qp_create_ezfio
This command creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format.
Usage
qp_create_ezfio [-a] -b <string> [-c <int>] [-d <float>]
[-h] [-m <int>] [-o EZFIO_DIR] [-p <string>] [-x] [--] FILE
- -a, --au
If present, input geometry is in atomic units.
- -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. Quantum Package This option is mandatory .
- -c, --charge=<int>
Total charge of the molecule. Default is 0.
- -d, --dummy=<float>
Add dummy atoms (X) between atoms when the distance between two atoms is less than \(x \times \sum R_\mathrm{cov}\), the covalent radii of the atoms. The default is x=0, so no dummy atom is added.
- -h, --help
Print the help text and exit
- -m, --multiplicity=<int>
Spin multiplicity \(2S+1\) of the molecule. Default is 1.
- -p <string>, --pseudo=<string>
Name of the pseudo-potential. Follows the same conventions as the basis set.
- -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, without combined sp, spd, … contractions. 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
Files can be extracted from the Basis Set Exchange database
https://www.basissetexchange.org , with the qp_basis tool.
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
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