The input filter has to read the following data from the output file and write them to its standard output in the format described below. This format follows the file format of TURBOMOLE very closely. A few sections had to be extended to allow data which is currently not supported by TURBOMOLE (e. g. unit cells).
$coord factor x1 y1 z1 symbol1 xyz x2 y2 z2 symbol2 xyz ...
factor is the conversion factor the coordinates have to be multiplied
with to convert them to Ångstrøms. Any combination of x, y, and z at the
end of the line (optional) indicates that the corresponding atom has been kept
fixed in that direction during a geometry optimization. Consequently, VIEWMOL
will not draw the forces acting on this atom in the fixed direction.
$title title
$vibrational spectrum symmetry1 wavenumber1 IR-intensity1 Raman-intensity1 symmetry2 wavenumber2 IR-intensity2 Raman-intensity2 ...
symmetry is the symmetry label for the vibrational mode,
wavenumber is its wave number and IR-intensity and
Raman-intensity are its IR and Raman intensity, respectively. If the
symmetry labels for the vibrational modes are unknown they should be set to a
default (e. g. A1).
$vibrational normal modes i1 i2 nm(1,1) nm(2,1) nm(3,1) nm(4,1) nm(5,1) i1 i2 nm(6,1) ... nm(3*natom,1) i1 i2 nm(1,2) nm(2,2) nm(3,2) nm(4,2) nm(5,2) i1 i2 nm(6,2) ... nm(3*natom,2) ... i1 i2 nm(1,nmodes) ... nm(5,nmodes) i1 i2 nm(6,nmodes) ... nm(3*natom,nmodes)
i1 and i2 are integers which are skipped during reading.
nm(i,j) are the normal mode coefficients. They have to be provided
ordered by cartesian coordinates (all x components of the first atom first,
then all y components of the first atom etc.).
$grad factor cycle = nc SCF energy = E_nc |dE/dxyz| = gradnorm_nc [unitcell a b c alpha beta gamma] [unitcell vectors xa ya za xb yb zb xc yc zc] x1 y1 z1 symbol1 x2 y2 z2 symbol2 ... xn yn zn symboln gx1 gy1 gz1 gx2 gy2 gz2 ... gxn gyn gzn cycle = nc+1 SCF energy = E_nc+1 |dE/dxyz| = gradnorm_nc+1 ...
factor is the conversion factor the coordinates have to be multiplied
with to convert them to Ångstrøms. nc is a counter for the cycle,
E_nc is the energy for the configuration of cycle nc, and gradnorm_nc
is the gradient norm of cycle nc. The line starting with unitcell is optional
and can be used to specify the current unit cell, e. g. during a constant pressure
MD run. Unit cells can be specified either by providing the lengths of the edges
and the angles between them or by providing the three vectors which span the unit
cell. The x, y, and z are the cartesian coordinates for each
atom, symbol is the atomic symbol. The gx, gy, and gz
are the gradients for each atom. This structure can be repeated for as many
cycles as necessary.
$scfmo [symmetrized] [gaussian]
n symmetry_label_n eigenvalue=MO_E_n nsaos=norb
moc(n,1) moc(n,2) moc(n,3) moc(n,4)
moc(n,5) ... moc(n,norb)
n+1 symmetry_label_n+1 eigenvalue=MO_E_n+1 nsaos=norb
...
$uhfmo_alpha [symmetrized] [gaussian]
n symmetry_label_n eigenvalue=MO_E_n nsaos=norb
moc(n,1) moc(n,2) moc(n,3) moc(n,4)
moc(n,5) ... moc(n,norb)
n+1 symmetry_label_n+1 eigenvalue=MO_E_n+1 nsaos=norb
...
$uhfmo_beta [symmetrized] [gaussian]
n symmetry_label_n eigenvalue=MO_E_n nsaos=norb
moc(n,1) moc(n,2) moc(n,3) moc(n,4)
moc(n,5) ... moc(n,norb)
n+1 symmetry_label_n+1 eigenvalue=MO_E_n+1 nsaos=norb
...
symmetrized is optional and can be used to notify
VIEWMOL of the fact that the MO coefficients are with respect to
symmetrized AOs rather than with respect to AOs. VIEWMOL needs
moloch from the TURBOMOLE package to handle symmetrized AOs. If moloch
is not installed and symmetrized AOs are input, MOs and electron densities
cannot be drawn. The string gaussian is also optional and notifies
VIEWMOL that the MO coefficients are normalized and ordered GAUSSIAN
style. n is a counter counting the MOs, symmetry_label_n is
the symmetry label for MO n, MO_E_n is the MO energy for MO n, and
norb is the total number of orbitals. The moc(n,i) are the MO
coefficients for MO n.
$atoms atom_symbol1 list_of_indices1 \ basis=basis_set_name1 atom_symbol2 list_of_indices2 \ basis=basis_set_name2 ... $basis * basis_set_name1 * number_of_primitives angular_momentum exponent1 coefficient1 exponent2 coefficient2 ... exponentn coefficientn number_of_primitives angular_momentum ... * basis_set_name2 * ... * $closed shells symmetry_label list_of_indices (2) $alpha shells symmetry_label list_of_indices (1) $beta shells symmetry_label list_of_indices (1) $pople [6d/10f/15g]
atom_symbol is the atom symbol of an element and list_of_indices
contains the indices of all atoms of the particular element according to the
list of coordinates read in under $coord. The list can be either comma
separated and/or contain hyphens for indicating ranges (e. g. c 1,3,7-10 is a
valid descriptor). Basis_set_name can be an arbitrary string describing
a particular basis set. It is only used to find the corresponding basis set in
the list read under basis. This list simply states the name for a basis
set and then lists the primitive functions which make up a contracted Gaussians
starting with the number of primitives in that particular contracted Gaussian
and its angular momentum (s, p, d, f, ...). Than the exponents and contraction
coefficients are listed line by line. This is repeated for all contracted
Gaussians of that particular basis set. $closed shells, $alpha shells,
and $beta shells are used to tell VIEWMOL which MOs are occupied
with how many electrons. symmetry_label is the symmetry label for a number
of MOs and list_of_indices is a list of integers stating which of the MOs
of that particular symmetry are occupied by either one or two electron(s). This list
can be either comma-separated or contain hyphens to indicate ranges of MOs.
Note: $closed shells, $alpha shells, and $beta shells
have to appear after $scfmo in the output written by the input filter.
$pople is used to indicate that d, f, or g functions have 6, 10, or 15
components instead of 5, 7, or 9. Note: This data group has to appear after
the $coord or $grad in the output. Otherwise VIEWMOL will fail.
$grid #n origin x y z vector1 x y z vector2 x y z vector3 x y z grid1 start s delta d points np grid2 start s delta d points np grid3 start s delta d points np type ty title for this grid t plotdata d(1,1,1) d(1,1,2) d(1,1,n) ... d(1,2,1) ... d(1,n,n) d(2,1,1) ... d(n,n,n)
n is an integer identifying the grid. origin is used
to specify the x, y, and z coordinates of the origin of the grid. vector1,
vector2, and vector3 are used to specify the three vectors
spanning the grid. grid1, grid2, and grid3 are used to
specify the starting point, s, the step size, d, and the number
of points, np, on each of the three vectors spanning the grid. ty
can be either mo or density specifying whether the data represents
a molecular orbital or a density. t is a string giving the grid a
title which is used in the wave function dialog to allow the user to select
the grid. Finally, d(i,j,k) are the values for the property at each
grid point.