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