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Messages - David Dubbeldam

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General / Re: 'CrashRestart' taking long time
« on: December 04, 2018, 10:18:32 AM »
If you know that there is no hysteresis in the system, you could simulate all of these pressure in parallel. That really speeds up computations of isotherms.

General / Re: GCMC results not exactly matching with literature
« on: December 04, 2018, 10:13:39 AM »
That could be for a variety of reasons, including slightly different positions for the atoms of a rigid molecule, and details like cutoff-distance, tail-corrections yes/no, etc. Also, results depend on the total amount of molecules and the system size etc.

Input files and parameters / Re: Configuration Files
« on: November 26, 2018, 06:54:08 PM »
See e.g. the "Movies yes" and "WriteMoviesEvery 5000" options  (explained in the manual).

Input files and parameters / Re: PartionFunction in Reactive Ensemble
« on: November 12, 2018, 11:45:46 AM »
In the literature and articles on "Reactive ensemble" the authors usually cite articles that describe how to compute these (either using QM calculations or using experimental date tables).

Input files and parameters / Re: Error while using "Grid" option
« on: November 12, 2018, 11:42:57 AM »
You can select which atoms to use for interpolation. The other ones will be computed in the usual way without interpolation.
The test at the beginning is limited and just meant to catch obvious wrong interpolations. But it is up to the user to judge whether the interpolation is sufficiently accurate or not. A few test of e.g. isotherms with and without grids can shows whether the grid is accurate enough.

Input files and parameters / Re: Error while using "Grid" option
« on: October 31, 2018, 02:21:51 PM »
These are warnings, it is up to you to judge how good the interpolation is.
For atom-types that have no VDW interaction, the atoms can be placed on top of other atoms during the test. This lead to large errors in the energy/force interpolation, but this would not occur during a real simulation.
Also, you can select which atom types to use with grid-interpolation (and which not).

General / Re: 'CrashRestart' taking long time
« on: October 24, 2018, 10:59:04 AM »
The binary-restart should immediately pick up where it left. So at most 10000 cycles before catching up again with the output. Make sure it really reads the binary restart and does not restart from scratch (for example, by testing it using WriteBinaryRestartFileEvery with a smaller number and run it interactively in a console). Also, you have the source code, and you can use a debugger to see what is happening).

General / Re: 'CrashRestart' taking long time
« on: October 18, 2018, 12:48:00 PM »
What is "CrashRestart yes"? Please check the manual "Restart and crash-recovery".
There is an option to restart from a restart-file containing positions, velocities, forces, and one option to continue from a binary file.
The binary-file format is not transferable between different versions of the code, so make sure you are using the latest version of the code (2.0.35).

Input files and parameters / Re: chemical potential in input file
« on: October 01, 2018, 06:30:01 PM »
No, but you can convert your 'chemical potential' to 'fugacity'.
Then, to use your own equation of state, simply input your computed 'fugacity coefficient'.
For example:
ExternalPressure 1e5
FugacityCoefficient 1.0
means the pressure is fugacity (because the fugacity coefficient is 1.0 and then pressure is equal to fugacity) and at 1 bar.
With your equation of state you can compute the fugacity coefficient.

Input files and parameters / Re: Error in connectivity
« on: September 29, 2018, 05:50:46 AM »
We do not have anything to do with python (that is an addition by 'numat' and their github version).
For our version (see the manual) you install with:
1 ) rm -rf autom4te.cache
2 ) mkdir m4
3 ) aclocal
4 ) autoreconf -i
5 ) automake --add-missing
6 ) autoconf
7 ) ./configure --prefix=${RASPA_DIR}
8 ) make
9 ) make install

Input files and parameters / Re: Error in connectivity
« on: September 23, 2018, 07:40:12 AM »
For our version of the code, this should not happen (on a standard unix system) and indicates something very strange on your system. Use a debugger to found out why it fails.
If you're using a version by other people (for example the numat github version) then it could be that their python additions might cause this problem.

Input files and parameters / Re: Error in connectivity
« on: September 22, 2018, 08:41:07 AM »
Remove the empty line after "11 H_xyl    0.48371800   -2.55620700   -0.00016000"

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.

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.

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.

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