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Anthony Scemama 2018-12-25 19:11:56 +01:00
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commit ed74e3a519
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4
docs/source/_static/links.rst
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@ -1,4 +1,5 @@
.. _Autoconf: http://www.gnu.org/software/autoconf .. _Autoconf: http://www.gnu.org/software/autoconf
.. _Bats: https://github.com/sstephenson/bats
.. _BLAS: http://www.netlib.org/blas/ .. _BLAS: http://www.netlib.org/blas/
.. _Core: https://opensource.janestreet.com/core/ .. _Core: https://opensource.janestreet.com/core/
.. _Dice: https://sanshar.github.io/Dice/ .. _Dice: https://sanshar.github.io/Dice/
@ -21,12 +22,13 @@
.. _Python: http://www.python.org .. _Python: http://www.python.org
.. _QMC=Chem: https://gitlab.com/scemama/qmcchem .. _QMC=Chem: https://gitlab.com/scemama/qmcchem
.. _QMCPack: https://qmcpack.org .. _QMCPack: https://qmcpack.org
.. _SLURM: https://slurm.schedmd.com/
.. _resultsFile: http://gitlab.com/scemama/resultsFile .. _resultsFile: http://gitlab.com/scemama/resultsFile
.. _SLURM: https://slurm.schedmd.com/
.. _ZeroMQ: http://zeromq.org/ .. _ZeroMQ: http://zeromq.org/
.. _Zlib: http://zlib.net .. _Zlib: http://zlib.net
.. |Bats| replace:: `Bats`_
.. |BLAS| replace:: `BLAS`_ .. |BLAS| replace:: `BLAS`_
.. |EZFIO| replace:: `EZFIO`_ .. |EZFIO| replace:: `EZFIO`_
.. |GAMESS| replace:: `GAMESS`_ .. |GAMESS| replace:: `GAMESS`_

99
docs/source/modules/hartree_fock.rst
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@ -61,77 +61,6 @@ Providers
--------- ---------
.. c:var:: ao_bi_elec_integral_alpha
.. code:: text
double precision, allocatable :: ao_bi_elec_integral_alpha (ao_num,ao_num)
double precision, allocatable :: ao_bi_elec_integral_beta (ao_num,ao_num)
File: :file:`fock_matrix_hf.irp.f`
Alpha Fock matrix in AO basis set
.. c:var:: ao_bi_elec_integral_beta
.. code:: text
double precision, allocatable :: ao_bi_elec_integral_alpha (ao_num,ao_num)
double precision, allocatable :: ao_bi_elec_integral_beta (ao_num,ao_num)
File: :file:`fock_matrix_hf.irp.f`
Alpha Fock matrix in AO basis set
.. c:var:: extra_e_contrib_density
.. code:: text
double precision :: extra_e_contrib_density
File: :file:`hf_energy.irp.f`
Extra contribution to the SCF energy coming from the density.
For a Hartree-Fock calculation: extra_e_contrib_density = 0
For a Kohn-Sham or Range-separated Kohn-Sham: the exchange/correlation - trace of the V_xc potential
.. c:var:: fock_matrix_ao_alpha
.. code:: text
double precision, allocatable :: fock_matrix_ao_alpha (ao_num,ao_num)
double precision, allocatable :: fock_matrix_ao_beta (ao_num,ao_num)
File: :file:`fock_matrix_hf.irp.f`
Alpha Fock matrix in AO basis set
.. c:var:: fock_matrix_ao_beta
.. code:: text
double precision, allocatable :: fock_matrix_ao_alpha (ao_num,ao_num)
double precision, allocatable :: fock_matrix_ao_beta (ao_num,ao_num)
File: :file:`fock_matrix_hf.irp.f`
Alpha Fock matrix in AO basis set
.. c:var:: hf_energy .. c:var:: hf_energy
.. code:: text .. code:: text
@ -182,34 +111,6 @@ Subroutines / functions
.. c:function:: create_guess
.. code:: text
subroutine create_guess
File: :file:`scf_old.irp.f`
Create a MO guess if no MOs are present in the EZFIO directory
.. c:function:: run
.. code:: text
subroutine run
File: :file:`scf_old.irp.f`
Run SCF calculation
.. c:function:: scf .. c:function:: scf
.. code:: text .. code:: text

