MOLCAS manual:

Next: 6.4 SEWARD An
Up: 6. Program Based Tutorials
Previous: 6.2 Environment and EMIL Commands
Subsections
6.3 GATEWAY - Definition of geometry, basis sets, and symmetry
The program GATEWAY handles the basic molecular parameters in the
calculation. It generates data that are used in all subsequent calculations.
These data are stored in the RUNFILE. GATEWAY is the first
program to be executed, if the $WorkDir directory and the RUNFILE file
has not already been generated by a previous calculation.
This tutorial is describes how to set up the basic MOLCAS input for the water molecule.
For a more general description of the input options for GATEWAY, please refer to the Users Guide.
The first line of the input is the program identifier &GATEWAY.
Then follows the keyword used is TITLe which will also get
printed in the GATEWAY section of the calculation output.
The title line is also saved in the integral file and will appear in subsequent programs.
The GROUp keyword is followed by the generators for the C2v
point group, since the example deals with the water molecule.
The specification of the C2v point group given in
Table 6.1 is not unique, but, in this tutorial, the
generators have been input in an order that reproduces the ordering in the
character tables. A complete list of symmetry generator input syntax is given
in Table 6.1. The symmetry groups available are listed
with the symmetry generators defining the group. The MOLCAS keywords required
to specify the symmetry groups are also listed. The last column contains the
symmetry elements generated by the symmetry generators.
&GATEWAY
Title= Water in C2v symmetry - A Tutorial
Coord = water.xyz
Group = XY Y
Basis Set = O.ANO-S-MB,H.ANO-S-MB
Table 6.1:
Symmetries available in MOLCAS including generators, MOLCAS keywords and symmetry elements.
Group |
Generators |
MOLCAS |
Elements |
|
g1 |
g2 |
g3 |
g1 |
g2 |
g3 |
E |
g1 |
g2 |
g1g2 |
g3 |
g1g3 |
g2g3 |
g1g2g3 |
C1 |
|
|
|
|
|
|
E |
|
|
|
|
|
|
|
C2 |
C2 |
|
|
xy |
|
|
E |
C2 |
|
|
|
|
|
|
Cs |
 |
|
|
x |
|
|
E |
 |
|
|
|
|
|
|
Ci |
i |
|
|
xyz |
|
|
E |
i |
|
|
|
|
|
|
C2v |
C2 |
 |
|
xy |
y |
|
E |
C2 |
 |
 |
|
|
|
|
C2h |
C2 |
i |
|
xy |
xyz |
|
E |
C2 |
i |
 |
|
|
|
|
D2 |
C2z |
C2y |
|
xy |
xz |
|
E |
C2z |
C2y |
C2x |
|
|
|
|
D2h |
C2z |
C2y |
i |
xy |
xz |
xyz |
E |
C2z |
C2y |
C2x |
i |
 |
 |
 |
To reduce the input, the unity operator E is always assumed. The twofold
rotation about the z-axis, C2(z), and the reflection in the xz-plane,
(xz), are input as XY and Y respectively. The MOLCAS input can be viewed as symmetry operators that operate on the
Cartesian elements specified. For example, the reflection in the
xz-plane is specified by the input keyword Y which is the
Cartesian element operated upon by the reflection.
The input produces the character table in the
GATEWAY section of the output shown in
Figure 6.3. Note that (yz) was produced from
the other two generators. The last column contains the basis functions of
each irreducible symmetry representation. The totally symmetric a1
irreducible representation has the z basis function listed which is unchanged
by any of the symmetry operations.
E C2(z) s(xz) s(yz)
a1 1 1 1 1 z
b1 1 -1 1 -1 x, xz, Ry
a2 1 1 -1 -1 xy, Rz, I
b2 1 -1 -1 1 y, yz, Rx
The geometry of the molecule is defined using the keyword coord. On
the next line, the name of the xyz file that defines the geometrical
parameters of the molecule (water.xyz) is given.
- The first line of the water.xyz file contains the number of atoms.
- The second line is used to indicate the units: Ångström or atomic units.
The default is to use Ångström.
- Then follows one line for each atom containing the name of each atom and its coordinates.
Basis sets are defined after the keyword BASIs sets. The oxygen
and hydrogen basis set chosen, for this example, are the small Atomic Natural Orbitals
(ANO) sets. There are three contractions of the basis included in the input,
which can be toggled in or excluded with an asterisk, according to the desired calculation:
minimal basis, double zeta basis with polarization, or triple zeta basis with polarization.
Figure 6.2:
The geometry of the water molecule
 |
3
O .000000 .000000 .000000
H 0.700000 .000000 0.700000
H -0.700000 .000000 0.700000
The GATEWAY output contains the symmetry character table, basis set
information and input atomic centers. The basis set information lists the
exponents and contraction coefficients as well as the type of Gaussian functions
(Cartesian, spherical or contaminated) used.
The internuclear distances and valence bond angles (including dihedral angles)
are displayed after the basis set information.
Inertia and rigid-rotor analysis is also included in the output along with
the timing information.
A section of the output that is useful for determining the input to
the MOLCAS module SCF is the symmetry adapted basis
functions which appears near the end of the GATEWAY portion
of the output. This is covered in more detail in the SCF
tutorial.
The most important file produced by the GATEWAY module is the
RUNFILE which in our case is linked to water.RunFile. This is
the general MOLCAS communications file for transferring data between the
various MOLCAS program modules. Many of the program modules add
data to the RUNFILE which can be used in still other modules. A new
RUNFILE is produced every time GATEWAY is run. It should finally
be mentioned that for backwards compatibility one can run MOLCAS
without invoking GATEWAY. The corresponding input and output will
then be handled by the program SEWARD.
GATEWAY can operates with several coordinate files, which is convenient
for computing BSSE corrections. BSSE followed by a number marks a XYZ
file which should be treated as dummy atoms. The following example demonstrates
this feature:
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
bsse = 1
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
&GRID_IT
NAME = water
***************
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
bsse = 2
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
&GRID_IT
NAME = ethanol
**************
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
&GRID_IT
NAME = akvavit
Note, that NOMOVE keyword prevents centering of the molecule, so the computed
grids are identical. An alternative way to compute density difference is to
modify coordinates, and change an element label to X.
Keyword | Meaning
|
Coord | File name or inline number of atoms and XYZ coordinates
|
BASIs Set | Atom_label.Basis_label (for example ANO-L-VTZP)
|
Group | Full (find maximum), NoSym, or symmetry generators
|
SYMMetry | Symmetry generators: X, Y, Z, XY, XZ, YZ, XYZ (in native format)
|
RICD | On-the-fly auxiliary basis sets.
|
|
|
Next: 6.4 SEWARD An
Up: 6. Program Based Tutorials
Previous: 6.2 Environment and EMIL Commands
|