Activity for Torbjörn Björkman
-
Torbjörn Björkman posted a comment on discussion Help
OK, I see what you mean. I'm not sure that's currently possible to do, but if it is possible, then the flag is --supercell-postvacuum-translation=[1,1,1] I think this might work, but I forget how I implemented it. It's not really meaningful to label your coordinates in the range 1 to 2 instead of from 0 to 1. May I ask the reason you want to do this? Just trying to understand what people need the program to do.
-
For a 2x2x2 supercell you want --supercell=[2,2,2] A 1,1,1 supercell is just the regular cell. A 1,1,1 translation vector will move you one whole unit cell, which is the same thing as not moving at all.
-
Quick answer: This request makes total sense. Please tell me which program you want supported and how you want the automated setting to work, and it is probably a quick job to implement it. More elaborate answer: There is in fact some support for this for some programs, for instance VASP and ... a couple of other programs? I forget. But it is not a generic feature. It would be possible to add, but it requires more in-depth knowledge of the individual electronic structure programs than I possess....
-
Lots of big important changes
-
OK, good to know what you are after, don't worry about the long post :-) This is not laid out as carefully as I would like in the cif2cell manual unfortunately. I've been meaning to fix this and also to implement some automatic way of generating surface slabs, but my time has been a scarce resource lately, unfortunately. I'll try to put my answer now in a form that I can incorporate in the manual later. The reference you sent actually discusses Miller indices, but it uses the real space graphical...
-
OK, good to know what you are after, don't worry about the long post :-) This is not laid out as carefully as I would like in the cif2cell manual unfortunately. I've been meaning to fix this and also to implement some automatic way of generating surface slabs, but my time has been a scarce resource lately, unfortunately. I'll try to put my answer now in a form that I can incorporate in the manual later. The reference you sent actually discusses Miller indices, but it uses the real space graphical...
-
OK, good to know what you are after, don't worry about the long post :-) This is not laid out as carefully as I would like in the cif2cell manual unfortunately. I've been meaning to fix this and also to implement some automatic way of generating surface slabs, but my time has been a scarce resource lately, unfortunately. I'll try to put my answer now in a form that I can incorporate in the manual later. The reference you sent actually discusses Miller indices, but it uses the real space graphical...
-
OK, good to know what you are after, don't worry about the long post :-) This is not laid out as carefully as I would like in the cif2cell manual unfortunately. I've been meaning to fix this and also to implement some automatic way of generating surface slabs, but my time has been a scarce resource lately, unfortunately. I'll try to put my answer now in a form that I can incorporate in the manual later. The reference you sent actually discusses Miller indices, but it uses the real space graphical...
-
I am a bit confused by your wording here, but I read it as that you want a cell where the last lattice vector is along the [110] direction and the first and second lattice vectors are along the [-110] and [010] directions. It is not entirely clear to me whether you refer to real space indices or Miller indices here, but for a cubic structure it doesn't really matter. From the desired basis it seems that you want the body-centred tetragonal setting of the fcc lattice. The easiest way is to work from...
-
New package directory, cif2cell, added + added all modules to the package.
-
New directory, binaries + moved cif2cell program to binaries.
-
* First functional python 3 version.
-
New branch for python3
-
VERSION 1.3.1
-
Please post the cif file and I'll see what causes the problem. Meanwhile, you can try if the --force flag will help you generate a file despite cif2cell not recognizing the space group information.
-
My turn not to spot things until several months... Thanks for checking up this issue, James! No problem with PyCIFRW here, but I have not yet had the time to make cif2cell compatible with the latest version, so it ships with a legacy version of PyCIFRW. Python 3 along with updating to latest PyCIFRW is on the installment plan, but time is not plentiful.
-
You need to specify a path to the VASP pseudopotential directory if you want to generate all input files (--setup-all flag). This is best done by setting the environment variable VASP_PAWLIB. Example for bash export VASP_PAWLIB=/wherever/it/is/potpaw_PBE.54 or whatever name you have for the directory.
-
You can have it tomorrow, depending on how clever you need it to be. I checked the GULP manual, and there are a bazillion knobs and switches, but dumb-as-a-post output that just prints cell vectors and positions to a file is a 10-15 minute job. What more precisely do you need it to do?
-
The problem is that the version of PyCifRW that is used is incompatible with Python 3, you still have to use python 2. I hope to get some time to fix this in the near future, pressure seems to be mounting to get this sorted out. Torbjörn
-
You're welcome! The flag --no-reduce gives you the conventional cell. Happy computing!...
-
Hello Helen, Not sure I see any error here. Anatase has space group I41/amd (number...
-
The CRYSTAL interface is likely to have bugs/unwanted behaviour like this. I have...
-
* Version 1.2.11
-
You have discovered a bug; a comparison between before and after the transformation...
