The formats supported by pikashu
are specified in the table below. "Input" means that the program can read this format, and "output" means it can convert files into this format. Clicking on a format name in the first column will redirect you to a (more or less) official web page describing this format. Please also read carefully the notes below the table.
INPUT | OUTPUT | |
---|---|---|
xyz | YES (1) | YES (extended xyz) (1) |
cfg (Atomeye format) | YES (normal and extended) | YES (extended cfg) |
xsf (xCrysDen format) | YES | YES |
gin (GULP format) | YES (gin, res or grs) (2) | YES (3) |
POSCAR (VASP format) | YES (4) | YES (4) |
dd (ddplot format) | NO | YES (5) |
(1) The XYZ format, although it is broadly used by many programs, has never been formally defined or published, so this format is nothing else than a text file containing 'atom x y z' lines. As a result, some programs use the atomic number in the first column, while some other programs use the atomic symbol; and the coordinates x, y and z can be either cartesian or fractional coordinates, depending on the periodicity of the system (cartesian coordinates are usually used for single molecules, while fractional coordinates are used for periodic crystals). Also, the system (or supercell) dimensions are usually not written in a XYZ file, contrary to other formats like CFG or XSF.
pikashu
can read XYZ files in all of these formats: it automatically detects if the spieces or the atomic number is used in the first column, and it also detects if fractional or cartesian coordinates are used.
When writing an output file to the XYZ format, pikashu
will use cartesian coordinates and use the atomic spieces as a first column. In addition, the dimensions of the system are written at the end of the file. All in all, pikashu
outputs the XYZ format in the following way (NP
is the total number of particles, <a0>
the lattice parameter, and the <H(i,j)>
the vectors of the supercell):
----------------------------------------
NP
comment
spieces1 x1 y1 z1
spieces2 x2 y2 z2
spieces3 x3 y3 z3
... ... ...
alat
<a0>
supercell
<H(1,1)> <H(1,2)> <H(1,3)>
<H(2,1)> <H(2,2)> <H(2,3)>
<H(3,1)> <H(3,2)> <H(3,3)>
----------------------------------------
(2) The reading of GULP input files (gin, res or grs) comes with a number of restrictions:
----------------------------------------
cell
# This comment is in the wrong place
4.02 4.02 4.02 90.0 90.0 90.0
----------------------------------------
In that case the line starting with # will cause an error, it has to be placed elsewhere. Apart from that, comments (i.e., lines starting with #) in the input file should not cause any problem.
(3) Only a basic GIN file is output, containing the cell parameters and the positions of the cores. This GIN file is just a draft, it is NOT fully set for a simulation. It is up to the user to complete this GIN file with the simulation parameters (atomic potential, options for relaxation/MD, etc.), and additional shell positions if relevant, before running a simulation.
(4) In VASP, the atom masses are not specified in the POSCAR file, but in the potential file (POTCAR). Hence, when reading a POSCAR file the program cannot guess the atomic masses, so dummy numbers will be used instead (first element will have mass=1, second mass=2, etc.). For the same reason, when converting atomic positions into a POSCAR file, the atomic masses cannot be written and will be lost (it is the user's responsability to set up atomic masses properly in the POTCAR file).
(5) Output to ddplot format is available only through the ddplot mode.