170 lines
4.7 KiB
ReStructuredText
170 lines
4.7 KiB
ReStructuredText
.. _qp_create_ezfio:
|
|
|
|
qp_create_ezfio
|
|
===============
|
|
|
|
.. program:: qp_create_ezfio
|
|
|
|
This command creates an |EZFIO| directory from a standard `xyz` file or
|
|
from a `z-matrix` file in Gaussian format.
|
|
|
|
Usage
|
|
-----
|
|
|
|
.. code:: bash
|
|
|
|
qp_create_ezfio [-a] -b <string> [-c <int>] [-d <float>]
|
|
[-h] [-m <int>] [-o EZFIO_DIR] [-p <string>] [-x] [--] FILE
|
|
|
|
|
|
.. option:: -a, --au
|
|
|
|
If present, input geometry is in atomic units.
|
|
|
|
|
|
.. option:: -b, --basis=<string>
|
|
|
|
Name of basis set. The basis set is defined as a single string if
|
|
all the atoms are taken from the same basis set, otherwise specific
|
|
elements can be defined as follows::
|
|
|
|
-b "cc-pcvdz | H:cc-pvdz | C:6-31g"
|
|
-b "cc-pvtz | 1,H:sto-3g | 3,H:6-31g"
|
|
|
|
By default, the basis set is obtained from the local database of the.
|
|
|qp| This option is mandatory .
|
|
|
|
If ``<string>`` is set to ``show``, the list of all available basis
|
|
sets is displayed.
|
|
|
|
|
|
.. option:: -c, --charge=<int>
|
|
|
|
Total charge of the molecule. Default is 0.
|
|
|
|
|
|
.. option:: -d, --dummy=<float>
|
|
|
|
Add dummy atoms (X) between atoms when the distance between two atoms
|
|
is less than :math:`x \times \sum R_\mathrm{cov}`, the covalent radii
|
|
of the atoms. The default is x=0, so no dummy atom is added.
|
|
|
|
|
|
.. option:: -h, --help
|
|
|
|
Print the help text and exit
|
|
|
|
|
|
.. option:: -m, --multiplicity=<int>
|
|
|
|
Spin multiplicity :math:`2S+1` of the molecule. Default is 1.
|
|
|
|
|
|
.. option:: -o, --output=EZFIO_DIR
|
|
|
|
Name of the created |EZFIO| directory.
|
|
|
|
.. option:: -p <string>, --pseudo=<string>
|
|
|
|
Name of the pseudo-potential. Follows the same conventions as the basis set.
|
|
|
|
.. option:: -x, --cart
|
|
|
|
Compute |AOs| in the Cartesian basis set (6d, 10f, ...)
|
|
|
|
|
|
Using custom atomic basis sets
|
|
------------------------------
|
|
|
|
If a file with the same name as the basis set exists, this file will
|
|
be read. For example, if the file containing the basis set is named
|
|
``custom.basis``, and the *xyz* geometry is in ``molecule.xyz``, the
|
|
following should be used::
|
|
|
|
qp_create_ezfio -b custom.basis molecule.xyz
|
|
|
|
Basis set files should be given in |GAMESS| format, where the full
|
|
names of the atoms are given, and the basis sets for each element are
|
|
separated by a blank line. Here is an example ::
|
|
|
|
HYDROGEN
|
|
S 3
|
|
1 13.0100000 0.0196850
|
|
2 1.9620000 0.1379770
|
|
3 0.4446000 0.4781480
|
|
S 1
|
|
1 0.1220000 1.0000000
|
|
P 1
|
|
1 0.7270000 1.0000000
|
|
|
|
BORON
|
|
S 8
|
|
1 4570.0000000 0.0006960
|
|
2 685.9000000 0.0053530
|
|
3 156.5000000 0.0271340
|
|
4 44.4700000 0.1013800
|
|
5 14.4800000 0.2720550
|
|
6 5.1310000 0.4484030
|
|
7 1.8980000 0.2901230
|
|
8 0.3329000 0.0143220
|
|
S 8
|
|
1 4570.0000000 -0.0001390
|
|
2 685.9000000 -0.0010970
|
|
3 156.5000000 -0.0054440
|
|
4 44.4700000 -0.0219160
|
|
5 14.4800000 -0.0597510
|
|
6 5.1310000 -0.1387320
|
|
7 1.8980000 -0.1314820
|
|
8 0.3329000 0.5395260
|
|
S 1
|
|
1 0.1043000 1.0000000
|
|
P 3
|
|
1 6.0010000 0.0354810
|
|
2 1.2410000 0.1980720
|
|
3 0.3364000 0.5052300
|
|
P 1
|
|
1 0.0953800 1.0000000
|
|
D 1
|
|
1 0.3430000 1.0000000
|
|
|
|
|
|
Using custom pseudo-potentials
|
|
------------------------------
|
|
|
|
As for the basis set, if a file with the same name as the
|
|
pseudo-potential exists, this file will be read. For example, if the
|
|
file containing the custom pseudo-potential is named ``custom.pseudo``,
|
|
the basis set is named ``custom.basis``, and the *xyz* geometry is in
|
|
``molecule.xyz``, the following command should be used
|
|
|
|
.. code:: bash
|
|
|
|
qp_create_ezfio -b custom.basis -p custom.pseudo molecule.xyz
|
|
|
|
Pseudo-potential files should be given in a format very close to
|
|
|GAMESS| format. The first line should be formatted as ``%s GEN %d %d``
|
|
where the first string is the chemical symbol, the first integer is
|
|
the number of core electrons to be removed and the second integer is
|
|
LMAX+1 as in |GAMESS| format. The pseudo-potential for each element are
|
|
separated by a blank line. Here is an example ::
|
|
|
|
Ne GEN 2 1
|
|
3
|
|
8.00000000 1 10.74945199
|
|
85.99561593 3 10.19801460
|
|
-56.79004456 2 10.18694048
|
|
1
|
|
55.11144535 2 12.85042963
|
|
|
|
F GEN 2 1
|
|
3
|
|
7.00000000 1 11.39210685
|
|
79.74474797 3 10.74911370
|
|
-49.45159098 2 10.45120693
|
|
1
|
|
50.25646328 2 11.30345826
|
|
|
|
|
|
|
|
|