Recent Posts

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1
Simulation algorithms and theory / Anisotropic volume change with Monte Carlo
« Last post by MichaelH on April 18, 2019, 07:31:52 PM »
Dear David,

Im looking at the advanced examples 1 and 2, trying to adapt them to study swelling (in the z-direction) of multi-layered clay(ff) system. Since my clay layers are periodic in x and y, I would like to avoid isotropic volume changes and use some sort of anisotropic-like barostatting instead.

So my question is: When running MonteCarlo, does the volume move (VolumeChangeProbability) only do isotropic volume scaling? or is there some way to activate anisotropic volume trial moves? or simply just do volume moves along the z-direction? I have seen the BoxShapeChangeProbability option, but Im not sure if its effective.

Best regards,

Michael
2
Input files and parameters / CIF files help
« Last post by petersbk on April 17, 2019, 02:35:56 PM »
What software do people use to successfully manipulate .cif files and get them to work with raspa? I've tried fairly simple things (like read in the FAU_SI.cif provided with raspa, convert it to P1, and export it back to .cif) and they seem to not work; sometimes with useful error messages and sometimes not. Besides Materials Studio which I don't have access to, what software works reliably? I've tried Avogadro and VESTA without success. They usually read each other's exported files or those included with raspa, but raspa does not read theirs. Does anyone have any tricks, hints, reports of idiosyncrasies, recommendations, or things to watch out for?

As an example (but I am really looking for general help), the FAU --> P1 in VESTA exercise above yielded the .cif shown below (and attached), but gave "ERROR in cif-file: no proper space group definition found" (after reporting tons of "unknown" lines) even though it has two lines relating to the space group. (Sorry: I couldn't get attachments to work).

#======================================================================

# CRYSTAL DATA

#----------------------------------------------------------------------

data_VESTA_phase_1


_chemical_name_common                  'FAU'
_cell_length_a                         24.34500
_cell_length_b                         24.34500
_cell_length_c                         24.34500
_cell_angle_alpha                      90
_cell_angle_beta                       90
_cell_angle_gamma                      90
_space_group_name_H-M_alt              'P 1'
_space_group_IT_number                 1

loop_
_space_group_symop_operation_xyz
   'x, y, z'

loop_
   _atom_site_label
   _atom_site_occupancy
   _atom_site_fract_x
   _atom_site_fract_y
   _atom_site_fract_z
   _atom_site_adp_type
   _atom_site_B_iso_or_equiv
   _atom_site_type_symbol
   O1         1.0     0.895800      0.104200      0.000000     Biso  1.000000 O
...

Thanks for any help.
3
Visualization / VTK visualization
« Last post by RobertoMennitto on April 15, 2019, 11:33:50 AM »
Dear Dr. Dubbeldam,

I am currently looking at how to visualize VTK files as discussed in the RASPA manual. Can you suggest a software to visualize those files?

I am currently exploring "VisIt" and "ParaView". However, I never manage to replicate the pictures of the density profiles together with the framework shown in the manual. When I try to merge framework and density files they are on different scales.

Regards
Roberto
4
Input files and parameters / MSD: increasing the length of the simulation
« Last post by VaeS on April 11, 2019, 12:45:53 PM »
Hi,

I try to simulate CO2 diffusion using MD in RASPA.

My simulation stops after a certain time (e.g. 100 ps), is there a way to increase the duration and reach e.g. 1000 ps or this is determined by the algorithm ?

Cheers,

Sebastien
5
Input files and parameters / Re: Only one Framework atom taken from .cif file
« Last post by petersbk on April 02, 2019, 03:15:41 PM »
Thanks for looking into this. The input and .cif files can be taken from my original post (the three atoms shown give similar behavior as a larger number of atoms). This force-field.def file is the one supplied in the latest version of the download. I've done nothing to modify any .def file.
6
May you please send your CIF, force field definition, and input file?
7
Input files and parameters / Re: Only one Framework atom taken from .cif file
« Last post by petersbk on April 01, 2019, 11:47:32 PM »
I converted to fractional coordinates by hand, removed the "ReadCIFAsCartesian yes" command, and the same behavior occurs: lots of "unknown" lines to stderr and only one FW atom appears @ 0,0,0. Any other advice? Thanks.
8
I have not used this option of RASPA but I guess it still needs the CIF in fractional coordinates and then RASPA internally converts it to Cartesian. You may use other software like VESTA to generate CIF in fractional coordinates.

My best,
Pezhman
9
Input files and parameters / Re: Only one Framework atom taken from .cif file
« Last post by petersbk on April 01, 2019, 07:16:40 PM »
Maybe. The manual says you can use Cartesian coordinates for P1 and I've used the "ReadCIFAsCartesian yes" command in the input file. It is off-topic, but I can't get openbabel to convert this file to fractional coordinates.  Thanks.
10
Dear Peter,

I think your issue is coming from the fact that you are providing Cartesian coordinates instead of fractional ones. You may convert it to fractional and then you will have

.
.
.
_atom_site_frac_x
_atom_site_frac_y
_atom_site_frac_z
Ar Ar1 frac_x frac_y frac_z
.
.
.

My best regards,
Pezhman
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