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31
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!!
32
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);
33
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.
34
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
35
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.
36
Use standard unix utilities like 'grep' for that:
grep -i FEYNMAN_HIBBS_LENNARD_JONES *.c
The potentials are implemented in 'potentials.c'.
37
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.
38
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.
39
General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 25, 2022, 07:29:38 PM »
My structures file
40
General / LAMMPS.trj file to cif
« Last post by bphan on May 25, 2022, 12:23:56 AM »
Hi all,

I have an amorphous polymer system that I ran an MD equilibration on. Im trying to use RASPA to calculate Henrys constant now and need to convert the lammps.trj file to cif. Right now im taking the last frame of the lammps file and changing the format to a cif file. The calculation runs but the simulated values are garbage. For 6 different gasses im getting the same value. I also tried calculating the IdealGasRosenbluthWeight before and inputting it but im just getting 1 for all values.

Im confused on where im going wrong, any input is appreciated.
The polymer system is polyethylene, the cif file has ~4000 atoms.
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