Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Messages - David Dubbeldam

Pages: 1 2 [3] 4 5 ... 16
31
General / Re: LAMMPS.trj file to cif
« on: May 27, 2022, 01:29:11 PM »
Have a look at the example cif files in RASPA, for example IRMOF-1
(structures/mofs/cif/IRMOF-1.cif)

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Zn1      Zn     0.2934     0.2066     0.2066     0
O1       O      0.25       0.25       0.25       0
O2       O      0.2819     0.2181     0.134      0
C1       C      0.25       0.25       0.1113     0
C2       C      0.25       0.25       0.0538     0
C3       C      0.2829     0.2171     0.0269     0
H1       H      0.3049     0.1951     0.0448     0

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.

32
Output files / Re: Energy landscape
« on: April 18, 2022, 07:56:22 PM »
Recently, these capabilities are implemented in iRASPA, where you play around with these energy-surfaces on the fly (computed very fast on the GPU).

33
Many of the moves use biasing (Multiple-first beads method). As soon as overlap is detected the move will be rejected.

Do you really need all the atoms outside the first cylindrical ring? If not, then you could
RestrictMovesToCylinder yes
and define a cylinder. Everything outside the cylinder will be considered an overlap.

34
General / Re: CIF file
« on: April 18, 2022, 07:43:09 PM »
CIF files are published by experimental groups to convert the structural data in a standardized way. The are uploaded to databases like CSD database.
For simulation codes, the atomic information is necessary _input_ for the simulations, because the positions of all the atoms need to be specified.
Programs like 'Openbabel' can convert between many formats.

35
Input files and parameters / Re: lennard jones parameters
« on: April 18, 2022, 07:39:16 PM »
Input units for the Lennard-Jones are epsilon/k_B in units of Kelvin, and sigma in units of Angstrom (see manual, also for units and unit conversions).

36
The smallest perpendicular width of the simulation box needs to be at least twice the cutoff (so as to satisfy the minimum image convention).
But you probably need larger cells to reduce finite size effects. A too large cell is computationally expensive.

37
General / Re: Enthalpy of adsorption for binary mixture
« on: March 14, 2022, 07:13:39 PM »
The fluctuation formula has to be used in the grand-conical ensemble, i.e. the molecules must fluctuate.
Numerical problems might also occur at high loadings where the lack of accepted insertions/deletions can become a problem.

38
Input files and parameters / Re: HYDRATED_ION_WATER potential
« on: March 14, 2022, 07:09:14 PM »
You do a: grep HYDRATED_ION_WATER *.c
in the source code and get the files back where this is used.
In the file 'potentials.c' you can check whether it is read okay, or printed out wrongly, or whether it is something with the mixing rule.

39
Yes, that is the standard way of simulation desorption. Note that is best to start from an equilibrated restart-file at the highest pressure (usually obtained from the adsorption branch).

40
That can not really be done without implementing that. The system must stay charge-neutral, so you cannot individually swap na and cl in and out. You will need to do that in pairs.

41
The positions of the atoms of the framework are 'input'. There might be tools available (builders) that create these initial structures for you.

42
Input files and parameters / Re: Segmentation fault (core dumped )
« on: March 14, 2022, 06:56:34 PM »
See the tips in section 5.5 of the manual on debugging to find the cause of this.
Basically, compile with the flag '-g' and run the executable via a debugger.

43
General / Re: Error loading VTK output and lack of H on methane
« on: March 14, 2022, 06:53:50 PM »
1) Methane is often modeled as a united-atom (a single bead).
2) The VTK output that can be read by iRASPA is a VTK density-file (see 'ComputeDensityProfile3DVTKGrid').

44
Pictures and movies / Re: creating movies in iRASPA
« on: December 02, 2021, 10:58:18 AM »
Select both files when loading them into iRASPA. The first tab in the project-pane shows the project. The second tab shows the two "movies" that you have loaded: the cif file with 1 frame, and the pdb with many frames. The third tab shows the frames of the movie.

Note: there is help in iRASPA (see menu item 'Help').

45
I would say > 0.1%. Lower then that and you will really have to simulate a long time. With biasing you can increases the acceptance at the cost of computing more.

Pages: 1 2 [3] 4 5 ... 16