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Messages - David Dubbeldam

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General / Re: error message on restart after crash
« on: January 11, 2023, 08:08:05 PM »
Note sure,  but could be that the crash damage the restart-file. This could happen when the crash happens at the exact time the binary-restart-file is written to disk.

For running multiple simulations, you would use/create scripts that generate the needed input.
MOF simulations time depend on the size of the system, and how accurate you need the results.
Small systems, about a day. Larger system, a week or longer.

General / Re: About the relation between Paritition and LnPartition for NH3
« on: December 02, 2022, 04:00:28 PM »
For a detailed explanation see:
Page 262 and following, and see Table  A5.

Visualization / Re: Vector image export
« on: November 24, 2022, 10:55:40 AM »
No, the data is inherently pixel-based. Exporting to pdf would just put a picture in a pdf.

Announcements / RASPA workshop announced (online) 3 February 2022
« on: November 22, 2022, 10:37:09 AM »
This workshop/school focused on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we were also considering the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online. Due to privacy reasons, there will be no video recordings. Registration is free but compulsory. Certificates of attendance will be made available after the workshop.
We are also planning offline workshops in 2023 (November, Abu Dhabi) and 2024 (September, The Netherlands).

General / Re: About the relation between Paritition and LnPartition for NH3
« on: November 22, 2022, 10:32:28 AM »
These value come from:
and to reduce under/overflow you input them as the log of these numbers in Table S3.

Visualization / Re: Transparent background?
« on: November 22, 2022, 10:14:22 AM »
Yes, for that very reason it saves in the tiff-file format. iRASPA uses RGBA-colors. You will need to change the background color and set the opacity to zero.

Yes, the atom colors can be changed, see the help/manual.

Input files and parameters / Re: mol file
« on: November 22, 2022, 10:12:01 AM »
You can use for example 'openbabel' to convert between formats.

Visualization / Re: RASPA visualization (Density Plot)
« on: September 25, 2022, 06:01:19 PM »
That depends on the VTK-version. But VTK-file plotting is now included in iRASPA, provided you have written the VTK with the latest version of RASPA.

General / Re: Phase state in MC simulation of grand canonical ensemble
« on: September 25, 2022, 05:58:14 PM »
Based on a Peng-Robinson equation of state it calculates the phase and density of the pure fluid (without framework). This density is used to calculate the the excess adsorption.

Input files and parameters / Re: desorption-error
« on: September 25, 2022, 05:55:10 PM »
You can use a debugger to find out where it crashes and then what input error caused it.

Input files and parameters / Re: desorption-example
« on: September 25, 2022, 05:51:53 PM »
Desorption is done by going from a high (saturation) pressure back to low pressure.

Visualization / Re: TIP4P visualization and bond lengths
« on: September 25, 2022, 05:47:07 PM »
You can select whether an atom is visible or not (checkbox).

The bond-distance criteria is a standard one. This is not yet easily changeable.

Input files and parameters / Re: Problem in adsorption
« on: September 25, 2022, 05:42:33 PM »
I would suggest to talk to experimental people and ask why their data goes up.
I expect this is due to adsorption at the external surface. You would expect that the results for adsorption should level off to a saturation value.

General / Re: _atom_site_disorder_group in .cif file
« on: September 25, 2022, 05:36:46 PM »
There are no standard methods. By making choices you need to create a structure with no symmetry (P1) so that all atom positions are defined.

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