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Messages - David Dubbeldam

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The 'CutOffVDW' should not be different for the gas and liquid phase, otherwise you're using different force fields for them.
The 'CutOffCoulomb' should be set to something slightly smaller than half the box size. This significantly speeds up the computation for the gas-phase since the gas-phase box can be large.
Importantly, both can be set per system (just list them after the 'Box' statement).

General / Re: list of configurational moves in .def file
« on: June 22, 2022, 10:13:44 PM »
This for the PartialReinsertionProbability move, where only a few atoms are regrown and the others are left fixed.
So, in this case there are 4 config move defined (and you see 5 lines). For each line you have the number of fixed atoms, and the the list of the fixed atom ids.
The other atoms are regrown using CBMC. This move has high efficiency, because the molecule is already present and is only partially regrown.
Note that in CBMC all branches need to be grown at the same time, so you can not keep more than one branch fixed (in a branched molecule).

General / Re: How to get movie from MD
« on: June 14, 2022, 09:33:53 PM »
An "MD path" is the path or trajectory that a particle follows in MD. if you ran too short, then the molecules have not moved enough.  Diffusion is defined as the limiting behavior of the Mean-Squared Displacement (MSD) at long-times. For diffusional processes, the slope must become linear at long times. If you did not reach that regime yet, then you have ran too short.
Slow diffusion might be outside the reach of MD, e.g. very slow diffusion can not be measured using MD. The maximum is probability up to 10^-14 m^2/s.

General / Re: How to get movie from MD
« on: June 09, 2022, 01:11:09 PM »
In general no, because diffusion coefficients are by definition the long-time behavior of molecules.
In any short MD-path you might even see opposite behavior. Of course for illustrative purposes you could just select an MD path that shows what you want to show.

These radii are only needed for flexible frameworks, and used as bond-criteria to determine bonding.
For other cases these values do not matter.

General / Re:negative MSD slope
« on: June 04, 2022, 07:06:06 PM »
See literature on how to compute diffusion coefficients from MSD. The slops of the MSD at long times can not be negative.
You're probably looking at a situation where MD is not capable of computing diffusion because it is too slow.

General / Re: LAMMPS.trj file to cif
« on: June 02, 2022, 05:44:08 PM »
About the gif-file: The _atom_site_type_symbol needs to be the chemical element. The _atom_site_label is used in the forcefield definition as a label of the atom.

General / Re: LAMMPS.trj file to cif
« on: May 31, 2022, 04:35:26 PM »
All atom-types need to be defined in the 'pseudo_atoms.def', so 'c', 'c3', 'hc', but also all atoms of the probe molecule.
Next define LJ parameters all of these for 'force_field_mixing_rules.def'.
The mixing rules with the be used to computed cross-interactions between all of the atoms.

You seems to have placed them in 'force_field.def' which is means to overwrite interactions for systems where mixing rules are not applicable. But these are no interactions defined then between {'c', 'c3', 'hc'} and all of the adsorbate atoms of the probe molecules.

General / Re: LAMMPS.trj file to cif
« on: May 28, 2022, 10:17:05 PM »
Did you define the forcefield for your framework atoms?
(i.e. all Lennard-Jones parameters for all your atom types, and all the charges)

grep RestrictMovesToCylinder *.c
you can see the files where it is used. Input is in 'input.c'.

So something like:
RestrictMovesToCylinder yes
Cylinder 0
CylinderCenter 0.5 0.5 0.5
CylinderRadius 3.0
CylinderDirection X

It is used in molecule.c
(grep RestrictCylinderDirection *.c)
In the routine:
int ValidCartesianPoint(int i, POINT pos);

Output files / Re: output - molcules/unit cell - IMPORTANT
« on: May 27, 2022, 01:55:58 PM »
'Molecules per unit cell' is the the number of molecules in the 1x1x1 system.
Often experiments uses mol/kg. RASPA prints out als other units like mg/g.

Input files and parameters / Re: TIP4P model
« on: May 27, 2022, 01:53:56 PM »
It has 4 sites, the O, 2 H, and a dummy site often called 'M'.

0 O        0.0                  0.0           0.0
1 H       -0.7569503272  0.0          -0.5858822766
2 H        0.7569503272  0.0          -0.5858822766
3 M        0.0                  0.0          -0.15

Input files and parameters / Re: two different temperatures
« on: May 27, 2022, 01:51:45 PM »
In equilibrium, adsorbates and adsorbents in a single system have the same temperature.
In state-state, systems with temperature gradients are used for example to compute thermal conductivity.

Use standard unix utilities like 'grep' for that:
The potentials are implemented in 'potentials.c'.

General / Re: net charge in diffusion
« on: May 27, 2022, 01:45:13 PM »
Net charge of non-zero is a warning, because it needs to be small. Say smaller then 1e-4.
Check that your framework is is neutral and that the molecules are neutral.

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