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 ... 11
1
Output files / Re: Regarding Non-Basic/Gibbs_CO2 example
« on: July 21, 2021, 09:53:32 AM »
See the many articles of Martin and Siepmann on this topic.

To compute pressure:
ComputeMolecularPressure yes

2
Input files and parameters / Re: The usage of block_file
« on: July 21, 2021, 09:47:57 AM »
You can use a tool like "openbabel" to convert between different file formats.

3
Input files and parameters / Re: FIXED_BOND vs RIGID_BOND
« on: July 21, 2021, 09:40:47 AM »
See the examples for molecules. RIGID_BOND is used for molecules that are fully rigid, for example water or CO2. The bonding information is used for the CBMC-biasing.
RIGID_BOND is a type of bond-potential that has only one bond-distance.

4
Output files / Re: Error: malloc(): corrupted top size
« on: July 21, 2021, 09:37:02 AM »
MIL-101 is very large indeed. RASPA is not optimized for speed.  You can use a debugger to see where it goes wrong.

5
General / Re: High-Pressure Simulations
« on: July 21, 2021, 08:51:45 AM »
9% at those high pressure is still very, very good I would say. The validity of such a simple methane model is not "endless". Any classical model will show weaknesses at extreme conditions. Perhaps a full-atom model might do better, but these are harder to paremeterize.

6
Output files / Re: Regarding Non-Basic/Gibbs_CO2 example
« on: June 18, 2021, 08:54:25 PM »
1) As many cycles and molecules as you need. The more the better, but the slower the simulations. That's always a trade-off.
In equilibrium, the macroscopic properties no longer change. The amount of cycles needed to reach equilibrium depends on the system.
To limit finite size effects you need a large system. In practice you can simulate various system sizes as see when your properties converge to a plateau value as a function of system size.

2) in a NVT or muVT or Gibbs NVT simulation the energy fluctuates. This energy fluctuation is related to a physical property called the heat capacity.

3) There are no rules of thumbs, but rather it will take experience to get a feel for this.

7
General / Re: Irreproducible Partial Charges uing Qeq method
« on: June 08, 2021, 02:39:04 PM »
Yes, all Qeq are differently implemented. The code in RASPA is based on the method of Wilmer and Snurr.
https://pubs.acs.org/doi/10.1021/jz3008485

8
General / Re: parameter input
« on: June 08, 2021, 02:36:34 PM »
The 'pseudo_atoms.def' contains predefined atoms, and this is often the way to go for molecules.
This especially important for united atom types etc.

For frameworks, read from a CIF file, there is always an element defined (_atom_site_type_symbol), and the type (_atom_site_label) is automatically added when found. The mass is a lookup from a database in 'src/scattering_factors.c'.

9
Input files and parameters / Re: Density histograms
« on: June 08, 2021, 02:28:59 PM »
This function writes out a VTK-file, a 3D histograms of the density. See the examples on Visualization.
You could also read this file yourself.

10
Input files and parameters / Re: Use of dreiding force field
« on: June 08, 2021, 02:26:43 PM »
The DREIDING force field uses specific functional forms and parameters. You can look these up and use (most of) these in RASPA.

11
Input files and parameters / Re: Error - mixed gas adsorption
« on: June 08, 2021, 02:11:36 PM »
Input looks, at first sight, okay to me. Remove as much as possible, i.e. component 1-3 etc, and check if it works. Then from add the components one by one to see where it goes wrong.
In general, change stuff in small steps, otherwise it is harder to debug.

12
I don't think this is currently possible. The implementation of the CBMC algorithm used for the insertion is the limitation here.

13
No, the pressure is indeed not used in this example.
I will remove the pressure line in the example.

14
Output files / Re: Shift all potential
« on: May 21, 2021, 06:50:13 PM »
Have a look at the example rigid molecules in RASPA, e.g. CO2.
Numbering starts at zero.

15
General / Re: Error at run time
« on: May 21, 2021, 06:47:00 PM »
That is hard to say based on this information. Always try with the latest version (2.0.45).
If it crashed, then use a debugger to find out why it crashes (section 5.5 in the manual).

Pages: [1] 2 3 ... 11