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21
General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 30, 2022, 09:36:25 PM »
Yes, My system is polyethylene so I only have hc and c3 type atoms, attached is the pseudo atom and forcefield file I made/I have preloaded from one of the provided frameworks.
Thanks for your quick responses, I really appreciate your help in this bind.
22
General / Re: LAMMPS.trj file to cif
« Last post by David Dubbeldam 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)
23
General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 27, 2022, 06:22:10 PM »
I did as you said but for the 6 gasses, Im getting the same value for Henrys constant. Do you know why this could be the case? Thanks again!!
24
With
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);
25
Output files / Re: output - molcules/unit cell - IMPORTANT
« Last post by David Dubbeldam 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.
26
Input files and parameters / Re: TIP4P model
« Last post by David Dubbeldam 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
27
Input files and parameters / Re: two different temperatures
« Last post by David Dubbeldam 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.
28
Use standard unix utilities like 'grep' for that:
grep -i FEYNMAN_HIBBS_LENNARD_JONES *.c
The potentials are implemented in 'potentials.c'.
29
General / Re: net charge in diffusion
« Last post by David Dubbeldam 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.
30
General / Re: LAMMPS.trj file to cif
« Last post by David Dubbeldam 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.
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