CIF2Cell Activity
Generating cells for electronic structure calculations from CIF files
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torbjornb
Activity for CIF2Cell
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Jehyeok Ryu posted a comment on discussion Help
Hi, I'm new to learn quantum espresso and trying to install cif2cell but failed. I tried it through pip and it shows error below. To fix this, I tried to install and upgrade PyCifRW, wheel, setuptools as latest version with pip command but it didn't work. I'm using M1 macbook air Ventura, python 3.10.9. Can somebody help how to fix this? I tried my best but I don't know how to try to fix it anymore. Thank you for reading. pip install cif2cell Collecting cif2cell Using cached cif2cell-2.0.0a3-py3-none-any.whl...
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Ben Rhodes posted a comment on discussion Help
Hi, I'm new to using cif2cell and have been trying to get it working on my Windows 10 laptop. I've successfully downloaded/untarred the package and run the python setup.py install command (also seemingly fine, though I did have to add in some brackets for a couple of print commands, but I think that may just be the newer version (3.9) of python I've got). My issues has come when I try and call the cif2cell command (specifically cif2cell -h, but also with tags for specific/test files too) and all...
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Anonymous created ticket #17
cannot import 'gcd' from 'fractions'
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Anonymous created ticket #16
Hall symbol Unknown (H-M symbol Unknown)
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Anju Chandran posted a comment on discussion Help
Hi, I have to create a TiAl system oriented in [1-10] [11-2] [111] directions and rotate this structure 60 degrees about z axis. The first step was accomplished by using cif2cell -f TiAl.cif --supercell=[[1,-1,0],[1,1,-2],[1,1,1]] -p cif --cartesian --force -o output.cif option. Further I rotated the structure using cif2cell -f output.cif --transform-cell=[[0.5,-0.866,0],[0.866,0.5,0],[0,0,1]] -p cif --cartesian --force -o output_60.cif option. But the obtained structure on visualizing is a non-orthogonal...
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Erdong Lu posted a comment on discussion Help
Of course, this will be a bit lengthy so bear with me. Basically, I am trying to scan through a bunch of pre-selected structures and check for the distance between certain elements in those structures. So, the simplest method I come up with is to convert all the CIF files into xyz files, where the positions are directly recorded by Cartesian coordinates. To take the periodic boundary condition into account, I plan to have a 3 * 3 * 3 supercell and then a 1* 1 * 1 single cell and have the single cell...
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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.
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I meant to generate a single unit cell, but the range should be x:[1~2] y:[1-2] z:[1-2] sorry for the confusion.
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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.
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Hello all, I am trying to use cif2cell to generate a single unit cell translated by [+1 +1 +1] unit cell vector (so the [2 2 2] unit cell). Taking CsCl.cif attached in this discussion for example. I have tried the following command: cif2cell -f CsCl.cif -p xyz --no-reduce --supercell=[1,1,1] --supercell-vacuum=[1,1,1] --outputfile=CsCl_test.xyz cif2cell -f CsCl.cif -p xyz --no-reduce --supercell=[1,1,1] --supercell-vacuum=[1,1,1] --supercell-prevacuum-translation=[1,1,1] --outputfile=CsCl_test.xyz...
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Ronald Cohen created ticket #15
Py_InitModule not present in python3
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Miroslav Iliaš created ticket #14
convert cif file for the elk geometry
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Tee posted a comment on discussion Help
I have had some issues generating pwscf input file with the cif2cell program. The program returned error as follow; Traceback (most recent call last): File "/home/usr/.local/bin/cif2cell", line 1574, in <module> docstring = StandardDocstring() File "/home/usr/.local/bin/cif2cell", line 1021, in StandardDocstring tmpstring2 += ". Reference number : "+ref.databasecode TypeError: cannot concatenate 'str' and 'NoneType' objects</module> The cif file used is downloaded from materials project database....
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Amir Behbahanian posted a comment on discussion Help
the _cod_database is a flag for known databases and probably the database you are using is not a well know (Synthetic and developed by the Material Project) database for a known material. But I'm not sure about the extent of the correctness of my answer.
