From 7521d3da468163f8e0c7c33254653b36e08f9da5 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 29 Jan 2019 23:10:00 +0100 Subject: [PATCH] Folder -> directory --- docs/source/modules/aux_quantities.rst | 15 ++++++++------- docs/source/modules/density_for_dft.rst | 14 +++++++++----- docs/source/programs/cisd.rst | 6 +++--- docs/source/programs/diagonalize_h.rst | 9 ++++++--- docs/source/programs/fcidump.rst | 17 +++++++++++------ docs/source/programs/four_idx_transform.rst | 10 +++++++--- docs/source/programs/print_wf.rst | 12 +++++++----- docs/source/programs/pt2.rst | 13 +++++++++---- docs/source/programs/save_natorb.rst | 15 ++++++++------- docs/source/programs/save_one_e_dm.rst | 14 +++++++++----- docs/source/users_guide/printing.rst | 2 +- man/cisd.1 | 6 +++--- man/diagonalize_h.1 | 10 ++++++---- man/fcidump.1 | 16 ++++++++++------ man/four_idx_transform.1 | 9 ++++++--- man/print_wf.1 | 12 +++++++----- man/printing.1 | 2 +- man/pt2.1 | 14 +++++++++----- man/save_natorb.1 | 15 ++++++++------- man/save_one_e_dm.1 | 14 +++++++++----- src/aux_quantities/README.rst | 15 ++++++++------- src/cisd/cisd.irp.f | 6 +++--- src/density_for_dft/README.rst | 14 +++++++++----- src/determinants/example.irp.f | 2 +- src/fci/pt2.irp.f | 13 +++++++++---- src/tools/diagonalize_h.irp.f | 9 ++++++--- src/tools/fcidump.irp.f | 17 +++++++++++------ src/tools/four_idx_transform.irp.f | 10 +++++++--- src/tools/print_wf.irp.f | 15 +++++++++------ src/tools/save_natorb.irp.f | 15 ++++++++------- src/tools/save_one_e_dm.irp.f | 15 +++++++++------ 31 files changed, 217 insertions(+), 139 deletions(-) diff --git a/docs/source/modules/aux_quantities.rst b/docs/source/modules/aux_quantities.rst index 3ded29f8..e71dc325 100644 --- a/docs/source/modules/aux_quantities.rst +++ b/docs/source/modules/aux_quantities.rst @@ -10,21 +10,22 @@ 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. +which are stored in the |EZFIO| directory 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 +any method, as long as they are stored in the same |MO| basis which is used for the calculations. In |RSDFT| calculations, this can be done to perform damping -on the density in order to speed up convergence. +on the density in order to speed up the convergence. The main providers of that module are: -* `data_one_e_dm_alpha_mo` and `data_one_e_dm_beta_mo` which are the - one-body alpha and beta densities which are necessary read from the EZFIO - folder. +* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which + are the one-body alpha and beta densities which are necessary read from the + |EZFIO| directory. Thanks to these providers you can use any density matrix that does not -necessary corresponds to that of the current wave function. +necessarily corresponds to that of the current wave function. + diff --git a/docs/source/modules/density_for_dft.rst b/docs/source/modules/density_for_dft.rst index 28708f69..ad42369b 100644 --- a/docs/source/modules/density_for_dft.rst +++ b/docs/source/modules/density_for_dft.rst @@ -9,12 +9,16 @@ density_for_dft =============== -This module defines the *provider* of the density used for the DFT related calculations. -This definition is done through the keyword :option:`density_for_dft density_for_dft`. -The density can be: +This module defines the *provider* of the density used for the |DFT| related +calculations. This definition is done through the keyword +:option:`density_for_dft density_for_dft`. The density can be: -* WFT : the density is computed with a potentially multi determinant wave function (see variables `psi_det` and `psi_det`)# input_density : the density is set to a density previously stored in the |EZFIO| folder (see ``aux_quantities``) -* damping_rs_dft : the density is damped between the input_density and the WFT density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` +* `WFT`: the density is computed with a potentially multi determinant wave + function (see variables `psi_det` and `psi_det`)# input_density: