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Messages - David Dubbeldam

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Input files and parameters / Re: Single Point Energy Calculation?
« on: January 17, 2019, 04:58:36 PM »
A single point is run by just using 0 cycles. To read in a configuration you can use the Restart-file (see manual).
A quick way of creating that file is to use 0 cycles and create a single molecule. That will write out the Restart-file containing (some) atomic positions of the molecule.
You can then edit this file, read it in, and run for 0 cycles to compute a 'single point' energy.

RASPA Workshops: Molecular simulations for adsorption and diffusion in nanoporous materials, modeling of ionic liquids, and other applications

The workshops focus on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials, and applying the RASPA software. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon. The content of the Europe and US workshops is identical. Participants will learn the theoretical foundations of Molecular Dynamics (MD) and Monte Carlo (MC), as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. We will use our publicly available code RASPA, but the gained knowledge and understanding are also directly applicable to other software. Participants will need to bring their own laptop (Mac, Linux, Windows).

Topics: (1) introduction to MD, MC; (2) studying adsorption and diffusion in porous materials (e.g. zeolites, MOFs); (3) Fluid and ionic liquid properties; (4) vapor-liquid equilibrium; (5) advanced simulation methods; (6) applying RASPA to industrial relevant systems.

Registration link:
RASPA Europe workshop at Wroclaw, Poland

More info:
Preliminary course schedule

Input files and parameters / Re: ChargeFromChargeEquilibration
« on: December 20, 2018, 09:11:37 AM »
See the example in: RASPA-2.0/examples/Auxiliary/ChargeEquilibration/IRMOF-1
You do not need any cycles, it is run only once to compute the charges of the framework using charge-equilibration.
1 x 1 x 1 unit cells is sufficient.

The charges are then written as output in the file: Movies/System_0/Framework_0_final_1_1_1_P1.cif
This cif-file you can use as the new framework (copy it to your working directory) and then use:
UseChargesFromCIFFile yes

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, 11:59:04 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, 01:48:00 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, 07:30:01 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, 06:50:46 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, 08:40:12 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, 09:41:07 AM »
Remove the empty line after "11 H_xyl    0.48371800   -2.55620700   -0.00016000"

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