.. _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 [-c ] [-d ] [-h] [-m ] [-o EZFIO_DIR] [-p ] [-x] [--] FILE .. option:: -a, --au If present, input geometry is in atomic units. .. option:: -b, --basis= 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 ```` is set to ``show``, the list of all available basis sets is displayed. .. option:: -c, --charge= Total charge of the molecule. Default is 0. .. option:: -d, --dummy= 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= Spin multiplicity :math:`2S+1` of the molecule. Default is 1. .. option:: -o, --output=EZFIO_DIR Name of the created |EZFIO| directory. .. option:: -p , --pseudo= 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