the density + is set to a density previously stored in the |EZFIO| directory (see + ``aux_quantities``) +* `damping_rs_dft`: the density is damped between the input_density and the WFT + density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` diff --git a/docs/source/programs/cisd.rst b/docs/source/programs/cisd.rst index 21da9b98..8d3f5ab4 100644 --- a/docs/source/programs/cisd.rst +++ b/docs/source/programs/cisd.rst @@ -19,7 +19,7 @@ cisd This program can be useful in many cases: - * GROUND STATE CALCULATION: if even after a :c:func:`cis` calculation, natural + * **Ground state calculation**: if even after a :c:func:`cis` calculation, natural orbitals (see :c:func:`save_natorb`) and then :c:func:`scf` optimization, you are not sure to have the lowest scf solution, do the same strategy with the :c:func:`cisd` executable instead of the :c:func:`cis` exectuable to generate the natural @@ -27,11 +27,11 @@ cisd - * EXCITED STATES CALCULATIONS: the lowest excited states are much likely to + * **Excited states calculations**: the lowest excited states are much likely to be dominanted by single- or double-excitations. Therefore, running a :c:func:`cisd` will save the "n_states" lowest states within the CISD space - in the EZFIO folder, which can afterward be used as guess wave functions + in the |EZFIO| directory, which can afterward be used as guess wave functions for a further multi-state fci calculation if you specify "read_wf" = True before running the fci executable (see :option:`determinants read_wf`). Also, if you specify "s2_eig" = True, the cisd will only retain states diff --git a/docs/source/programs/diagonalize_h.rst b/docs/source/programs/diagonalize_h.rst index e21da7c0..cd1f9e7b 100644 --- a/docs/source/programs/diagonalize_h.rst +++ b/docs/source/programs/diagonalize_h.rst @@ -9,11 +9,14 @@ diagonalize_h - Program that extracts the :option:`determinants n_states` lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. + Program that extracts the :option:`determinants n_states` lowest + states of the Hamiltonian within the set of Slater determinants stored + in the |EZFIO| directory. - If :option:`determinants s2_eig` = True, it will retain only states + If :option:`determinants s2_eig` = |true|, it will retain only states + which correspond to the desired value of + :option:`determinants expected_s2`. - which corresponds to the desired value of :option:`determinants expected_s2`. Needs: diff --git a/docs/source/programs/fcidump.rst b/docs/source/programs/fcidump.rst index b6e2a5b4..4e58a1ff 100644 --- a/docs/source/programs/fcidump.rst +++ b/docs/source/programs/fcidump.rst @@ -9,17 +9,22 @@ fcidump - Produce a regular FCIDUMP file from the |MOs| stored in the |EZFIO| folder. + Produce a regular `FCIDUMP` file from the |MOs| stored in the |EZFIO| + directory. - To specify an active space, the class of the mos have to set in the |EZFIO| folder (see :ref:`qp_set_mo_class`). + To specify an active space, the class of the |MOs| have to set in the + |EZFIO| directory (see :ref:`qp_set_mo_class`). - The fcidump program supports 3 types of MO_class : + The :ref:`fcidump` program supports 3 types of |MO| classes : - * the "core" orbitals which are always doubly occupied in the calculation + * the *core* orbitals which are always doubly occupied in the + calculation - * the "del" orbitals that are never occupied in the calculation + * the *deleted* orbitals that are never occupied in the calculation + + * the *active* orbitals that are occupied with a varying number of + electrons - * the "act" orbitals that will be occupied by a varying number of electrons Needs: diff --git a/docs/source/programs/four_idx_transform.rst b/docs/source/programs/four_idx_transform.rst index 953d7b1d..220433e1 100644 --- a/docs/source/programs/four_idx_transform.rst +++ b/docs/source/programs/four_idx_transform.rst @@ -9,11 +9,15 @@ four_idx_transform - 4-index transformation of two-electron integrals from |AO| to |MO| integrals. + 4-index