..
: PyBEST: Pythonic Black-box Electronic Structure Tool
: Copyright (C) 2016-- The PyBEST Development Team
:
: This file is part of PyBEST.
:
: PyBEST is free software; you can redistribute it and/or
: modify it under the terms of the GNU General Public License
: as published by the Free Software Foundation; either version 3
: of the License, or (at your option) any later version.
:
: PyBEST is distributed in the hope that it will be useful,
: but WITHOUT ANY WARRANTY; without even the implied warranty of
: MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
: GNU General Public License for more details.
:
: You should have received a copy of the GNU General Public License
: along with this program; if not, see <http://www.gnu.org/licenses/>
: --
.. _user_iodata_naming:
Naming conventions in PyBEST
############################
To guarantee full functionality of PyBEST, especially if you wish to read in
your own data files using a format that is not direclty supported by PyBEST,
we recommend that all data is stored in an :py:class:`~pybest.io.iodata.IOData`
container exploiting **predefined**, **PyBEST-specific** labels.
If you work with file formats that are supported in PyBEST and handled by
PyBEST internally, you do not need to worry about the naming convention as
this is handled automatically.
The following table summarizes all frequently used PyBEST objects, their attribute
names in the :py:class:`~pybest.io.iodata.IOData` container, and which
:py:class:`~pybest.linalg.base.LinalgFactory` class is typically associated
with such an object.
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | Object | attribute name in | object type | label |
| | :py:class:`~pybest.io.iodata.IOData` | | |
+=======================+======================================+=====================================================+=======================+
| | list of atoms | atom | ``list`` of ``str`` or ``int`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | xyz coordinates | coordinates | | ``np.array`` of ``float`` | -- |
| | [bohr] | | | or occ_model.factory.coordinates | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | Occupation model | occ_model | :py:class:`~pybest.gbasis.occ_model.AufbauOccModel` | -- |
| | | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | Atomic basis set | gobasis or occ_model.factory | :py:class:`~pybest.gbasis.py_basis.Basis` | -- |
| | (Gaussian orbitals) | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | kinetic energy | kin | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | kin |
| | integrals | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | nuclear attraction | ne | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | ne |
| | integrals | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | electron repulsion | eri | :py:class:`~pybest.linalg.dense.DenseFourIndex` | eri |
| | integrals | +-----------------------------------------------------+-----------------------+
| | | :py:class:`~pybest.linalg.cholesky.CholeskyIndex` | eri |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | nuclear repulsion | nn (incl. in e_core) | ``float`` | nn (e_core) |
| | integrals | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | one-electron | one | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | one |
| | integrals | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | two-electron | two | :py:class:`~pybest.linalg.dense.DenseFourIndex` | two |
| | integrals | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | orbitals | orb_a (restricted/alpha spin) | :py:class:`~pybest.linalg.dense.DenseOrbital` | -- |
| +--------------------------------------+-----------------------------------------------------+-----------------------+
| | orb_b (beta spin) | :py:class:`~pybest.linalg.dense.DenseOrbital` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | overlap integrals | olp | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | olp |
| | | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | electron pair | t_p | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | t_p |
| | amplitudes | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | singles amplitudes | t_1 | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | t_1 |
| | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | doubles amplitudes | t_2 | :py:class:`~pybest.linalg.dense.DenseFourIndex` | t_2 |
| | (including pairs) | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | :math:`\Lambda` for | l_p | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | l_p |
| | electron pairs | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | :math:`\Lambda` for | l_1 | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | l_1 |
| | singles | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | :math:`\Lambda` for | l_2 | :py:class:`~pybest.linalg.dense.DenseFourIndex` | l_2 |
| | doubles (incl pairs)| | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | 1-RDM | dm_1 | (``dict`` of) | -- |
| | | :py:class:`~pybest.linalg.dense.DenseOneIndex` | |
| | +-----------------------------------------------------+-----------------------+
| | | (``dict`` of) | -- |
| | | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | 2-RDM | dm_2 | ``dict`` of | -- |
| | | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | |
| | +-----------------------------------------------------+-----------------------+
| | | :py:class:`~pybest.linalg.dense.DenseFourIndex` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | 3-RDM | dm_3 | ``dict`` of | -- |
| | | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | 4-RDM | dm_4 | ``dict`` of | -- |
| | | :py:class:`~pybest.linalg.dense.DenseTwoIndex` | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | kinetic energy | e_kin | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | nuclear attr energy | e_ne | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | nuclear repul energy| e_nn | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | Coulomb energy (el) | e_hartree | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | exchange energy (el)| e_x_hf | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | total energy | e_tot | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | reference energy | e_ref | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | correlation energy | e_corr | ``float`` | -- |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_s | ``float`` | -- |
| :math:`\hat{T}_1` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_p | ``float`` | -- |
| :math:`\hat{T}_p` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_d | ``float`` | -- |
| :math:`\hat{T}_2` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_s0 | ``float`` | -- |
| | :math:`\Omega=0` of | | | |
| :math:`\hat{T}_2` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_s2 | ``float`` | -- |
| | :math:`\Omega=2` of | | | |
| :math:`\hat{T}_2` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+
| | corr energy wrt | e_corr_s4 | ``float`` | -- |
| | :math:`\Omega=4` of | | | |
| :math:`\hat{T}_2` | | | |
+-----------------------+--------------------------------------+-----------------------------------------------------+-----------------------+