates that you are in the liquid phase. That happens when you go above the vapor pressure.

Input files and parameters / Re: MC and MD inconsistency
« on: May 14, 2020, 07:07:21 PM »
A common inconstancy between MC and MD is the VDW potential. Make sure you use a shifted VDW potential for MC.

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.

Input files and parameters / Re: setup for energy-bias GCMC?
« on: April 24, 2020, 06:41:49 PM »
The energy-bias method is not implemented in RASPA (it is implemented in the code 'MUSIC').

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.

Output files / Re: Excess adsorption
« on: April 24, 2020, 06:34:21 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.

Input files and parameters / Re: Gibbs Ensemble MC
« on: April 24, 2020, 06:31:05 PM »
You could take the restart-file:
mv Restart RestartInitial

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).

General / Re: MIL-53(Cr) flexible MOF MD problem
« on: April 24, 2020, 06:26:57 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.

Visualization / Re: create movie
« on: April 24, 2020, 06:22:43 PM »
For now, many capabilities are only available on the Mac version. The window version will be updated in the coming months.

Bug reports / Re: MSD for diffusion at infinite dilution
« on: April 09, 2020, 09:58:52 AM »
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.

Input files and parameters / Re: Choosing space group
« on: April 09, 2020, 08:42:02 AM »
For space groups, see
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

Yes, the first component is then not changing it's number of molecules, while the second component is swapped in and out.

General / Re: error run simulate
« on: March 01, 2020, 09:40:13 AM »
Since I see some python stuff, so it is probably that you are using the numat-code (
You could ask them about their additional python routines.
Our version is strictly C, and is at:

Visualization / Re: Visualisation using Para View
« on: 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.

Pages: [1] 2 3 ... 7