-
The space group of your compound is C2/c, which is a base-centred setting. By default...
-
The problem is that cif2cell produces a unit cell of the compound, but a mixture...
-
For some reason the installer doesn't copy the python modules. A simple fix would...
-
This looks like an installation issue. I can reproduce the problem by running cif2cell...
-
No, there isn't. The reason was that as far as I can understand, the program determines...
-
No, there isn't. The reason was that as far as I can understand, the program determines...
-
Generally speaking, the Crystal interface is not very well maintained. I have never...
-
The reason is that your cif's are adding labels to the element name of oxygen and...
-
Can you attach the offending CIF file? I don't quite see what you mean here. Charge...
-
Well, the CIF 2 standard is only preliminary yet. The author of PyCifRW is the head...
-
I have reproduced the error and can confirm that it is the PyCifRW that is the problem....
-
Can you try with the PyCifRW that comes with cif2cell? -Torbjörn
-
Hi, The easiest way to fix this was to just implement the possibility to alter the...
-
No problemo. Happy computing! -T
-
Hello Sunkwang, The cif file that you attach contains a bcc cell (symmetry_space_group_name_H-M...
-
The 'supercell' command does not take Miller indices as its input. In the form you...
-
The 'supercell' command does not take Miller indices as its input. In the form you...
-
The primitive lattice vectors normally chosen for the fcc lattice (as set up by cif2cell)...
-
The primitive lattice vectors normally chosen for the fcc lattice (as set up by cif2cell)...
-
I'm not sure what you mean by "a supercell along the 110 direction". Do you want...
-
* Fixed bug sometimes appearing when symmetry e...
-
* Tweaked froyen mesh generation for RSPt.
-
Added --export-cif-labels feature, which export...
-
There are problems in the CIF files you are using, unfortunately not as rare a case...
-
There are two problems with the command that you sent. 1) it misses a space before...
-
Drastic solution, but if it works it works. You apparently had something strange...
-
Hi, uctools is part of cif2cell. That the program does not find it indicates that...
-
Installation problems
-
Hi Abrar, The --print-digits flag only affects the output printed to screen, there...
-
Hi Abrar, The --print-digits flag only affects the output printed to screen, there...
-
* Disable chemical formula test for alloys, tha...
-
* Version 1.2.8.
-
* Release version 1.2.7
-
<< creating input for MOPAC >>
-
With the release 1.2.7 everything should work the way you wanted, including the freeze...
-
What version of Python do you use? You can find out by just typing 'python', which...
-
new branch for alloy handling
-
No problems at all, but there still isn't support for mind reading, so you have to...
-
<< creating input for MOPAC >>
-
<< PyCifRW problem >>
-
Try this version. Just specifying -p mopac will give you an output file that does...
-
Absolutely! I will knock up an interface and send it to you for testing. Expect it...
-
* Version 1.2.5
-
Hello Hatuey, PyCifRW comes with the package these days, and also be installed automatically...
-
* Version 1.2.4
-
* Fixes in the RSPt interface.
-
* Major changes to the RSPt interface.
-
version 1.2.2
-
* Fixed check for _space_group_symop_operation_...
-
CP2K and VASP probrems/improvement
-
The changes are implemented in version 1.2.1 which I just uploaded. I'll close this...
-
The way I handle that myself right now is to convert everything to .cif and then...
-
Very good, I'll just scratch the 'UNIT' keyword. It is very easy to add output in...
-
Hi Kirill, Thanks for the input, I have put in your solution for custom PP priority....
-
* Version 1.2.0. PWSCF interface seems OK now.
-
* Version 1.1.7
-
* Fixed bug with improveprecision() function (d...
-
OK, then I see where this goes wrong, only integer values are allowed in the supercell...
-
Hi, Atoms should never end up on top of each other, so maybe what you have is a bug...
-
The problem is a bug which comes from cif2cell failing to convert the Hermann-Mauguin...
-
* Version 1.1.5
-
* Added 'Unknown' space group.
-
Added a lot of previously unsupported H-M symbols.
-
I'll try to add it for the next release (no I don't know when that will be...but...
-
Well, a rotation matrix of course has unit determinant, the point is that only a...
-
The only way to perform a rotation of the positions is through the supercell command,...
-
For some things like this I have used CrystalMaker, where you can look at structures...
-
The easiest way is to just download a cif file with a base wurtzite structure from...
-
cif2cell doesn't really have any simple tool to modify stacking sequences, unfortunately....
-
That should have been installed automatically. Do you have the [installdir]/lib/cif2cell...
-
Hello, Some stuff on this is in the manual (the example is the Si 111 surface). The...
-
version 1.1.4
-
VCA support for VASP
-
Surface supercell generation branch
-
version 1.1.3
-
* Fixed issue when the cif file contains all th...
1 >
