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Messages - David Dubbeldam

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1
Note that force fields like 'GenericMOFs' are only examples (just like any molecule or structure file), just for the example cases in the code to work. For any real work you need to create and develop your own force fields, or take them from from the literature, and carefully construct, check and validate them.

2
Also, orthorhombic is much faster than triclinic. For triclinic structure, the distance computation is a matrix multiplication to get fractional coordinates, then apply periodic boundary conditions, and then convert back to Cartesian space.

3
It might be that if you choose the atomic positions wrong, that the molecules can overlap. This happened in particular with for example water where the larger oxygen shield the hydrogens. Often the hydrogens do not have a VDW parameter because the repulsion of the oxygen is sufficient. Choosing a wrong repulsion (too small sigma) leads to overlap with the hydrogens and hence numerical issues. So with classical force fields you should always be aware and avoid unphysical situations.

4
General / Re: Warning: Reinsertion used on the charged ions
« on: January 07, 2021, 08:02:11 PM »
The reason for the warning is that using CBMC with regrow is not advisable when the molecule has a net charge. The energies could become why to small/large leading to under/overflow.
It is better than for cations to use 'random translation'.

If the net-charge changes it can be because the adsorbate has a (small) net charge. With inserting adsorbates it will then grow in magnitude.

5
Input files and parameters / Re: Change input file when restart
« on: January 07, 2021, 07:58:34 PM »
Using the 'binary' file, the simulation should immediately end, since it was already finished. There is no wya to extend a binary restart.
The other form of restart just use the initial positions written as output from the previous run.
The positions are written to 'Restart', while reading is from 'RestartInitial' to avoid overwriting these.
To restart, copy 'Restart' to 'RestartInitial'.
If results are different, then you did not equilibrate long enough.

6
Input files and parameters / Re: Error in connectivity
« on: December 23, 2020, 09:23:51 PM »
Check the manual and examples. There are explicit examples for mixtures and adsorption mixtures,
for example:
examples/Basic/MC_BinaryMixture_in_Box
examples/Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1

7
General / Re: How to eliminate the boundary effect in GEMC simulations?
« on: December 23, 2020, 09:20:53 PM »
Do you mean that you want to simulate adsorption on the outside of the zeolite?
Because using the grand-canonical approach only the adsorbed phase inside the framework is computed.

I have no experience with adsorption on the external surface of a zeolite.

8
Did you set the 'IdealGasRosenbluthWeight'?

Since every flexible model changes the reference chemical potential, the IdealGasRosenbluthWeight needs to be explicitly computed using a simulation of a single molecule in an empty box, and then used as the reference in the adsorption simulation.

9
General / Re: Issue with ExtraFrameworkMolecule
« on: December 23, 2020, 09:09:27 PM »
I re-ran "examples/Non-Basic/MC_Adsorption_of_CO2_in_LTA4A_Sodium" without problems.
There was however a small memory-issue which could affect this, so you could retry with version 2.0.40.

But usually "illegal instruction" is related to the compiler, for example compiling on intel-type A and then running on intel-type B.

10
Input files and parameters / Re: Flexible and chiral molecules
« on: December 23, 2020, 07:38:15 PM »
Did you define a flexible-ring? (RASPA can not handle flexible rings).

11
Input files and parameters / Re: Miture Grand canonical MC Fugacity
« on: December 23, 2020, 07:35:52 PM »
See the example: Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1
You specify total pressure and mol-fractions. Partial fugacities are computed and written to the output-file.


ExternalTemperature 300.0
ExternalPressure  10e5

Component 0 MoleculeName               CO2
            MolFraction                0.25

Component 1 MoleculeName               methane
            MolFraction                0.75

12
Bug reports / Re: Charge Equilibration leads to Segmentation Fault
« on: December 23, 2020, 07:31:05 PM »
Most likely it is related to the encoding of your cif-file (i.e. newline and carriage return which differed between windows and Mac/linux).

Framework[CurrentSystem].Atoms[CurrentFramework].Type
The type seems be nonsensical, so the error must be during the reading of the cif-file.

To quickly debug, run with 1x1x1 and 'ChargeFromChargeEquilibration    no', and then check in the output-file that the file is read properly.

13
Input files and parameters / Re: ReturnPseudoAtomNumber Error
« on: November 28, 2020, 08:21:11 PM »
See e.g. 'forcefield/GarciaPerez2006' for an example of the 'force_field_mixing_rules.def', 'force_field.def', and 'pseudo_atoms.def' files.

14
Visualization / Re: Visualization
« on: November 28, 2020, 08:13:38 PM »
Check some other viewer to make sure the pdb-file is okay.
iRASPA can also visualize the frames of the movie.

What could be a potential issue with VMD is that all frames need to have the same amount of atoms for VMD to work out of the box for movies.

15
General / Re: How to eliminate the boundary effect in GEMC simulations?
« on: November 28, 2020, 08:10:49 PM »
Boundary effects are already eliminated in the grand-canonical and Gibbs approach.
For the grand-canonical approach, only the adsorbed phase is simulated.
For the Gibbs approach, the adsorbed phase and a fluid phase is simulated.
In both there are no surface effects. You do need sufficiently large systems to minimize finite-size effects.

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