diff --git a/docs/source/modules/ao_one_e_integrals.rst b/docs/source/modules/ao_one_e_integrals.rst index 3f158a26..c2ef6703 100644 --- a/docs/source/modules/ao_one_e_integrals.rst +++ b/docs/source/modules/ao_one_e_integrals.rst @@ -10,6 +10,13 @@ AO_one_e_integrals All the one-electron integrals in the |AO| basis are here. +The most important providers for usual quantum-chemistry calculation are: + +# `ao_kinetic_integral` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_ao_ints.irp.f`) +# `ao_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_ao_ints.irp.f`) +# `ao_mono_elec_integral` which are the the h_core operator integrals on the |AO| basis (see :file:`ao_mono_ints.irp.f`) + +Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_ao.irp.f`. diff --git a/docs/source/modules/aux_quantities.rst b/docs/source/modules/aux_quantities.rst index 4eded7d9..4e6fde73 100644 --- a/docs/source/modules/aux_quantities.rst +++ b/docs/source/modules/aux_quantities.rst @@ -4,13 +4,20 @@ .. default-role:: option -============ -Data energy and density -============ +============== +aux_quantities +============== This module contains some global variables (such as densities and energies) which are stored in the EZFIO folder in a different place than determinants. This is used in practice to store density matrices which can be obtained from any methods, as long as they are stored in the same MO basis which is used for the calculations. In |RS-DFT| calculations, this can be done to perform damping on the density in order to speed up convergence. +The main providers of that module are: + +# `data_one_body_alpha_dm_mo` and `data_one_body_beta_dm_mo` which are the one-body alpha and beta densities which are necessary read from the EZFIO folder. + + +Thanks to these providers you can use any density matrix that does not necessary corresponds to that of the current wave function. + EZFIO parameters diff --git a/docs/source/modules/becke_numerical_grid.rst b/docs/source/modules/becke_numerical_grid.rst index 8b0ef81f..eb934238 100644 --- a/docs/source/modules/becke_numerical_grid.rst +++ b/docs/source/modules/becke_numerical_grid.rst @@ -5,13 +5,20 @@ .. default-role:: option ==================== -Becke Numerical Grid +becke_numerical_grid ==================== This module contains all quantities needed to build the Becke's grid used in general for DFT integration. Note that it can be used for whatever integration in R^3 as long as the functions to be integrated are mostly concentrated near the atomic regions. This grid is built as the reunion of a spherical grid around each atom. Each spherical grid contains a certain number of radial and angular points. +The main providers of that module are: + +# :option:`becke_numerical_grid n_points_integration_angular` which is the number of angular integration points. WARNING: it obeys to specific rules so it cannot be any integer number. Some of the possible values are [ 50 | 74 | 266 | 590 | 1202 | 2030 | 5810 ] for instance. See :file:`angular.f` for more details. +# :option:`becke_numerical_grid n_points_radial_grid` which is the number of radial angular points. This can be any strictly positive integer. Nevertheless, a minimum of 50 is in general necessary. +# `final_grid_points` which are the (x,y,z) coordinates of the grid points. +# `final_weight_at_r_vector` which are the weights at each grid point + For a simple example of how to use the grid, see :file:`example.irp.f`. The spherical integration uses Lebedev-Laikov grids, which was used from the code distributed through CCL (http://www.ccl.net/). diff --git a/docs/source/modules/davidson.rst b/docs/source/modules/davidson.rst index c7380356..338b26bb 100644 --- a/docs/source/modules/davidson.rst +++ b/docs/source/modules/davidson.rst @@ -14,7 +14,10 @@ a dressing is used, the dressing column should be defined and the :ref:`davidsondressed` module should be used. If no dressing is required, the :ref:`davidson` module should be used, and it has a default zero dressing vector. +The important providers for that module are: +# `psi_energy` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the Hamiltonian, dressed or not. It uses the general subroutine `u_0_H_u_0`. +# `psi_energy_bielec` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the standard two-electrons coulomb operator. It uses the general routine `u_0_H_u_0_bielec`. diff --git a/docs/source/modules/determinants.rst b/docs/source/modules/determinants.rst index c23e267b..35713a2f 100644 --- a/docs/source/modules/determinants.rst +++ b/docs/source/modules/determinants.rst @@ -10,6 +10,22 @@ Determinants Contains everything for the computation of the Hamiltonian matrix elements in the basis of orthogonal Slater determinants built on a restricted spin-orbitals basis. +The main providers for this module are: + +# :option:`determinants n_states`: number of states to be computed +# `psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|. +# `psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants. + +The main routines for this module are: + +# `i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants. +# `i_H_j_s2`: computes the Hamiltonian and (:math:`S^2`) matrix element between two arbitrary Slater determinants. +# `i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor. +# `i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants. + + +For an example of how to use these routines and providers, take a look at :file:`example.irp.f`. + EZFIO parameters diff --git a/docs/source/modules/dft_keywords.rst b/docs/source/modules/dft_keywords.rst index 301c983e..ed7f87d2 100644 --- a/docs/source/modules/dft_keywords.rst +++ b/docs/source/modules/dft_keywords.rst @@ -5,18 +5,19 @@ .. default-role:: option ============ -DFT Keywords +dft_keywords ============ This module contains the main keywords related to a DFT calculation or RS-DFT calculation, such as: -# :option:exchange_functional -# :option:correlation_functional -# :option:HF_exchange : only relevent for the :ref:`ks_scf` program -# :option:density_for_dft : mainly relevent for multi-determinant range separated DFT, see the plugins of eginer. +# :option:`dft_keywords exchange_functional` +# :option:`dft_keywords correlation_functional` +# :option:`dft_keywords HF_exchange` : only relevent for the :ref:`ks_scf` program The keyword for the range separation parameter :math:`\mu` is the :option:`ao_two_e_erf_integrals mu_erf` keyword. +The keyword for the type of density used in RS-DFT calculation with a multi-configurational wave function is the :option:`density_for_dft density_for_dft` keyword. + EZFIO parameters diff --git a/docs/source/modules/generators_cas.rst b/docs/source/modules/generators_cas.rst index 806f4430..9d1e75e0 100644 --- a/docs/source/modules/generators_cas.rst +++ b/docs/source/modules/generators_cas.rst @@ -13,7 +13,7 @@ The |MOs| belonging to the |CAS| are those which were set as active with the :ref:`qp_set_mo_class` command. This module is intended to be included in the :file:`NEED` file to define -generators on a |CAS|. +the generators as the |CAS| determinants, which can be useful to define post-CAS approaches (see cassd module for instance). diff --git a/docs/source/modules/mo_one_e_integrals.rst b/docs/source/modules/mo_one_e_integrals.rst index aedd40d6..d4e14b41 100644 --- a/docs/source/modules/mo_one_e_integrals.rst +++ b/docs/source/modules/mo_one_e_integrals.rst @@ -5,11 +5,18 @@ .. default-role:: option ================== -MO_one_e_integrals +mo_one_e_integrals ================== All the one-electron integrals in |MO| basis are defined here. +The most important providers for usual quantum-chemistry calculation are: + +# `mo_kinetic_integral` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_mo_ints.irp.f`) +# `mo_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_mo_ints.irp.f`) +# `mo_mono_elec_integral` which are the the h_core operator integrals on the |AO| basis (see :file:`mo_mono_ints.irp.f`) + +Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_mo.irp.f`. diff --git a/docs/source/modules/scf_utils.rst b/docs/source/modules/scf_utils.rst index 52a411e2..a5aaeb73 100644 --- a/docs/source/modules/scf_utils.rst +++ b/docs/source/modules/scf_utils.rst @@ -10,11 +10,11 @@ scf_utils -The scf_utils module performs *Restricted* SCF calculations (the +The scf_utils module is an abstract module which contains the basics to perform *Restricted* SCF calculations (the spatial part of the |MOs| is common for alpha and beta spinorbitals) based on a single-determinant wave function. This module does not produce any executable *and must not do*, but instead it contains everything one needs to perform an orbital optimization based on an Fock matrix. -The ``scf_utils`` module is included in the :file:`NEED` of the various single determinant SCF procedures, such as ``hartree_fock`` or ``kohn_sham``, where a specific definition of the Fock matrix is given (see :file:`hartree_fock fock_matrix_hf.irp.f` for an example). +The ``scf_utils`` module is meant to be included in the :file:`NEED` of the various single determinant SCF procedures, such as ``hartree_fock`` or ``kohn_sham``, where a specific definition of the Fock matrix is given (see :file:`hartree_fock fock_matrix_hf.irp.f` for an example). All SCF programs perform the following actions: diff --git a/docs/source/users_guide/quickstart.rst b/docs/source/users_guide/quickstart.rst index 43dc7106..afc0136e 100644 --- a/docs/source/users_guide/quickstart.rst +++ b/docs/source/users_guide/quickstart.rst @@ -43,7 +43,7 @@ The file :file:`hcn.xyz` contains:: N 0.0 0.0 -1.156 -This xyz file is now used with the :command:`qp_create_ezfio_from_xyz` command to +This xyz file is now used with the :ref:`qp_create_ezfio_from_xyz` command to create an |EZFIO| database with the 6-31G basis set: .. code:: bash diff --git a/src/ao_basis/README.rst b/src/ao_basis/README.rst index c279864c..753dd12b 100644 --- a/src/ao_basis/README.rst +++ b/src/ao_basis/README.rst @@ -1,5 +1,5 @@ ======== -AO_Basis +ao_basis ======== This module describes the atomic orbitals basis set. diff --git a/src/ao_one_e_integrals/README.rst b/src/ao_one_e_integrals/README.rst index 0901554a..2d4c9660 100644 --- a/src/ao_one_e_integrals/README.rst +++ b/src/ao_one_e_integrals/README.rst @@ -1,5 +1,5 @@ ================== -AO_one_e_integrals +ao_one_e_integrals ================== All the one-electron integrals in the |AO| basis are here. diff --git a/src/bitmask/README.rst b/src/bitmask/README.rst index 82e0825e..dae6eaf5 100644 --- a/src/bitmask/README.rst +++ b/src/bitmask/README.rst @@ -1,5 +1,5 @@ ============== -Bitmask Module +bitmask module ============== The central part of this module is the :file:`bitmasks_module.f90` file. It contains diff --git a/src/cis/README.rst b/src/cis/README.rst index 4b37f514..b7f1ea19 100644 --- a/src/cis/README.rst +++ b/src/cis/README.rst @@ -1,5 +1,5 @@ === -CIS +cis === This module contains a CIS program, built by setting the following rules: diff --git a/src/cisd/README.rst b/src/cisd/README.rst index 096fe22e..268b6609 100644 --- a/src/cisd/README.rst +++ b/src/cisd/README.rst @@ -1,5 +1,5 @@ ==== -CISD +cisd ==== This module contains a CISD program, built by setting the following rules: diff --git a/src/davidson/README.rst b/src/davidson/README.rst index 1ff7847a..b7c15356 100644 --- a/src/davidson/README.rst +++ b/src/davidson/README.rst @@ -1,6 +1,6 @@ -============== -Davidson_Utils -============== +======== +davidson +======== Abstract module for Davidson's diagonalization. It contains everything required for the Davidson algorithm, dressed or not. If diff --git a/src/davidson_dressed/README.rst b/src/davidson_dressed/README.rst index 4ae57595..d5839846 100644 --- a/src/davidson_dressed/README.rst +++ b/src/davidson_dressed/README.rst @@ -1,6 +1,6 @@ -=============== -DavidsonDressed -=============== +================ +davidson_dressed +================ Davidson with single-column dressing. diff --git a/src/davidson_undressed/README.rst b/src/davidson_undressed/README.rst index ff48b77f..564fab02 100644 --- a/src/davidson_undressed/README.rst +++ b/src/davidson_undressed/README.rst @@ -1,6 +1,6 @@ -================= -DavidsonUndressed -================= +================== +davidson_undressed +================== Module for main files Davidson's algorithm with no dressing. diff --git a/src/determinants/README.rst b/src/determinants/README.rst index 63d88b02..537464b7 100644 --- a/src/determinants/README.rst +++ b/src/determinants/README.rst @@ -1,5 +1,5 @@ ============ -Determinants +determinants ============ Contains everything for the computation of the Hamiltonian matrix elements in the basis of orthogonal Slater determinants built on a restricted spin-orbitals basis. diff --git a/src/dressing/README.rst b/src/dressing/README.rst index c25559d1..a3854407 100644 --- a/src/dressing/README.rst +++ b/src/dressing/README.rst @@ -2,6 +2,6 @@ dress_zmq ========= -Module to facilitate the construction of modules using dressed Hamiltonians, parallelized -with |ZeroMQ|. +Module to facilitate the construction of modules using dressed +Hamiltonians, parallelized with |ZeroMQ|. diff --git a/src/electrons/README.rst b/src/electrons/README.rst index 0db59aee..251b2c66 100644 --- a/src/electrons/README.rst +++ b/src/electrons/README.rst @@ -1,9 +1,9 @@ ========= -Electrons +electrons ========= -Describes the electrons. For the moment, only the number of alpha and beta electrons -are provided by this module. +Describes the electrons. For the moment, only the number of alpha +and beta electrons are provided by this module. Assumptions diff --git a/src/ezfio_files/README.rst b/src/ezfio_files/README.rst index ea568b71..bf3166de 100644 --- a/src/ezfio_files/README.rst +++ b/src/ezfio_files/README.rst @@ -1,5 +1,5 @@ =========== -Ezfio_files +ezfio_files =========== This modules essentially contains the name of the |EZFIO| directory in the diff --git a/src/fci/README.rst b/src/fci/README.rst index 3bb6fb24..2257d528 100644 --- a/src/fci/README.rst +++ b/src/fci/README.rst @@ -1,5 +1,5 @@ === -FCI +fci === Selected Full Configuration Interaction. diff --git a/src/generators_cas/README.rst b/src/generators_cas/README.rst index a030059c..cb7b53ac 100644 --- a/src/generators_cas/README.rst +++ b/src/generators_cas/README.rst @@ -1,5 +1,5 @@ ============== -Generators_CAS +generators_cas ============== Module defining the generator determinants as those belonging to a |CAS|. diff --git a/src/generators_full/README.rst b/src/generators_full/README.rst index 1f5036e5..4e59ee3b 100644 --- a/src/generators_full/README.rst +++ b/src/generators_full/README.rst @@ -1,5 +1,5 @@ =============== -Generators_full +generators_full =============== Module defining the generator determinants as all the determinants of the diff --git a/src/hartree_fock/README.rst b/src/hartree_fock/README.rst index 6ea2d00d..7fa01d4f 100644 --- a/src/hartree_fock/README.rst +++ b/src/hartree_fock/README.rst @@ -1,5 +1,5 @@ ============ -Hartree-Fock +hartree_fock ============ diff --git a/src/iterations/README.rst b/src/iterations/README.rst index e5bf9d3c..8ebd7231 100644 --- a/src/iterations/README.rst +++ b/src/iterations/README.rst @@ -1,5 +1,6 @@ -============= -IterativeSave -============= +========== +iterations +========== -Module which saves the computed energies for an extrapolation to the |FCI| limit. +Module which saves the computed energies for an extrapolation to +the |FCI| limit. diff --git a/src/kohn_sham/README.rst b/src/kohn_sham/README.rst index 197509c8..2b6bd7bc 100644 --- a/src/kohn_sham/README.rst +++ b/src/kohn_sham/README.rst @@ -1,6 +1,6 @@ -============ -Kohn-Sham -============ +========= +kohn_sham +========= The Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the diff --git a/src/kohn_sham_rs/README.rst b/src/kohn_sham_rs/README.rst index 95ad0cab..14441fb1 100644 --- a/src/kohn_sham_rs/README.rst +++ b/src/kohn_sham_rs/README.rst @@ -1,6 +1,6 @@ -========================= -Range-separated Kohn-Sham -========================= +============ +kohn_sham_rs +============ The Range-separated Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the diff --git a/src/mo_basis/README.rst b/src/mo_basis/README.rst index 8de13894..181092b3 100644 --- a/src/mo_basis/README.rst +++ b/src/mo_basis/README.rst @@ -1,5 +1,5 @@ ======== -MO_Basis +mo_basis ======== Molecular orbitals are expressed as diff --git a/src/mo_guess/README.rst b/src/mo_guess/README.rst index 9b867a48..7accfa52 100644 --- a/src/mo_guess/README.rst +++ b/src/mo_guess/README.rst @@ -1,6 +1,6 @@ -======= -MOGuess -======= +======== +mo_guess +======== Guess for |MOs|. diff --git a/src/mo_two_e_integrals/README.rst b/src/mo_two_e_integrals/README.rst index 0af514fa..2e627dc6 100644 --- a/src/mo_two_e_integrals/README.rst +++ b/src/mo_two_e_integrals/README.rst @@ -1,6 +1,6 @@ -================ -Integrals_Bielec -================ +================== +mo_two_e_integrals +================== Here, all two-electron integrals (:math:`1/r_{12}`) are computed. As they have 4 indices and many are zero, they are stored in a map, as defined diff --git a/src/mpi/README.rst b/src/mpi/README.rst index 8fe18079..66ed6fd5 100644 --- a/src/mpi/README.rst +++ b/src/mpi/README.rst @@ -1,5 +1,5 @@ === -MPI +mpi === Contains all the functions and providers for parallelization with |MPI|. diff --git a/src/nuclei/README.rst b/src/nuclei/README.rst index d03d64bd..d7f3d8e2 100644 --- a/src/nuclei/README.rst +++ b/src/nuclei/README.rst @@ -1,5 +1,5 @@ ====== -Nuclei +nuclei ====== This module contains data relative to the nuclei (coordinates, charge, diff --git a/src/perturbation/README.rst b/src/perturbation/README.rst index 0927b962..44f955b8 100644 --- a/src/perturbation/README.rst +++ b/src/perturbation/README.rst @@ -1,5 +1,5 @@ ============ -Perturbation +perturbation ============ diff --git a/src/pseudo/README.rst b/src/pseudo/README.rst index b1bab664..42cca6d0 100644 --- a/src/pseudo/README.rst +++ b/src/pseudo/README.rst @@ -1,5 +1,5 @@ ====== -Pseudo +pseudo ====== This module defines the |EZFIO| parameters of the effective core potentials. diff --git a/src/psiref_cas/README.rst b/src/psiref_cas/README.rst index c84537e3..23b9fa84 100644 --- a/src/psiref_cas/README.rst +++ b/src/psiref_cas/README.rst @@ -1,5 +1,5 @@ ========== -Psiref_CAS +psiref_cas ========== Reference wave function is defined as a |CAS| wave function. diff --git a/src/psiref_utils/README.rst b/src/psiref_utils/README.rst index a4b4a175..d4b70a89 100644 --- a/src/psiref_utils/README.rst +++ b/src/psiref_utils/README.rst @@ -1,5 +1,5 @@ ============ -Psiref_Utils +psiref_utils ============ diff --git a/src/selectors_cassd/README.rst b/src/selectors_cassd/README.rst index 4f193cce..e359ef8e 100644 --- a/src/selectors_cassd/README.rst +++ b/src/selectors_cassd/README.rst @@ -1,5 +1,5 @@ =============== -Selectors_CASSD +selectors_cassd =============== Selectors for |CAS-SD| calculations. The selectors are defined as first the diff --git a/src/selectors_full/README.rst b/src/selectors_full/README.rst index bc370fc3..668d5e0a 100644 --- a/src/selectors_full/README.rst +++ b/src/selectors_full/README.rst @@ -1,5 +1,5 @@ ============== -Selectors_full +selectors_full ============== All the determinants are possible selectors. Only the largest contributions are kept, where diff --git a/src/selectors_utils/README.rst b/src/selectors_utils/README.rst index ec067b76..cbb2c723 100644 --- a/src/selectors_utils/README.rst +++ b/src/selectors_utils/README.rst @@ -1,5 +1,5 @@ =============== -Selectors_Utils +selectors_utils =============== Helper functions for selectors. diff --git a/src/single_ref_method/README.rst b/src/single_ref_method/README.rst index fbd35b79..0993349e 100644 --- a/src/single_ref_method/README.rst +++ b/src/single_ref_method/README.rst @@ -1,6 +1,6 @@ -=============== -SingleDetMethod -=============== +================= +single_ref_method +================= Include this module for single reference methods. Using this module, the only generator determinant is the Hartree-Fock determinant. diff --git a/src/slave/README.rst b/src/slave/README.rst index 0337b2f8..341b3d7d 100644 --- a/src/slave/README.rst +++ b/src/slave/README.rst @@ -1,5 +1,5 @@ ===== -Slave +slave ===== Slave processes for distributed parallelism. diff --git a/src/tools/README.rst b/src/tools/README.rst index e560b35a..134280bd 100644 --- a/src/tools/README.rst +++ b/src/tools/README.rst @@ -1,5 +1,5 @@ ===== -Tools +tools ===== Useful tools are grouped in this module. diff --git a/src/utils/README.rst b/src/utils/README.rst index 72d6e4ee..3b0bb885 100644 --- a/src/utils/README.rst +++ b/src/utils/README.rst @@ -1,5 +1,5 @@ ===== -Utils +utils ===== Contains general purpose utilities (sorting, maps, etc). diff --git a/src/zmq/README.rst b/src/zmq/README.rst index 1a6ef4fa..64322294 100644 --- a/src/zmq/README.rst +++ b/src/zmq/README.rst @@ -1,5 +1,5 @@ === -ZMQ +zmq === Definition of |ZeroMQ| sockets and messages.