CIF2CELL(1)
💖 CIF2CELL(1) 💖
User Commands · CIF2CELL · User Commands
okay bestie, welcome to the cif2cell page, this is the one, this is THE girl 💅
✨ NAME ✨
cif2cell — get your CIF files ready for electronic structure calculations 🧚
✨ SYNOPSIS ✨
cif2cell FILE [-p PROGRAM] [other options]✨ DESCRIPTION ✨
so basically, this program generates input lattice structures for a whole bunch of electronic structure programs, starting from a CIF (Crystallographic Information Framework) file. iconic behaviour, no notes. 🎀
this code was published in Comput. Phys. Commun. 182, 1183 (2011). Please cite generously. like, she's asking nicely, do it 🫶
✨ OPTIONS ✨
-h,--help— shows this help message and then dips out ✌️--version— prints the version number, that's it, that's the whole job 💫-v,--verbose— be as verbose as physically possible, spill EVERYTHING 🗣️-q,--quiet— suppress all screen output except what you explicitly asked for. this one overrides the--verboseflag, so don't try to have both, she's not gonna let you 💀
🌸 General options: 🌸
-f FILE,--file=FILE— the input CIF file. you only need this if you didn't already hand it over as the first argument to the program 🍓-p PROGRAM,--program=PROGRAM— which electronic structure code do you want input file(s) for? currently she supports:abinit,ase,atat,bmdl,castep,cellgen,cfg,cif,coo,cp2k,cpmd,crymol,crystal09,elk,emto,exciting,fhi-aims,fleur,hutsepot,kfcd,kgrn,kstr,lammps,mopac,ncol,pwscf,quantum-espresso,rspt,shape,siesta,spacegroup,spc,sprkkr,vasp,xband,xyz. and this keyword is case insensitive, so type it however your heart desires 💖-o FILE,--outputfile=FILE— name of the output file, for when you don't want the default name that your electronic structure code would normally get 🌈-a,--append— append the output onto the given output file instead of straight up overwriting it. polite 💅--grammar=GRAMMAR— sets the CIF grammar used when parsing the input file (default is1.1)--which-filename— if you pair this with the--programoption, the name of the output file gets printed to screen 📺-b BLOCK,--block=BLOCK— which block of data in the input file to use, for when your CIF file has more than one block in it 🧩
🌸 Cell generation options: 🌸
--no-reduce— don't reduce to the primitive cell 🚫--force— attempt to force generation of the output file despite problems and/or ambiguities in the input file. there are no guarantees that what you get makes sense, but the program makes an honest attempt, she's trying her best 😭. this implies--forcealloy--force-alloy— force generation of the output file for an alloy compound, for an electronic structure code that doesn't implement any alloy theory (like CPA) 🧪--vca— set up an alloy using the virtual crystal approximation (VCA). currently only the CASTEP interface supports this one 👑--cartesian— make the program generate any output in cartesian coordinates 📐--coordinate-tolerance=COORDTOL— the parameter for deciding when two coordinates count as the same one (default=0.0002)--setup-all— do a more complete setup, not just the geometrical part. currently only available formopac,pwscf,quantum-espresso,rspt,vasp💫--k-resolution=KRESOLUTION— the desired resolution in k-space (default=0.2). used for generating k-space grid options if--setup-allis specified 🌐--transform-cell=[[],[],[]]— a transformation matrix applied to the lattice vectors and the symmetry operations, for when you, say, want to realign the cell 🔄--body-centred-setting=0,1— if set to1, use the more symmetrical set of primitive translation vectors used for the bcc structure for other body-centred crystals too 🎯--cubic-diagonal-z— set up a cubic cell with the[111]direction along the z-axis 📏--rhombohedral-diagonal— set up a rhombohedral cell with the threefold axis along the pseudocubic[111]direction 💎--random-displacements=displacementsize— randomly displace all atoms. depending on the distribution, the displacement size is either the maximal displacement (for uniform distribution) or the standard deviation (for gaussian distribution), in Angstrom 🎲--random-displacements-distribution=uniform/gaussian— the distribution used for displacing the atoms 📊--export-cif-labels— export atom labels from the CIF file (currently only supported forcastepandRSPt) 🏷️
🌸 Supercell generation options: 🌸
