mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-08-31 08:13:43 +02:00
* Changed native into SSE4.2 in gfortran.cfg * Fixed rm opam_installer * Fix configure * Improving scaling of pt2 with network * Router/dealer in qp_tunnel * Reduced size of qp2.png * Exclude temp files in tar * Introduce NO_CACHE in configure for daily test * Faster determinants in OCaml * We always give max 10k dets in qp_edit. Read-only if more * Fixed save_natorb * Fixing bug in qp_edit * Comments * Biblio (#61) * Biblio (#62) * Update biblio * Update paper * Journal missing in research.bib * Added paper * Fixed Pierre Francois * Checking number of electrons in MOs * Biblio (#64) * Update biblio * Update paper * Journal missing in research.bib * Added paper * Fixed Pierre Francois * 2 papers * Fixed 6-31G and quickstart (#65) * Fixed 6-31 basis sets * Bug in quickstart * Biblio (#66) * Bugfix (#67) * Fixing opam installation * Fixed 6-31 basis sets * Bug in quickstart * Use irpf90 v1.7.6 * Fix IRPF90 Path
218 lines
6.2 KiB
ReStructuredText
218 lines
6.2 KiB
ReStructuredText
=================
|
|
Quick-start guide
|
|
=================
|
|
|
|
This tutorial should teach you everything you need to get started with
|
|
the the basics of the |qp|. As an example, we will run a frozen core
|
|
|CIPSI| calculation on the HCN molecule in the 6-31G basis set.
|
|
|
|
|
|
Demo video
|
|
==========
|
|
|
|
This tutorial can be directly watched at:
|
|
|
|
|
|
`<https://www.youtube.com/watch?v=4nmdCAPkZlc>`_
|
|
|
|
|
|
Hands on
|
|
========
|
|
|
|
.. important::
|
|
|
|
Before using the |qp|, it is required to load the environment variables
|
|
relatives to the |QP| or to be in the |qpsh| mode.
|
|
|
|
|
|
Please execute in the current shell:
|
|
|
|
.. code:: bash
|
|
|
|
${QP_ROOT}/bin/qpsh
|
|
|
|
where :code:`${QP_ROOT}` is the path to the source files of the |QP| installed on your architecture.
|
|
|
|
The |QPSH| mode: a Bash-like experience for quantum chemistry
|
|
-------------------------------------------------------------
|
|
|
|
The |QP| has been designed pretty much as an *interactive* environment for quantum-chemistry calculations,
|
|
in order to facilitate the user experience.
|
|
|
|
Just like in Bash, there are many commands in the |QP| (see for instance :ref:`qp_edit` or :ref:`qp_run`)
|
|
which help in handling useful data or running executables (see for instance :ref:`scf` or :ref:`fci`).
|
|
|
|
All commands designed within the |qp| **begin** with `qp`, and there are two ways of running a **command**:
|
|
|
|
* running the *executable* associated with the command:
|
|
|
|
.. code:: bash
|
|
|
|
qp_command
|
|
|
|
or executing the *qp* shell command which calls the *executable* :code:`qp_command`:
|
|
|
|
.. code:: bash
|
|
|
|
qp command
|
|
|
|
Usually, when using the :command:`qp` command, the name of the |EZFIO| database is omitted.
|
|
|
|
The advantage of using :code:`qp command` is that you can, just like in Bash, have:
|
|
|
|
* the :kbd:`Tab` key for the auto-completion for basically any command of the |QP|
|
|
|
|
* man pages with -h, --help or qp man
|
|
|
|
|
|
Just try, for instance:
|
|
|
|
.. code:: bash
|
|
|
|
qp
|
|
|
|
and then use the auto-completion. You will show appear all possible commands that you can run:
|
|
|
|
|
|
.. code:: bash
|
|
|
|
convert_output_to_ezfio -h plugins unset_file
|
|
create_ezfio man set_file update
|
|
|
|
Then, try, still with the auto-completion,
|
|
|
|
.. code:: bash
|
|
|
|
qp create
|
|
|
|
You will see appear all the options for the :ref:`qp_create_ezfio` commands.
|
|
|
|
|
|
Create the EZFIO database
|
|
-------------------------
|
|
|
|
The data relative to calculations are stored in an |EZFIO| database.
|
|
|EZFIO| is a hierarchical data format which uses the hierarchy of the
|
|
file system to organize the data, as files stored in a directory. The
|
|
data in the |EZFIO| directory are stored as plain text files, so it can
|
|
be opened with any text editor.