transformation of two-electron integrals from |AO| to |MO| + integrals. - This program will compute the two-electron integrals on the |MO| basis and store it into the |EZFIO| folder. + This program will compute the two-electron integrals on the |MO| basis + and store it into the |EZFIO| directory. + + This program can be useful if the AO --> MO transformation is an + expensive step by itself. - This program can be useful if the AO --> MO transformation is an expensive step by itself. Needs: diff --git a/docs/source/programs/print_wf.rst b/docs/source/programs/print_wf.rst index 56f5b238..a141be09 100644 --- a/docs/source/programs/print_wf.rst +++ b/docs/source/programs/print_wf.rst @@ -9,13 +9,15 @@ print_wf - Print the ground state wave function stored in the |EZFIO| folder in the intermediate normalization. + Print the ground state wave function stored in the |EZFIO| directory + in the intermediate normalization. - It also prints a lot of information regarding the excitation operators from the reference determinant + It also prints a lot of information regarding the excitation + operators from the reference determinant ! and a first-order + perturbative analysis of the wave function. - and a first-order perturbative analysis of the wave function. - - If the wave function strongly deviates from the first-order analysis, something funny is going on :) + If the wave function strongly deviates from the first-order analysis, + something funny is going on :) Needs: diff --git a/docs/source/programs/pt2.rst b/docs/source/programs/pt2.rst index c18e466b..45726526 100644 --- a/docs/source/programs/pt2.rst +++ b/docs/source/programs/pt2.rst @@ -9,13 +9,18 @@ pt2 - Second order perturbative correction to the wave function contained in the EZFIO directory. + Second order perturbative correction to the wave function contained + in the |EZFIO| directory. - This programs runs the stochastic PT2 correction on all "n_states" wave function stored in the EZFIO folder (see :option:`determinant n_states`). + This programs runs the stochastic |PT2| correction on all + :option:`determinants n_states` wave functions stored in the |EZFIO| + directory. - The option for the PT2 correction are the "pt2_relative_error" which is the relative stochastic + The main option for the |PT2| correction is the + :option:`perturbation pt2_relative_error` which is the relative + stochastic error on the |PT2| to reach before stopping the + sampling. - error on the PT2 to reach before stopping the stochastic sampling. (see :option:`perturbation pt2_relative_error`) Needs: diff --git a/docs/source/programs/save_natorb.rst b/docs/source/programs/save_natorb.rst index 736e4178..852b1583 100644 --- a/docs/source/programs/save_natorb.rst +++ b/docs/source/programs/save_natorb.rst @@ -9,15 +9,16 @@ save_natorb - Save natural MOs into the EZFIO + Save natural |MOs| into the |EZFIO|. - This program reads the wave function stored in the EZFIO folder, + This program reads the wave function stored in the |EZFIO| directory, + extracts the corresponding natural orbitals and setd them as the new + |MOs|. - extracts the corresponding natural orbitals and set them as the new MOs - - If this is a multi-state calculation, the density matrix that produces the natural orbitals - - is obtained from a state-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). + If this is a multi-state calculation, the density matrix that produces + the natural orbitals is obtained from an average of the density + matrices of each state with the corresponding + :option:`determinants state_average_weight` Needs: diff --git a/docs/source/programs/save_one_e_dm.rst b/docs/source/programs/save_one_e_dm.rst index bf8ec089..5758aad6 100644 --- a/docs/source/programs/save_one_e_dm.rst +++ b/docs/source/programs/save_one_e_dm.rst @@ -9,12 +9,16 @@ save_one_e_dm - 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. + Program that computes the one body density on the |MO| basis + for $\alpha$ and $\beta$ electrons from the wave function + stored in the |EZFIO| directory, and then saves it into the + :ref:`module_aux_quantities`. - Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. - - This can be used to perform damping on the density in RS-DFT calculation (see the density_for_dft module). + Then, the global variable :option:`aux_quantities data_one_e_dm_alpha_mo` + and :option:`aux_quantities data_one_e_dm_beta_mo` will automatically + read this density in the next calculation. This can be used to perform + damping on the density in |RSDFT| calculations (see + :ref:`module_density_for_dft`). Needs: diff --git a/docs/source/users_guide/printing.rst b/docs/source/users_guide/printing.rst index 8509a2d8..69f2b839 100644 --- a/docs/source/users_guide/printing.rst +++ b/docs/source/users_guide/printing.rst @@ -31,7 +31,7 @@ interactively in :ref:`qp_edit` mode. An alternative is to use the This program will, by default, print out the first :math:`10^4` determinants whatever the size of the wave function stored in the -|EZFIO| folder. If you want to change the number of printed Slater +|EZFIO| directory. If you want to change the number of printed Slater determinants, just change the :option:`determinants n_det_print_wf` keyword using the :ref:`qp_edit` tool. diff --git a/man/cisd.1 b/man/cisd.1 index 7a962b7c..20954d68 100644 --- a/man/cisd.1 +++ b/man/cisd.1 @@ -43,17 +43,17 @@ matrix (see \fBdeterminants n_states\fP). This program can be useful in many cases: .INDENT 0.0 .IP \(bu 2 -GROUND STATE CALCULATION: if even after a \fBcis()\fP calculation, natural +\fBGround state calculation\fP: if even after a \fBcis()\fP calculation, natural orbitals (see \fBsave_natorb()\fP) and then \fBscf()\fP optimization, you are not sure to have the lowest scf solution, do the same strategy with the \fBcisd()\fP executable instead of the \fBcis()\fP\ exectuable to generate the natural orbitals as a guess for the \fBscf()\fP\&. .IP \(bu 2 -EXCITED STATES CALCULATIONS: the lowest excited states are much likely to +\fBExcited states calculations\fP: the lowest excited states are much likely to be dominanted by single\- or double\-excitations. Therefore, running a \fBcisd()\fP will save the “n_states” lowest states within the CISD space -in the EZFIO folder, which can afterward be used as guess wave functions +in the \fI\%EZFIO\fP directory, which can afterward be used as guess wave functions for a further multi\-state fci calculation if you specify “read_wf” = True before running the fci executable (see \fBdeterminants read_wf\fP). Also, if you specify “s2_eig” = True, the cisd will only retain states diff --git a/man/diagonalize_h.1 b/man/diagonalize_h.1 index be760d5f..ed8931ba 100644 --- a/man/diagonalize_h.1 +++ b/man/diagonalize_h.1 @@ -32,11 +32,13 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Program that extracts the \fBdeterminants n_states\fP lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. +Program that extracts the \fBdeterminants n_states\fP lowest +states of the Hamiltonian within the set of Slater determinants stored +in the \fI\%EZFIO\fP directory. .sp -If \fBdeterminants s2_eig\fP = True, it will retain only states -.sp -which corresponds to the desired value of \fBdeterminants expected_s2\fP\&. +If \fBdeterminants s2_eig\fP = \fBtrue\fP, it will retain only states +which correspond to the desired value of +\fBdeterminants expected_s2\fP\&. .sp Needs: .INDENT 0.0 diff --git a/man/fcidump.1 b/man/fcidump.1 index c63f86f0..c8791248 100644 --- a/man/fcidump.1 +++ b/man/fcidump.1 @@ -32,18 +32,22 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Produce a regular FCIDUMP file from the MOs stored in the \fI\%EZFIO\fP folder. +Produce a regular \fIFCIDUMP\fP file from the MOs stored in the \fI\%EZFIO\fP +directory. .sp -To specify an active space, the class of the mos have to set in the \fI\%EZFIO\fP folder (see qp_set_mo_class). +To specify an active space, the class of the MOs have to set in the +\fI\%EZFIO\fP directory (see qp_set_mo_class). .sp -The fcidump program supports 3 types of MO_class : +The \fI\%fcidump\fP program supports 3 types of MO classes : .INDENT 0.0 .IP \(bu 2 -the “core” orbitals which are always doubly occupied in the calculation +the \fIcore\fP orbitals which are always doubly occupied in the +calculation .IP \(bu 2 -the “del” orbitals that are never occupied in the calculation +the \fIdeleted\fP orbitals that are never occupied in the calculation .IP \(bu 2 -the “act” orbitals that will be occupied by a varying number of electrons +the \fIactive\fP orbitals that are occupied with a varying number of +electrons .UNINDENT .sp Needs: diff --git a/man/four_idx_transform.1 b/man/four_idx_transform.1 index 43bc294a..41f89b92 100644 --- a/man/four_idx_transform.1 +++ b/man/four_idx_transform.1 @@ -32,11 +32,14 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -4\-index transformation of two\-electron integrals from AO to MO integrals. +4\-index transformation of two\-electron integrals from AO to MO +integrals. .sp -This program will compute the two\-electron integrals on the MO basis and store it into the \fI\%EZFIO\fP folder. +This program will compute the two\-electron integrals on the MO basis +and store it into the \fI\%EZFIO\fP directory. .sp -This program can be useful if the AO –> MO transformation is an expensive step by itself. +This program can be useful if the AO –> MO transformation is an +expensive step by itself. .sp Needs: .INDENT 0.0 diff --git a/man/print_wf.1 b/man/print_wf.1 index 53c1dc26..515b8a91 100644 --- a/man/print_wf.1 +++ b/man/print_wf.1 @@ -32,13 +32,15 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Print the ground state wave function stored in the \fI\%EZFIO\fP folder in the intermediate normalization. +Print the ground state wave function stored in the \fI\%EZFIO\fP directory +in the intermediate normalization. .sp -It also prints a lot of information regarding the excitation operators from the reference determinant +It also prints a lot of information regarding the excitation +operators from the reference determinant ! and a first\-order +perturbative analysis of the wave function. .sp -and a first\-order perturbative analysis of the wave function. -.sp -If the wave function strongly deviates from the first\-order analysis, something funny is going on :) +If the wave function strongly deviates from the first\-order analysis, +something funny is going on :) .sp Needs: .INDENT 0.0 diff --git a/man/printing.1 b/man/printing.1 index b5ec89da..0ba10e53 100644 --- a/man/printing.1 +++ b/man/printing.1 @@ -74,7 +74,7 @@ qp_run print_wf file.ezfio | tee file.ezfio.fci_natorb.wf .sp This program will, by default, print out the first 10^4 determinants whatever the size of the wave function stored in the -\fI\%EZFIO\fP folder. If you want to change the number of printed Slater +\fI\%EZFIO\fP directory. If you want to change the number of printed Slater determinants, just change the \fBdeterminants n_det_print_wf\fP keyword using the qp_edit tool. .sp diff --git a/man/pt2.1 b/man/pt2.1 index 3c59e81d..91ac2941 100644 --- a/man/pt2.1 +++ b/man/pt2.1 @@ -32,13 +32,17 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Second order perturbative correction to the wave function contained in the EZFIO directory. +Second order perturbative correction to the wave function contained +in the \fI\%EZFIO\fP directory. .sp -This programs runs the stochastic PT2 correction on all “n_states” wave function stored in the EZFIO folder (see \fBdeterminant n_states\fP). +This programs runs the stochastic PT2 correction on all +\fBdeterminants n_states\fP wave functions stored in the \fI\%EZFIO\fP +directory. .sp -The option for the PT2 correction are the “pt2_relative_error” which is the relative stochastic -.sp -error on the PT2 to reach before stopping the stochastic sampling. (see \fBperturbation pt2_relative_error\fP) +The main option for the PT2 correction is the +\fBperturbation pt2_relative_error\fP which