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Rabeet posted a comment on discussion Help
Hi Amir, Thanks for responding. I could not succeed with coddatabasecode None. But your idea helped to figure out the problem. I am able to generate the input file by adding "database_codeICSD None" or by adding any string given within "database_code' at https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Idatabase_code_.html I am wondering why the cif downloaded from material project missing this string. Thanks. Rabeet
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Hi Amir, Thanks for responding. I could not succeed with coddatabasecode None. But your idea helped to figure out the problem. I am able to generate the input file by adding "database_codeICSD None" or by adding any string given within "database_code' at https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Idatabase_code_.html I am wondering why the cif downloaded from material project missing this string. Thanks. Rabeet
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Hi Amir, Thanks for responding. I could not succeed with coddatabasecode None. But your idea helped to figure out the problem. I am able to generate the input file by adding "database_codeICSD None" or by adding any string given within "database_code' at https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Idatabase_code_.html Thanks. Rabeet
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Hi Rabeet, the error says it needs the database code or, "docstring += " from "+ref.databaseabbr[ref.database]+" reference: "+ref.databasecode" try "_coddatabasecode None" it might solve the problem. Good Luck, Amir
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Anonymous created ticket #13
Error message: cell setup: Cartesian coordinates in CIF, but no transformation matrix given
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Dear Users, I have been using cif2cell to generate the input files for quantum espresso and vasp. I usually download the cif files from material project. But recently I am facing problem to generate the input files from the cifs downloaded from material project. I tried to different operating systems. On ubuntu I am getting error cif2cell -p vasp mp-22905_LiCl.cif Traceback (most recent call last): File "/home/rabeet/.local/bin/cif2cell", line 4, in <module> import('pkg_resources').run_script('cif2cell==2.0.0a1',...
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Anonymous created ticket #9
generate input file for real space multigrid package.
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Bingbing Zhang posted a comment on discussion Help
Dear developers and users, I used cif2cell (vesion 1.2.10) to generate .cell file as input file of CASTEP by using the following command cif2cell XXX.cif -p castep. The most job are suceeded when running CASTEP but a few of them meet mistake. It said "Error detected in cell_factor_group_symmetry: Symmetry operations do not form a product group" in .castep file. So, I trace back to .cell file and find that there are some repetition of # Symm. op. For example, to ICSD-18211, symm. op. 3 and 4 are same,...
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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....
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Anonymous posted a comment on ticket #3
Had the k-point creation been added in cif2cell so far?
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Leopold Talirz posted a comment on discussion Help
Dear Torbjörn , I came across cif2cell because Stefaan Cottenier mentioned it as a tool he likes to use in his DFT course [1] and I would be interested in including it in the Quantum Mobile virtual machine [2] that he uses for the course (the VM is developed here at EPFL). When I donwloaded the program, I noticed that it is written in python but that it isn't released on the python package index [3]. Since you've already written the setup.py [4], is there anything holding you back from releasing...
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Dr. R. Rajaraman modified a comment on discussion Help
Dear Torbjorn, Recently I came across your post regarding theoretical density estimate incorporated in cif2cell. I gave a try and found calculated densities are wrong. see for example Cu supposed be 8.9 g/cm^3. but cif2cell gives 60.3. Cell volume is fine. Please check.
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Dear Torbjorn, Recently I came across your post regarding theretical density estimate incorporated in cif2cell. I gave a try and found calculated densities are wrong. see for example Cu supposed be 8.9 g/cm^3. but cif2cell gives 60.3. Cell volume is fine. Please check.
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Lots of big important changes
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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...
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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...
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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...
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Christoph Wolf posted a comment on discussion Help
Thank you so much for your help - this works like a charm! I am staying tuned for upcoming releases cif2cell really is the best in my opinion for structure input generation! Best, Chris
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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...
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Hi Torbjörn, thank you for your swift reply and I am sorry that my wording probably reflects my confusion ;) The indices were meant to represent "real space" reference coordinates if I am not mistaken. I took the notation from page 19-20 of this thesis http://physik.uni-graz.at/~pep/Theses/MasterThesis_Knebl_Dario_Wolf_13_11_2013.pdf The (110) facet. The lattice vectors are represented by the red arrows of Fig. 2.2h. By defining the x-axis in [110]-direction, the y-axis in [001]-direction and the...