|
|
To access the data of the |EZFIO| database, the APIs (Fortran, |Python|,
|
|
|OCaml| or Bash) provided by |EZFIO| should be used, or tools using
|
|
these APIs such as :ref:`qp_edit` provided with the |qp|.
|
|
|
|
First, create an `xyz` file containing the coordinates of the molecule.
|
|
The file :file:`hcn.xyz` contains::
|
|
|
|
3
|
|
HCN molecule
|
|
C 0.0 0.0 0.0
|
|
H 0.0 0.0 1.064
|
|
N 0.0 0.0 -1.156
|
|
|
|
|
|
This xyz file is now used with the :ref:`qp_create_ezfio` command to
|
|
create an |EZFIO| database with the 6-31G basis set:
|
|
|
|
.. code:: bash
|
|
|
|
qp create_ezfio -b "6-31g" hcn.xyz -o hcn
|
|
|
|
The EZFIO database now contains data relative to the nuclear coordinates
|
|
and the atomic basis set:
|
|
|
|
.. code:: bash
|
|
|
|
$ ls hcn
|
|
ao_basis becke_numerical_grid dft_keywords mo_one_e_ints perturbation
|
|
ao_one_e_ints davidson dressing mo_two_e_erf_ints pseudo
|
|
ao_two_e_erf_ints density_for_dft electrons mo_two_e_ints scf_utils
|
|
ao_two_e_ints determinants ezfio nuclei work
|
|
|
|
|
|
Run a Hartree-Fock calculation
|
|
------------------------------
|
|
|
|
The program :ref:`qp_run` is the driver program of the |qp|. To run a
|
|
|scf| calculation, just run
|
|
|
|
.. code:: bash
|
|
|
|
qp run scf
|
|
|
|
The expected energy is ``-92.827856698`` au.
|
|
|
|
.. seealso::
|
|
|
|
The documentation of the :ref:`module_hartree_fock` module and that of the
|
|
:ref:`scf` program.
|
|
|
|
This creates the |MOs| in the |EZFIO| database that will be used to
|
|
in any other post-SCF method. The |qp| does not handle symmetry and
|
|
the |MOs| are stored by increasing order of Fock energies.
|
|
|
|
|
|
Choose the target |MO| space
|
|
----------------------------
|
|
|
|
Now, we will modify the |EZFIO| database to make a |CIPSI| calculation only in the
|
|
full set of valence |MOs|, keeping the core |MOs| frozen. The simple
|
|
command :ref:`qp_set_frozen_core` does this automatically:
|
|
|
|
.. code:: bash
|
|
|
|
qp set_frozen_core
|
|
|
|
|
|
The general command to specify core and active orbitals is :ref:`qp_set_mo_class`.
|
|
In the case of HCN molecule in the 631G basis, one has 20 |MOs| in total and the two first orbitals are frozen:
|
|
|
|
.. code::
|
|
|
|
qp set_mo_class --core="[1-2]" --act="[3-20]"
|
|
|
|
|
|
|
|
Run the |CIPSI| calculation
|
|
----------------------------
|
|
|
|
We will now use the |CIPSI| algorithm to estimate the |FCI| energy.
|
|
|
|
.. code::
|
|
|
|
qp run fci | tee hcn.fci.out
|
|
|
|
|
|
The program will start with a single determinant and will iteratively:
|
|
|
|
* Select the most important determinants from the external space and add them to the
|
|
internal space
|
|
* Add all the necessary determinants to allow the eigenvector of |H| to be
|
|
also an eigenstate of |S^2|
|
|
* Diagonalize |H| in the enlarged internal space
|
|
* Compute (stochastically) the second-order perturbative contribution to the energy
|
|
* Extrapolate the variational energy by fitting
|
|
:math:`E=E_\text{FCI} - \alpha\, E_\text{PT2}`
|
|
|
|
By default, the program will stop when more than one million determinants have
|
|
entered in the internal space, or when the |PT2| energy is below :math:`10^{-4}` au.
|
|
|
|
To have a pictural illustration of the convergence of the |CIPSI| algorithm, just run
|
|
|
|
.. code::
|
|
|
|
qp_e_conv_fci
|
|
|
|
This will create the files :file:`hcn.fci.out.conv` containing the data of the
|
|
convergence of the energy that can be plotted, together with the file
|
|
:file:`hcn.fci.out.conv.1.eps` which is obtained from the gnuplot plot file
|
|
:file:`hcn.fci.out.conv.plt`.
|
|
|
|
|
|
The estimated |FCI| energy of HCN is ``-93.0501`` au.
|
|
|
|
.. seealso::
|
|
|
|
The documentation of the :ref:`module_fci` module and that of the :ref:`fci` program.
|
|
|
|
|