1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
|
.. index::
single: Program; Gateway
single: Gateway
single: Integrals
.. _TUT\:sec\:gateway:
:program:`GATEWAY` --- Definition of geometry, basis sets, and symmetry
=======================================================================
The program :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 :file:`RUNFILE`. :program:`GATEWAY` is the first
program to be executed, if the :file:`WorkDir` directory and the :file:`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 :program:`GATEWAY`, please refer to the Users Guide.
The first line of the input is the program identifier ``&GATEWAY``.
Then follows the keyword used is :kword:`TITLe` which will also get
printed in the :program:`GATEWAY` section of the calculation output.
The title line is also saved in the integral file and will appear in subsequent programs.
.. The input for water is given in
:numref:`block:gateway_input`.
.. index::
single: Gateway; Symmetry
single: Option; Symmetry
single: Symmetry; Generators
single: Symmetry; Point groups
single: Gateway; Input
The :kword:`GROUp` keyword is followed by the generators for the :math:`C_{2v}`
point group, since the example deals with the water molecule.
The specification of the :math:`C_{2v}` point group given in
:numref:`tab:symmetry_list` 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 :numref:`tab:symmetry_list`. 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:: Symmetries available in |molcas| including generators, |molcas| keywords and symmetry elements.
:name: tab:symmetry_list
============== ============== ================ =========== ============ ============ ============ ========= ============== ================ ================= =========== =================== =================== ===================
Group Generators |molcas| Elements
-------------- ------------------------------------------- -------------------------------------- -----------------------------------------------------------------------------------------------------------------------------------
|zws| :math:`g_1` :math:`g_2` :math:`g_3` :math:`g_1` :math:`g_2` :math:`g_3` :math:`E` :math:`g_1` :math:`g_2` :math:`g_1g_2` :math:`g_3` :math:`g_1g_3` :math:`g_2g_3` :math:`g_1g_2g_3`
============== ============== ================ =========== ============ ============ ============ ========= ============== ================ ================= =========== =================== =================== ===================
:math:`C_1` :math:`E`
:math:`C_2` :math:`C_2` :kword:`xy` :math:`E` :math:`C_2`
:math:`C_s` :math:`\sigma` :kword:`x` :math:`E` :math:`\sigma`
:math:`C_i` :math:`i` :kword:`xyz` :math:`E` :math:`i`
:math:`C_{2v}` :math:`C_2` :math:`\sigma_v` :kword:`xy` :kword:`y` :math:`E` :math:`C_2` :math:`\sigma_v` :math:`\sigma_v'`
:math:`C_{2h}` :math:`C_2` :math:`i` :kword:`xy` :kword:`xyz` :math:`E` :math:`C_2` :math:`i` :math:`\sigma_h`
:math:`D_2` :math:`C_2^z` :math:`C_2^y` :kword:`xy` :kword:`xz` :math:`E` :math:`C_2^z` :math:`C_2^y` :math:`C_2^x`
:math:`D_{2h}` :math:`C_2^z` :math:`C_2^y` :math:`i` :kword:`xy` :kword:`xz` :kword:`xyz` :math:`E` :math:`C_2^z` :math:`C_2^y` :math:`C_2^x` :math:`i` :math:`\sigma^{xy}` :math:`\sigma^{xz}` :math:`\sigma^{yz}`
============== ============== ================ =========== ============ ============ ============ ========= ============== ================ ================= =========== =================== =================== ===================
.. Note: contains a nbsp
To reduce the input, the unity operator :math:`E` is always assumed. The twofold
rotation about the z-axis, :math:`C_2(z)`, and the reflection in the xz-plane,
:math:`\sigma_v(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 :kword:`Y` which is the
Cartesian element operated upon by the reflection.
The input produces the character table in the
:program:`GATEWAY` section of the output shown in
:numref:`block:TUT_C2v_output`. Note that :math:`\sigma_v(yz)` was produced from
the other two generators. The last column contains the basis functions of
each irreducible symmetry representation. The totally symmetric :math:`a_1`
irreducible representation has the :math:`z` basis function listed which is unchanged
by any of the symmetry operations.
.. index::
single: Character table
.. code-block:: none
:caption: Character Table for :math:`C_{2v}`
:name: block:TUT_C2v_output
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
.. Note: contains a nbsp
.. index::
single: Gateway; Test
single: Input; Comment lines
single: Units
single: Gateway; Geometry
single: Gateway; Units
single: Coordinates; Gateway input
The geometry of the molecule is defined using the keyword :kword:`coord`. On
the next line, the name of the xyz file that defines the geometrical
parameters of the molecule (:file:`water.xyz`) is given.
#. The first line of the :file:`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 :kword:`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.
.. code-block:: none
:caption: The geometry of the water molecule
:name: block:coord
3
O .000000 .000000 .000000
H 0.700000 .000000 0.700000
H -0.700000 .000000 0.700000
.. index::
single: Gateway; Output
single: Gateway; Geometry
:program:`GATEWAY` Output
-------------------------
The :program:`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.
.. There is a keyword,
:kword:`RTRN`, which is used to increase the threshold for printing of bond
lengths, bond angles and dihedral angles from the default of 3.5 au.
A section of the output that is useful for determining the input to
the |molcas| module :program:`SCF` is the symmetry adapted basis
functions which appears near the end of the :program:`GATEWAY` portion
of the output. This is covered in more detail in the :program:`SCF`
tutorial.
The most important file produced by the :program:`GATEWAY` module is the
:file:`RUNFILE` which in our case is linked to :file:`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 :file:`RUNFILE` which can be used in still other modules. A new
:file:`RUNFILE` is produced every time :program:`GATEWAY` is run. It should finally
be mentioned that for backwards compatibility one can run :program:`MOLCAS`
without invoking :program:`GATEWAY`. The corresponding input and output will
then be handled by the program :program:`SEWARD`.
.. index::
single: Gateway; BSSE
Basis Set Superposition Error (BSSE)
------------------------------------
:program:`GATEWAY` can operates with several coordinate files, which is convenient
for computing BSSE corrections. :kword:`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 :kword:`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.
:program:`GATEWAY` Basic and Most Common Keywords
-------------------------------------------------
.. class:: keywordlist
:kword:`Coord`
File name or inline number of atoms and XYZ coordinates
:kword:`BASIs Set`
Atom_label.Basis_label (for example ANO-L-VTZP)
:kword:`Group`
Full (find maximum), NoSym, or symmetry generators
:kword:`SYMMetry`
Symmetry generators: X, Y, Z, XY, XZ, YZ, XYZ (in native format)
:kword:`RICD`
On-the-fly auxiliary basis sets.
|
