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 ...
factoris 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.
$vibrational spectrum symmetry1 wavenumber1 IR-intensity1 Raman-intensity1 symmetry2 wavenumber2 IR-intensity2 Raman-intensity2 ...
symmetryis the symmetry label for the vibrational mode,
wavenumberis its wave number and
Raman-intensityare 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)
i2are 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 ...
factoris the conversion factor the coordinates have to be multiplied with to convert them to Ångstrøms.
ncis a counter for the cycle,
E_ncis the energy for the configuration of cycle nc, and
gradnorm_ncis the gradient norm of cycle nc. The line starting with
unitcellis 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
zare the cartesian coordinates for each atom,
symbolis the atomic symbol. The
gzare 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 ...
symmetrizedis 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
gaussianis also optional and notifies VIEWMOL that the MO coefficients are normalized and ordered GAUSSIAN style.
nis a counter counting the MOs,
symmetry_label_nis the symmetry label for MO n,
MO_E_nis the MO energy for MO n, and
norbis 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_symbolis the atom symbol of an element and
list_of_indicescontains 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_namecan 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.
$alpha shells, and
$beta shellsare used to tell VIEWMOL which MOs are occupied with how many electrons.
symmetry_labelis the symmetry label for a number of MOs and
list_of_indicesis 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:
$alpha shells, and
$beta shellshave to appear after
$scfmoin the output written by the input filter.
$popleis 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
$gradin 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)
nis an integer identifying the grid.
originis used to specify the x, y, and z coordinates of the origin of the grid.
vector3are used to specify the three vectors spanning the grid.
grid3are 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.
tycan be either
densityspecifying whether the data represents a molecular orbital or a density.
tis 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.
$unitcell a b c alpha beta gamma
$unitcell vectors xa ya za xb yb zb xc yc zc
$error errorLabel severity additionalInformation
errorLabelis an arbitrary one word label which refers to an error message in the resources.
severityis a label for the severity of the error. Set it to 0 if the program can continue despite this error. Set it to 1 if the program must stop.
additionalInformationis any additional information you want to be displayed in the error message (e. g. the name of a file which was not found). Currently, the following errorLabels are in use:
unknownErrorMessage. If your input filter wants to return an error because it is missing coordinates in the input file ``dummy.inp" you can have it writing the following line to standard output:
$error missingCoordinates 1 dummy.inp
Viewmol.missingCoordinates: The file %s does not contain any coordinates.
The input filter can be installed by adding a line to the