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Messages - David Dubbeldam

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31
Input files and parameters / Re: Error in connectivity
« on: September 21, 2018, 06:54:11 PM »
The most common reason is that your molecule contains a ring. RASPA can not handle flexible rings.

32
General / Re: Issue with the forcefield
« on: September 21, 2018, 04:44:04 PM »
The forcefield and molecules present in RASPA are examples. For your system you need to define your own force field (for the adsorbate, the ZIF-8, and the cross-interactions). All relevant interactions needs to be defined.

33
General / Re: Issue with the forcefield
« on: September 20, 2018, 09:23:48 AM »
Higher adsorption capacity compared to what? experiments? other simulations?
For the first, you need to make sure you use a reliable force field and a structure that corresponds to the experiments (taking inaccessibility for example into account). For the latter, you need to make sure you do the simulations exactly as published in the literature.

34
Output files / Re: Excess adsorption
« on: July 29, 2018, 11:52:41 AM »
No, there is nothing wrong. With the fugacity coefficient specified as 1.0, the code will not compute the excess adsorption. For that it needs to use an equation of state using the critical constants.
Note that you can also trivially compute excess adsorption from absolute adsorption by hand (see literature).

35
Output files / Re: Excess adsorption
« on: July 27, 2018, 08:12:40 PM »
The computation of excess adorption is done using an equation of state (Peng-Robinson), which requires that you specify the critical constants for your molecule (at the top of the molecule definition).

36
So in iRASPA you import both files at the same time (on a mac you use cmd-click to add to the selection in the file-import).

37
What do you mean with a "totally destroyed structure"? Are you using a flexible model? In that case you need a good force field to describe the flexibility of the framework.
For a rigid structure, the end and begin structure should of course be identical. In case you meant a rigid structure, then check whether the space-group is given correctly. You can always change your structure to a P1 structure, so that there are no space group issues.

38
Output files / Re: MSD calculation
« on: May 23, 2018, 09:39:03 AM »
See the manual for these options.

'ComputeMSDConventional'  for conventional MSD, and 'ComputeMSD' for order-n MSD (works in log-scale).

Correlation times are usually much smaller than total simulation time, because you need to average a lot to get good statistics. You could only have one measurement of a correlation time equal to your simulation length and that point would be useless.

39
Input files and parameters / Re: The flexibility of IRMOF-1
« on: May 12, 2018, 04:30:02 PM »
If you use a flexible framework, then all atoms should move. In MD that is done automatically; in MC you need MC-moves to do that.

40
Input files and parameters / Re: BarrierCrossing examples?
« on: May 08, 2018, 12:38:05 PM »
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.


41
Input files and parameters / Re: Makegrid
« on: April 25, 2018, 05:00:05 PM »
I am not sure, but you can always try it and sees if it works or not.

42
Input files and parameters / Re: Question on Pseudo_atom.def
« on: April 25, 2018, 04:59:16 PM »
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.

43
Output files / Re: MSD calculation
« on: April 25, 2018, 04:55:49 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'.

44
No, you do that by setting for the component:
FugacityCoefficient 1.0
Then you compute vs fugacity (see the manual).

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