VIEWMOL can be easily adapted to read outputs of other programmes or other file formats. All you have to do is to write a new input filter which extracts the data from the corresponding file. These input filter are stand-alone programmes and can be written in every programming language you want. Examples in C and awk are included.
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 are currently not supported by TURBOMOLE (e. g. unit cells).
$coord factor x1 y1 z1 symbol1 x2 y2 z2 symbol2 ...
factor
is the conversion factor the coordinates have to be multiplied
with to convert them to Ångstrøms.$title title
$vibrational spectrum symmetry1 wavenumber1 IR-intensity1 Raman-intensity1 symmetry2 wavenumber2 IR-intensity2 Raman-intensity2 ...
symmetry
is the symmetry label for the vibrational mode, wavenumber
is the its wave number and IR-intensity
and Raman-intensity
are its
IR and Raman intensity, respectively. If the symmetry labels for the vibrational
modes are unknown they should be set to a default (e. g. A1).$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 provided ordered by cartesian coordinates
(all x components of the first atom first, then all y components of the first atom etc.).$grad cartesian gradients cycle = nc SCF energy = E_nc |dE/dxyz| = gradnorm_nc [unitcell a b c alpha beta gamma] x1 y1 z1 symbol1 x2 y2 z2 symbol2 ... xn yn zn symboln gx1 gy1 gz1 gx2 gy2 gz2 ... gxn gyn gzn cycle = nc+1 SCF energy = E_nc+1 |dE/dxyz| = gradnorm_nc+1 ...
nc
is a counter for the cycle, E_nc
is the energy for the configuration of cycle
nc, and gradnorm_nc
is the gradient norm of cycle nc. The line starting with
unitcell
is optional and can be used to specify the current unit cell e. g. during a
constant pressure MD run. The x
, y
, and z
are the cartesian coordinates
for each atom, symbol
is atomic symbol. The gx
, gy
, and gz
are the
gradients for each atom. This structure can be repeated for as many cycles as necessary.$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 ...The string
symmetrized
after $scfmo
is optional and can be used to
notify VIEWMOL of the fact that the MO coefficients are with respect to
symmetrized AOs rather than with respect to AOs. VIEWMOL needs moloch from
the TURBOMOLE package to handle symmetrized AOs. If moloch is not installed
and symmetrized AOs are input, MOs and electron densities cannot be drawn.
The string gaussian
is also optional and notifies VIEWMOL that the
MO coefficients are normalized and ordered GAUSSIAN style.
n
is a counter counting the MOs, symmetry_label_n
is the symmetry label for
MO n, MO_E_n
is the MO energy for MO n, and norb
is the total number
of orbitals. The moc(n,i)
are the MO coefficients for MO n.$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) $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 descriping a particular basis set. It is only used to find
the correponding basis set in the list read under basis
. This list simply
states the name for a basis set and than 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
is
used to tell VIEWMOL which MOs are occupied and which are not. 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. This list can be either
comma-separated or contain hyphens to indicate ranges of MOs. $pople
is used to
indicate that d, f, or g functions have 6, 10, or 15 components instead of 5, 7, or 9.$unitcell a b c alpha beta gamma
$error errorLabel severity additionalInformation
errorLabel
is an arbitrary one word label which refers to an error message
in the resources. severity
is a label for the severity of the error. Set it
to 0 if the programme can continue despite this error. Set it to 1 if the programme
must stop. additionalInformation
is 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: noFile
, notConverged
,
unsupportedVersion
, wrongFiletype
, noCoordinates
, noEnergy
,
and unknownErrorMes-
sage
. 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.inpThen you have to specify a resource for the error message in
$HOME/.Xdefaults
:
Viewmol.missingCoordinates: The file %s does not contain any coordinates.With these two lines in place any encounter of no coordinates in an input file will let to the display of the error dialog in Figure 7. There is no need to recompile VIEWMOL to achieve this !
$end
.
Figure 7: The error dialog produced by the sample error message
The input filter can be installed by adding a line to the viewmolrc
file.