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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...
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Dear all, I have read the manual and duly completed th exercise for the Si(111) supercell but apparently I still cannot fully understand how it works. The lattice vectors for FCC are Bravais lattice vectors : 0.5000000 0.5000000 0.0000000 0.5000000 0.0000000 0.5000000 0.0000000 0.5000000 0.5000000 Here is what I ultimately want: I denote the x,y,z axis for the primitive cell as [100], [010], [001]; then the z axis for the new cell clearly points in z=[110] and I pick x=[-110], y=[001]; The lattice...
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New package directory, cif2cell, added + added all modules to the package.
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New directory, binaries + moved cif2cell program to binaries.
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* First functional python 3 version.
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New branch for python3
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VERSION 1.3.1
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Dawei Guo posted a comment on discussion Help
Hi Torbjörn, Thanks a lot for your useful package! I cant connect outlook to my email so I cant start a new forum..Sorry! I am new in python, and I just try to install your package into it. I have installed ‘pycifrw’ successfully using the method: ‘python setup.py install’, and when I input ‘>>>import CifFile’ the system didn’t send me any error so I think it has been well installed. However, when I cd the path and try to install ‘cif2cell’, the system said: Copying ………. . . . . . Running install_egg_info...
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thx
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x
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Hi Torbjörn, Thanks a lot for your useful package! I cant connect outlook to my email so I cant start a new forum..Sorry! I am new in python, and I just try to install your package into it. I have installed ‘pycifrw’ successfully using the method: ‘python setup.py install’, and when I input ‘>>>import CifFile’ the system didn’t send me any error so I think it has been well installed. However, when I cd the path and try to install ‘cif2cell’, the system said: Copying ………. . . . . . Running install_egg_info...
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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.
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SHIVAM posted a comment on discussion Help
I tried running, $cif2cell -p elk -f '/home/shivkmr/project/pcfo/PCFO_N.cif' for getting GEOMETRY.OUT from cif file i got the error ***Error: cell setup: CIF file contains neither space group symbols nor space group number. I can't understand why it does that, When the spacegroup is clearly mentioned in cif files it may be something related to FullProf , I got the cif from doing Retveild Refinement in FullProfSuite
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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.
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Jack shi posted a comment on discussion Help
Dear Thanks, very much, I have followed your seggestion and solved. Many thanks! Regards,
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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.
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Hi, When I was using the cif2cell some problems came see below: Traceback (most recent call last): File "/usr/bin/cif2cell", line 1608, in <module> incarfile = INCARFile(cd,docstring=docstring,vca=options.vca,prioritylist=prioritylist,encutfac=encutfac) File "/usr/lib/python2.6/site-packages/ESPInterfaces.py", line 2044, in init raise SetupError("No path to the VASP pseudopotential library specified.\n") utils.SetupError: 'No path to the VASP pseudopotential library specified.\n' I don’t know why...
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Hi, when I use the cif2cell to convert a cif file to input files to VASP. I encountered problems below: Traceback (most recent call last): File "/usr/bin/cif2cell", line 1608, in <module> incarfile = INCARFile(cd,docstring=docstring,vca=options.vca,prioritylist=prioritylist,encutfac=encutfac) File "/usr/lib/python2.6/site-packages/ESPInterfaces.py", line 2044, in init raise SetupError("No path to the VASP pseudopotential library specified.\n") utils.SetupError: 'No path to the VASP pseudopotential...
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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?
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Keith Refson created ticket #8
Add GULP output format
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Albert Bartok-Partay posted a comment on discussion Help
FYI, this could happen due to a clash in name space: there is a python package called "utils" and when you do from utils import * that gets loaded instead of utils.py which is part of cif2cell.
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James Hester posted a comment on discussion Help
Author of PyCIFRW here. I've just come across this comment 6 months later. PyCIFRW has supported Python3 since March 2017 (see https://pypi.python.org/pypi/PyCifRW/4.3). Please let me know of any issues with this support.
