diff --git a/docs/source/_static/links.rst b/docs/source/_static/links.rst index 2f646e80..976c7950 100644 --- a/docs/source/_static/links.rst +++ b/docs/source/_static/links.rst @@ -1,4 +1,5 @@ .. _Autoconf: http://www.gnu.org/software/autoconf +.. _Bats: https://github.com/sstephenson/bats .. _BLAS: http://www.netlib.org/blas/ .. _Core: https://opensource.janestreet.com/core/ .. _Dice: https://sanshar.github.io/Dice/ @@ -21,12 +22,13 @@ .. _Python: http://www.python.org .. _QMC=Chem: https://gitlab.com/scemama/qmcchem .. _QMCPack: https://qmcpack.org -.. _SLURM: https://slurm.schedmd.com/ .. _resultsFile: http://gitlab.com/scemama/resultsFile +.. _SLURM: https://slurm.schedmd.com/ .. _ZeroMQ: http://zeromq.org/ .. _Zlib: http://zlib.net +.. |Bats| replace:: `Bats`_ .. |BLAS| replace:: `BLAS`_ .. |EZFIO| replace:: `EZFIO`_ .. |GAMESS| replace:: `GAMESS`_ diff --git a/docs/source/modules/hartree_fock.rst b/docs/source/modules/hartree_fock.rst index dc2d79b8..08649720 100644 --- a/docs/source/modules/hartree_fock.rst +++ b/docs/source/modules/hartree_fock.rst @@ -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 .. 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 .. code:: text diff --git a/docs/source/modules/tools.rst b/docs/source/modules/tools.rst index e5eb0415..e3915bac 100644 --- a/docs/source/modules/tools.rst +++ b/docs/source/modules/tools.rst @@ -90,20 +90,6 @@ Subroutines / functions -.. c:function:: routine - - .. code:: text - - subroutine routine - - File: :file:`write_integrals_erf.irp.f` - - - - - - - .. c:function:: save_natorb .. 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 .. code:: text diff --git a/docs/source/programmers_guide/index_providers.rst b/docs/source/programmers_guide/index_providers.rst index 446cc193..a09efe1a 100644 --- a/docs/source/programmers_guide/index_providers.rst +++ b/docs/source/programmers_guide/index_providers.rst @@ -225,6 +225,7 @@ Index of Providers * :c:data:`exchange_functional` * :c:data:`expected_s2` * :c:data:`extra_e_contrib_density` +* :c:data:`extra_energy_contrib_from_density` * :c:data:`extrapolate_fock_matrix` * :c:data:`extrapolated_energy` * :c:data:`ezfio_filename` diff --git a/docs/source/users_guide/plugins.rst b/docs/source/users_guide/plugins.rst index c1ad33c4..2eaed3c1 100644 --- a/docs/source/users_guide/plugins.rst +++ b/docs/source/users_guide/plugins.rst @@ -2,23 +2,50 @@ Working with external plugins ============================= -.. TODO -The |qp| has very few executables out of the box. Most of the time, external -plugins need to be downloaded and copied in the ``$QP_ROOT/plugins`` directory. -The ``qp_module`` script will be needed:: +|qp| has very few executables out of the box. Most of the time, external +plugins need to be downloaded and installed in the ``$QP_ROOT/plugins`` +directory. - qp_module create -n NAME [CHILDREN_MODULE...] - qp_module install NAME ... - qp_module uninstall NAME +Plugins are usually hosted in external repositories. To dowload a plugin, +the remote repository needs to be downloaded, and the plugins of the +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/``. diff --git a/docs/source/users_guide/qp_test.rst b/docs/source/users_guide/qp_test.rst index 524af6ef..0fb7ed86 100644 --- a/docs/source/users_guide/qp_test.rst +++ b/docs/source/users_guide/qp_test.rst @@ -4,7 +4,7 @@ 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 -----