--supercell=[k,l,m]/[[],[],[]]— three integers separated by commas and wrapped in square brackets that specify the dimensions of a supercell, OR three vectors of integers giving the map to the supercell to be constructed from the primitive cell. if you combine this with the--no-reduceoption, the supercell gets generated based on the conventional cell instead 🧱--supercell-dimensions=[x,y,z]/[[],[],[]]— three numbers separated by commas and wrapped in square brackets that specify the desired ABSOLUTE dimensions of a supercell (in angstrom), OR three vectors of numbers giving the desired lattice vectors. the program will automatically generate a supercell, attempting to get as close as possible to the desired dimensions 🎯--supercell-vacuum=[k,l,m]— three numbers>=0separated by commas and wrapped in square brackets that specify a number of unit cell units of vacuum to add along the first, second or third of the generated lattice vectors 🌌--supercell-translation-vector=[k,l,m],--supercell-prevacuum-translation=[k,l,m]— three numbers separated by commas and wrapped in square brackets that specify a shift of all atomic positions in the cell prior to vacuum generation (in units of the lattice vectors of the supercell) 🚚--supercell-postvacuum-translation=[k,l,m]— three numbers separated by commas and wrapped in square brackets that specify a final shift of all atomic positions in the final cell (in units of the lattice vectors of the new cell) 📦--supercell-realign=0,1— realign the supercell lattice vectors with respect to the cartesian reference frame. for orthorhombic cells, it puts the first, second and third lattice vectors along x, y and z, respectively 🧭--supercell-sort=SUPERCELLSORT— sort the atom positions by some scheme. currently available are: 1) by cartesian coordinate — example:xzywill sort first on x, then on z, then on y. 2) by lattice vector — example:132will sort first by lattice vector 1, then by lattice vector 3 and last by lattice vector 2 🔢
🌸 Surface generation options: 🌸
--surface-wizard=[h,k,l]— three integers separated by commas and wrapped in square brackets that specify a(hkl)plane. the wizard will suggest a supercell map that gives the first two lattice vectors in the(hkl)plane. the third lattice vector is selected as the[hkl]direction, or as reasonably orthogonal to the(hkl)plane as possible (if the[hkl]direction is far from orthogonal to this plane) 🧙♀️✨
🌸 Printing options: 🌸
--print-digits=PRINTDIGITS— number of digits used when printing coordinates etc. to screen (default=8). useful if you need to tweak the screen output for cutting and pasting into some unsupported program. there's genuinely no point in going over16because of the floating point accuracy 🖨️--print-atomic-units— output lattice parameters in bohrradii rather than angstrom 📏--print-cartesian— atomic sites printed to screen in cartesian rather than lattice coordinates 📐--print-symmetry-operations— print the symmetry operations of the generated cell 🔄--print-seitz-matrices— print the symmetry operations of the generated cell in Seitz matrix form 🔷--print-charge-state,--print-oxidation-numbers— print information about the oxidation state from the CIF file ⚡--print-reference-bibtex— print the citation in BibTeX format and exit 📚
🌸 Program specific options: 🌸
--abinit-braces— put curly braces around input values for ABINIT{ }🎀--cellgen-map=[[k,l,m],[n,o,p],[q,r,s]]— nine integers separated by commas and grouped three and three inside square brackets (this is a matrix in Python) that specify the map to a supercell to be output for the RSPt supercell generatorcellgen. this overrides--cellgen-supercell-dims🗺️--cellgen-supercell-dimensions=[k,l,m]— three integers separated by commas and wrapped in square brackets that specify the dimensions of a supercell to be output to the RSPt supercell generatorcellgen(the diagonal elements of themap) 📦--cellgen-reference-vector=[x,y,z]— three reals separated by commas and wrapped in square brackets that specify an optional shift of the origin used by the RSPt supercell generatorcellgen🎯--castep-cartesian— output atom positions in cartesian rather than lattice coordinates 📐--castep-atomic-units— output to CASTEP in atomic units (bohr radii) rather than angstrom 📏--cpmd-cutoff=CPMDCUTOFF— set the cutoff written to the&SYSTEMblock (default=100.0 Ry) ✂️--crystal09-rhombohedral-setting— for trigonal spacegroups where this is possible, specify the rhombohedral cell in the Crystal09 input 💎--emto-hard-sphere-radii=HARDSPHERERADII— set hard spheres in KSTR to something other than the default (=0.67) ⚽--fhi-aims-cartesian— store the coordinates for FHI-AIMS in cartesian format 📐--mopac-first-line="string"— string