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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
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Geoffrey Wood posted a comment on discussion Help
Hello, I am a true novice here so apologies for what's probably a really basic question. I am running python 3.5 and I downloaded your package. I went into the PyCifRW-3.3 directory and typed: python setup.py install after what seemed a lot of output I got: Installed /anaconda/lib/python3.5/site-packages/PyCifRW-3.3-py3.5-macosx-10.5-x86_64.egg Processing dependencies for PyCifRW==3.3 Finished processing dependencies for PyCifRW==3.3 Then I wne t back to your package and did the same i.e. python...
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GXZ posted a comment on discussion Help
Many thanks :) Helen
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You're welcome! The flag --no-reduce gives you the conventional cell. Happy computing!...
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Dear people, I'm a FHI-aims code user. I've been recently converting cif to geometry.in...
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Hallo Torbjörn, thanks a lot for your quick response. Yep, I mean FOUR formula. Now...
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Hello Helen, Not sure I see any error here. Anatase has space group I41/amd (number...
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Dear people, I'm a FHI-aims code user. I've been recently converting cif to geometry.in...
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Abrar Quadery modified a comment on discussion Help
Hi Torbjorn, I am happy to inform that my colleague, who is a very smart programmer,...
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Hi Torbjorn, I am happy to inform that my colleague, who is a very smart programmer,...
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The CRYSTAL interface is likely to have bugs/unwanted behaviour like this. I have...
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Dmitry Krylov posted a comment on discussion Help
The generated input for titanite P2(1)/a produces results which are erroneously interpreted...
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hatuey posted a comment on discussion Help
Hello, I had CIF2CELL running well. After updating my system (OpenSUSE Tumbleweed)...
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Hurray, it works! Just to be exact, the rotation above is considered negative, and...
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* Version 1.2.11
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./cif2cell alpha_quartz.cif gives the following Bravais lattice vector. 0.8660254...
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You have discovered a bug; a comparison between before and after the transformation...
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The cif file is attached here.
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./cif2cell alpha_quartz.cif gives the following Bravais lattice vector. 0.8660254...
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./cif2cell alpha_quartz.cif gives the following Bravais lattice vector. 0.8660254...
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When using the switch --cartesian, the orientation determines the different components...
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When using the switch --cartesian, the orientation determines the different components...
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Works perfectly! Thanks a ton, much appreciate the quick response. I have another...
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The space group of your compound is C2/c, which is a base-centred setting. By default...
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I use the first among the given cif files for coesite from here http://rruff.geo.arizona.edu/AMS/minerals/Coesite...
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I use the first among the given cif files for coesite from here http://rruff.geo.arizona.edu/AMS/minerals/Coesite...
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Paul Hodgkinson created ticket #7
Extended labelling
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Fix to CASTEP atom label output
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'improveprecision' over-used
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Just to add to the question: 3 files are attached with muscovite data 1. CIF (mu.cif)...
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Actually, the micas end-members, which I would like to study at the moment (e.g.,...
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The problem is that cif2cell produces a unit cell of the compound, but a mixture...
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cif2cell complains that a system is an alloy when creating inputs for the Crystal...
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Lee Burton posted a comment on discussion Help
i'm sorry but this does not solve the problem. Neither does setting the cif2cell...
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For some reason the installer doesn't copy the python modules. A simple fix would...
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Ok i have been playing with this for a week now and still no success. So let me provide...
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i tried deleting all of the cif2cell files/folders i could find and then rerunning...
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This looks like an installation issue. I can reproduce the problem by running cif2cell...
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using cif2cell version 1.2.10 on Mac OSX, i get the error: Traceback (most recent...
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No, there isn't. The reason was that as far as I can understand, the program determines...
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No, there isn't. The reason was that as far as I can understand, the program determines...
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Lorenzo Dona posted a comment on discussion Help
dear all is there a way to create a queantum espresso input with ibrav different...
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Hi It seems after several try-and-error attempts, I have found what was wrong with...
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Generally speaking, the Crystal interface is not very well maintained. I have never...
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