30
docs/source/modules/tools.rst
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@ -90,20 +90,6 @@ Subroutines / functions
.. c:function:: routine
.. code:: text
subroutine routine
File: :file:`write_integrals_erf.irp.f`
.. c:function:: save_natorb .. c:function:: save_natorb
.. code:: text .. code:: text
@ -118,22 +104,6 @@ Subroutines / functions
.. c:function:: save_one_body_dm
.. code:: text
subroutine save_one_body_dm
File: :file:`save_one_body_dm.irp.f`
programs that computes the one body density on the mo basis for alpha and beta electrons from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities.
Then, the global variable data_one_body_alpha_dm_mo and data_one_body_beta_dm_mo will automatically read the density in a further calculation.
This can be used to perform dampin on the density in RS-DFT calculation (see the density_for_dft module).
.. c:function:: save_ortho_mos .. c:function:: save_ortho_mos
.. code:: text .. code:: text

1
docs/source/programmers_guide/index_providers.rst
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@ -225,6 +225,7 @@ Index of Providers
* :c:data:`exchange_functional` * :c:data:`exchange_functional`
* :c:data:`expected_s2` * :c:data:`expected_s2`
* :c:data:`extra_e_contrib_density` * :c:data:`extra_e_contrib_density`
* :c:data:`extra_energy_contrib_from_density`
* :c:data:`extrapolate_fock_matrix` * :c:data:`extrapolate_fock_matrix`
* :c:data:`extrapolated_energy` * :c:data:`extrapolated_energy`
* :c:data:`ezfio_filename` * :c:data:`ezfio_filename`

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docs/source/users_guide/plugins.rst
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Working with external plugins Working with external plugins
============================= =============================
.. TODO
The |qp| has very few executables out of the box. Most of the time, external |qp| has very few executables out of the box. Most of the time, external
plugins need to be downloaded and copied in the ``$QP_ROOT/plugins`` directory. plugins need to be downloaded and installed in the ``$QP_ROOT/plugins``
The ``qp_module`` script will be needed:: directory.
qp_module create -n NAME [CHILDREN_MODULE...] Plugins are usually hosted in external repositories. To dowload a plugin,
qp_module install NAME ... the remote repository needs to be downloaded, and the plugins of the
qp_module uninstall NAME repository can be selected for installation.
To download an external repository of plugins, run the following command:
.. code-block:: bash
qp_plugins download http://somewhere/over/the/rainbow/ext_repo
For example you can type :: This downloads a copy of the repository of external plugins :file:`ext_repo`
in :file:`$QP_ROOT/plugins`.
qp_module install QMCChem The list of available uninstalled plugins can be seen using:
.. code-block::
qp_plugins list -u
Now, the specific plugin :file:`ext_module` contained in the repository
:file:`ext_repo` can be installed using:
.. code-block::
qp_plugins install ext_module
The module is now accessible via a symbolic link in :file:`$QP_ROOT/src`,
and can be compiled as any module, running |Ninja|.
To remove the module, run
.. code-block::
qp_plugins uninstall ext_module
This will install the `QMCChem` module. All the modules are installed in the
``$QP_ROOT/src/``, and all the available modules are in ``$QP_ROOT/plugins/``.

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docs/source/users_guide/qp_test.rst
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qp_test qp_test
======= =======
This command runs the consistency test of |qp|. The tests are run with the |bats| shell testing environment. This command runs the consistency test of |qp|. The tests are run with the |Bats| shell testing environment.
Usage Usage
----- -----