to be used for the first line (the run commands) of the MOPAC input 1️⃣--mopac-second-line="string"— string to be used for the second line (documentation) of the MOPAC input 2️⃣--mopac-third-line="string"— string to be used for the third line (documentation) of the MOPAC input 3️⃣--mopac-freeze-structure=T/F— if set to'T'then add a0after each coordinate (freezing the structure), if set to'F'then add a1(allowing everything to relax) 🧊--pwscf-pseudostring=_PSEUDO— string to attach to the element name to identify the pseudopotential file (e.g. something like"_HSCV_PBE-1.0.UPF") 🔤--pwscf-atomic-units— write the PWSCF.infile in atomic units (bohr) rather than angstrom 📏--pwscf-alat-units— use'alat'units for the positions in the PWSCF.infile 📐--pwscf-cartesian— write lattice vectors and positions to the PWSCF.infile in cartesian coordinates and set the lengths scale to1🧭--pwscf-cartesian-latticevectors— drops the lattice vectors into your PWSCF.infile as cartesian coordinates and sets the lengths scale to1. no conversion drama, we're going straight-up cartesian 💅--pwscf-cartesian-positions— same energy but for the lattice positions in that PWSCF.infile: cartesian coordinates, periodt.--rspt-new— generates asymt.inpfile in the new format. shiny new era ✨--rspt-spinpol— generates a new-formatsymt.inpfile with spin polarization. spins are booked and busy 🌀--rspt-relativistic— generates a new-formatsymt.inpfile with relativistic effects baked in. fast particles, main character physics 🚀--rspt-spinaxis=[x,y,z]— sets the spin axis forsymt.inp; the default is[0.0,0.0,0.0]. give it your three numbers, bestie 🧭--rspt-no-spin— forces a nonmagnetic setup, and it works in conjunction with--setupall. no magnetism today, we're chillin' 🧊--rspt-mtradii=N— an integerNthat tells it which method to use for setting the muffin tin radii. yes it's really called that, and yes it's lowkey iconic 🧁--rspt-cartesian-latticevectors— puts the lattice vectors in atomic units and sets the length scale parameter to1.--rspt-pass-wyckoff— passes the wyckoff labels from the CIF file through to thesymt/rspt.inpfile. hand them over, no gatekeeping 🫶--sprkkr-minangmom=SPRKKRMINANGMOM— enforces a minimum onsite angular momentum (=l+1, so that3will be d-states). set the floor, bestie 📐--spacegroup-supercell=[k,l,m]— three integers, comma-separated, wrapped in square brackets, that specify the dimensions of a supercell to be output to the elk input generatorspacegroup. three numbers, one glow-up 🏗️--vasp-format=VASPFORMAT— the format of the generated POSCAR file, either4or5. default is4. pick your era, no wrong answers (well, mostly) 🌈--vasp-print-species— prints the atomic species to screen in the order they get put into the POSCAR file. super useful for scripting, fr fr 🖨️--vasp-cartesian— writes the lattice vectors and positions to the POSCAR file in cartesian coordinates, and sets length to1. both at once, because we're efficient 💅--vasp-cartesian-lattice-vectors— writes just the lattice vectors to the POSCAR file in cartesian coordinates and sets the length scale to1.--vasp-cartesian-positions— writes the atomic positions to the POSCAR file in Cartesian rather than Direct coordinates.--vasp-selective-dynamics— outputs the POSCAR in selective dynamics format (without any constrained atoms). selective, but make it zero constraints 😌--vasp-pseudo-libdr=VASPPSEUDOLIB— the path to the VASP pseudopotential library. you can also set this with theVASP_PAWLIBenvironment variable 🔑🫶--vasp-pseudo-priority="_d,_pv,_sv,_h,_s"— sets the priority of different pseudopotentials via a list of suffixes. also available through theVASP_PP_PRIORITYenvironment variable. ranking the suffixes, it's giving leaderboard 📊--vasp-encutfac=1.5— a factor that multiplies the maximal ENCUT found in the POTCAR file. multiply, don't add 💥--xyz-atomic-units— outputs the xyz file in atomic units (bohr radii) rather than angstrom. bohr girl summer 🌸
and that's the whole flag squad, bestie 💖 you made it to the end, genuinely iconic of you 👑
this wascif2cellversion2.1.0+dfsg, datedFebruary 2024— screenshot it, cite it, love it, and go convert some crystals 🦋✨
📦 where this page comes from
- debian trixie: python3-cif2cell 2.1.0+dfsg-1 · GPL-3.0-or-later
- ubuntu noble: python3-cif2cell 2.1.0+dfsg-1 · GPL-3.0-or-later
- ubuntu questing: python3-cif2cell 2.1.0+dfsg-1
- 💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on : a language model's rewrite of the original, under its terms