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 .

If <string> is set to show, the list of all available basis sets is displayed.

-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.

-o, --output=EZFIO_DIR¶: Name of the created EZFIO directory.

-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, 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
   13.0100000              0.0196850
    1.9620000              0.1379770
    0.4446000              0.4781480
S   1
    0.1220000              1.0000000
P   1
    0.7270000              1.0000000

BORON
S   8
 4570.0000000              0.0006960
  685.9000000              0.0053530
  156.5000000              0.0271340
   44.4700000              0.1013800
   14.4800000              0.2720550
    5.1310000              0.4484030
    1.8980000              0.2901230
    0.3329000              0.0143220
S   8
 4570.0000000             -0.0001390
  685.9000000             -0.0010970
  156.5000000             -0.0054440
   44.4700000             -0.0219160
   14.4800000             -0.0597510
    5.1310000             -0.1387320
    1.8980000             -0.1314820
    0.3329000              0.5395260
S   1
    0.1043000              1.0000000
P   3
    6.0010000              0.0354810
    1.2410000              0.1980720
    0.3364000              0.5052300
P   1
    0.0953800              1.0000000
D   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

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