wrong units in density.cube file

[jjakowski]

The header indensity.cube file is currently in Angstrooms. Currently Angstrooms is used for both atomic coordinates and for mesh description. However, when the density.cube is opened with VESTA or VMD the coordinates and mesh is interpreted as it is Bohrs and all bonds seems to be compressed.

For example,

1) Here is the first few lines of "density.cube" created by RMG:

This is a Cube file to be viewed

Atomic coordinates in Angstroms

720 0.0 0.0 0.0 1
192 0.206710 0.000000 0.000000 192 0.000000 0.206710 0.000000 192 0.000000 0.000000 0.206710 6 0.000000 2.697192e+01 1.944030e+01 1.011858e+01 6 0.000000 2.587621e+01 1.906240e+01 9.511481e+00 6 0.000000 2.523281e+01 2.013900e+01 9.136980e+00 6 0.000000 2.593221e+01 2.117970e+01 9.509981e+00 6 0.000000 2.700912e+01 2.074900e+01 1.011538e+01 6 0.000000 3.238073e+01 1.892400e+01 2.118180e+01

and corresponding composite plot of structure +density:

2) Here is how it should look like (the same file but with header corrected):

This is a Cube file to be viewed

Atomic coordinates in bohrs

720 0.0 0.0 0.0 192 0.39062 0.000000 0.000000 192 0.000000 0.39062 0.000000 192 0.000000 0.000000 0.39062
6 0.000000 50.96953537 36.73684491 19.12134876 6 0.000000 48.89895821 36.02271594 17.97409368 6 0.000000 47.68310593 38.05719926 17.2663898 6 0.000000 49.00478309 40.02384127 17.97125909 6 0.000000 51.03983333 39.20993456 19.11530163

and corresponding composite plot of structure +density:

Notice that the first version shows bond betnween all carbons in the hexagons.

[WenchangLu]

fixed the bug for unit in cube files. All atoms' coordinate and dx,dy,dz are in unit of Bohr.