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cpmd2cube

Files like DENSITY.x, ELF, LSD_ELF, SPINDEN.x, WANNIER_1.x ... are created in a binary format and they have to be translated to a Gaussian style cube-file format to be readable by visualization programs. The cpmd2cube.x tool to convert the output can be download at www.cpmd.org and is used in the following way:
cpmd2cube: Convert CPMD's Wannier-function files to cube
usage is: cpmd2cube [options] Wannier_file [Wannier_file...]
   If you specify more than one Wannier file, they MUST have the
   same g-vectors and (for the moment) atom positions
   The program will create one cube file for each Wannier file
   and one pdb file with the atom positions
Example:
   cpmd2cube WANNIER_1.*
possible options are
   -v <verbosity>:
      <verbosity> is 0-3 (default is 1)
   -double:
      Read the density in double precision (default is single)
   -fullmesh:
      create full mesh cube file (default is -halfmesh)
   -halfmesh:
      leave out half the grid points in each direction.
      Reduces the file size by 1/8th
   -trim <threshold>:
      write a minimal cube file including all data points which have an
      absolute value above <treshold>. Can reduce the file size dramatically
      for isolated molecules and localized orbitals.
   -normpot:
      correct for the fact, that the integrated electrostatic potential.
      is not zero. To be used when converting ELPOT files
   -nocoords:
      do not output any coordinates to the cube file. only puts a dummy
      atom at the origin, since some codes need at least one atom.
      main application is to generate small files on QM/MM runs.
   -n <n1> <n2> <n3>:
      change the REAL-space mesh. Default is to take the same mesh as CPMD
   -o <prefix>:
      specify the prefix of the name used for the cube and pdb-files
   -rep <n1> <n2> <n3>:
      replicate the cell n<j> times along the <j>-th direction by periodicity
   -shift <r1> <r2> <r3>:
      shift cube density by r1*a1+r2*a2+r3*a3
   -centre:
   -center:
      centre density around centre of mass of system.
   -inbox:
      put atoms inside unit cell centred around origin
   -rho:
   -dens:
      convert a density instead of a wavefunction into a cube file.
   -psi:
   -wave:
      convert a wavefunction instead of a density into a cube file.
   --:
      last option. Useful if you have a file with the same name as an option
   -h  or  -?  or  -help  or  --help  or no files:
      write this help

Bundled with cpmd2cube.x are two more utilities that can be used to post process the resulting cube files: trimcube and cutcube.x.

cutcube.x allows to cut out regions around atoms from a cubefile and thus visualize/analyze only a subset of the total data. The program guides you through the process interactively.

trimcube serves three purposes: a) it can be used to reduce the size of cube files that contain significant data only in a subset of the data points (e.g. the density of an isolated molecule or some (localized) orbital), b) it can normalize cubefiles containing the electrostatic potential (in pseudopotential calculations, the ``neutral'' electrostatic potential is not always exactly as zero and the normalization corrects for that), and to select the phase, i.e. set all positive or all negative values to zero. The functionality a) and b) is also available directly from cpmd2cube as -trim and -normpot flag.


next up previous contents index
Next: Fourier Up: Post-Processing Tools and File Previous: General Tools   Contents   Index
Costas Bekas 2008-09-04