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165 lines
5.1 KiB
ReStructuredText
165 lines
5.1 KiB
ReStructuredText
User's guide
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============
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The input data is stored in a `EZFIO`_ database. It is a hierarchical data
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format which uses the hierarchy of the file system to organize the data, stored
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in a directory.
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To access the data in the EZFIO file, you can use the provided API (Fortran,
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Python, OCaml or Bash), or tools such as ``qp_edit`` provided with the Quantum
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Package. The data in the EZFIO directory is stroed as plain text files, so
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it can be read with a text editor.
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To create an EZFIO directory from scratch, the ``qp_create_ezfio_from_xyz`` should
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be used.
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qp_create_ezfio_from_xyz
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------------------------
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Usage ::
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qp_create_ezfio_from_xyz [FLAGS] (xyz_file|zmt_file)
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Flags ::
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-b string Name of basis set.
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[-au] Input geometry is in atomic units.
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[-c int] Total charge of the molecule. Default is 0.
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[-cart] Compute AOs in the Cartesian basis set (6d, 10f, ...)
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[-d float] Add dummy atoms. x * (covalent radii of the atoms)
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[-m int] Spin multiplicity (2S+1) of the molecule. Default is 1.
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[-o file] Name of the created EZFIO file.
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[-p string] Name of the pseudopotential
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[-help] print this help text and exit
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(alias: -?)
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This command creates an EZFIO directory from a standard xyz file or from a
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z-matrix file in Gaussian format. The basis set is defined as a single string
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if all the atoms are taken from the same basis set, otherwise specific elements
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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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If a file with the same name as the basis set exists, this file will be read.
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Basis set files should be given in GAMESS format. Otherwise, the basis set is
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obtained from the local database of the Quantum Package.
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The same rules apply for pseudopotentials.
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qp_set_mo_class
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---------------
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Usage ::
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qp_set_mo_class [FLAGS] EZFIO_DIRECTORY
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Flags ::
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[-act range] Range of active orbitals
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[-core range] Range of core orbitals
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[-del range] Range of deleted orbitals
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[-inact range] Range of inactive orbitals
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[-q] Query: print the current masks
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[-virt range] Range of virtual orbitals
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[-help] print this help text and exit
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(alias: -?)
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This command sets the orbital classes in an EZFIO directory.
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Core
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MOs which are always doubly occupied
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Deleted
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MOs which are never occupied
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Active
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MOs in which any number of holes/particles can be made
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Inactive
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MOs in which only holes can be made
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Virtual
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MOs in which only particles can be made
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To avoid errors, all the MOs should be given a class.
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The range of MOs are given like the ranges in SLURM commands. For example,
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``"[36-53,72-107,126-131]"``.
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To quickly setup a frozen core calculation, the script ``qp_set_frozen_core.py``
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can be used::
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qp_set_frozen_core.py EZFIO_DIRECTORY
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.. warning::
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For atoms on the right of the periodic table, `qp_set_frozen_core.py` will
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work as expected. But for atoms on the left, a small core will be chosen. For
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example, a carbon atom will have 2 core electrons, but a Lithium atom will have
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zero.
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Excited states
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--------------
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It is possible to run excited states calculations with the quantum package. To
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do this, set the ``n_states`` variable in the ``Determinants`` section to the
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number of requested states. The selection criterion will be the maximum of the
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selection criteria for each state. If the Davidson diagonalization has
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difficulties to converge, increase the ``n_states_diag`` variable in the
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``Davidson`` section.
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When computing multiple states, it is good to have the ``s2_eig`` flag of the
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``Determinants`` section set to ``true``. This will force the Davidson algorithm to
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choose only vectors with a value of S^2 equal to the ``expected_s2``.
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Otherwise, different spin states will come out in the diagonalization.
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The Quantum Package doesn't take account of the symmetry. Due to numerical
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noise, excited states of different symmetries may enter in the calculation.
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Note that it is possible to make state-average calculation of states with
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different symmetries and/or different spin multiplicities.
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To include excited state of all possible symmetries, a simple trick is to
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run a preliminary multi-state CIS calculation, and then running the selected
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FCI restarting from the CIS states, setting the ``read_wf`` flag of the
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``Determinants`` section to ``true``.
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Usually, it is good practice to use state-averaged MOs so that all states have
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MOs of comparable quality. For example, when searching for a singly excited
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state, one can use state-average natural orbitals of a preliminary CIS
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calculation.
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Natural orbitals
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----------------
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To produce state-average natural orbitals, run ::
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qp_run save_natorb file.ezfio
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The MOs will be replaced, so the two-electron integrals and the wave function are invalidated as well.
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.. _EZFIO: http://gitlab.com/scemama/EZFIO
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.. important:: TODO
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.. include:: work.rst
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* qp_edit
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* qp_run
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* qp_convert
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* Interfaces : molden/fcidump
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* Natural orbitals
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* Parameters for Hartree-Fock
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* Parameters for Davidson
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* Running in parallel
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* Parameters for selection (Generators/selectors)
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