qp_create_ezfio.rst

qp_create_ezfio

qp_create_ezfio

This command creates an 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. 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 × ∑R_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.

-o, --output=EZFIO_DIR

Name of the created directory.

-p <string>, --pseudo=<string>

Name of the pseudo-potential. Follows the same conventions as the basis set.

-x, --cart

Compute 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 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 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 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