is the relative +stochastic error on the PT2 to reach before stopping the +sampling. .sp Needs: .INDENT 0.0 diff --git a/man/save_natorb.1 b/man/save_natorb.1 index e4e368a2..1b06061d 100644 --- a/man/save_natorb.1 +++ b/man/save_natorb.1 @@ -32,15 +32,16 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Save natural MOs into the EZFIO +Save natural MOs into the \fI\%EZFIO\fP\&. .sp -This program reads the wave function stored in the EZFIO folder, +This program reads the wave function stored in the \fI\%EZFIO\fP directory, +extracts the corresponding natural orbitals and setd them as the new +MOs\&. .sp -extracts the corresponding natural orbitals and set them as the new MOs -.sp -If this is a multi\-state calculation, the density matrix that produces the natural orbitals -.sp -is obtained from a state\-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). +If this is a multi\-state calculation, the density matrix that produces +the natural orbitals is obtained from an average of the density +matrices of each state with the corresponding +\fBdeterminants state_average_weight\fP .sp Needs: .INDENT 0.0 diff --git a/man/save_one_e_dm.1 b/man/save_one_e_dm.1 index 4ce589ab..5899cdfb 100644 --- a/man/save_one_e_dm.1 +++ b/man/save_one_e_dm.1 @@ -32,12 +32,16 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -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. +Program that computes the one body density on the MO basis +for $alpha$ and $beta$ electrons from the wave function +stored in the \fI\%EZFIO\fP directory, and then saves it into the +module_aux_quantities\&. .sp -Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. -.sp -This can be used to perform damping on the density in RS\-DFT calculation (see the density_for_dft module). +Then, the global variable \fBaux_quantities data_one_e_dm_alpha_mo\fP +and \fBaux_quantities data_one_e_dm_beta_mo\fP will automatically +read this density in the next calculation. This can be used to perform +damping on the density in RSDFT calculations (see +module_density_for_dft). .sp Needs: .INDENT 0.0 diff --git a/src/aux_quantities/README.rst b/src/aux_quantities/README.rst index 62036952..c2b8b5ed 100644 --- a/src/aux_quantities/README.rst +++ b/src/aux_quantities/README.rst @@ -4,18 +4,19 @@ 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. +which are stored in the |EZFIO| directory 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 +any method, as long as they are stored in the same |MO| basis which is used for the calculations. In |RSDFT| calculations, this can be done to perform damping -on the density in order to speed up convergence. +on the density in order to speed up the convergence. The main providers of that module are: -* `data_one_e_dm_alpha_mo` and `data_one_e_dm_beta_mo` which are the - one-body alpha and beta densities which are necessary read from the EZFIO - folder. +* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which + are the one-body alpha and beta densities which are necessary read from the + |EZFIO| directory. Thanks to these providers you can use any density matrix that does not -necessary corresponds to that of the current wave function. +necessarily corresponds to that of the current wave function. + diff --git a/src/cisd/cisd.irp.f b/src/cisd/cisd.irp.f index e21423cf..9631f971 100644 --- a/src/cisd/cisd.irp.f +++ b/src/cisd/cisd.irp.f @@ -11,7 +11,7 @@ program cisd ! ! This program can be useful in many cases: ! - ! * GROUND STATE CALCULATION: if even after a :c:func:`cis` calculation, natural + ! * **Ground state calculation**: if even after a :c:func:`cis` calculation, natural ! orbitals (see :c:func:`save_natorb`) and then :c:func:`scf` optimization, you are not sure to have the lowest scf ! solution, ! do the same strategy with the :c:func:`cisd` executable instead of the :c:func:`cis` exectuable to generate the natural @@ -19,11 +19,11 @@ program cisd ! ! ! - ! * EXCITED STATES CALCULATIONS: the lowest excited states are much likely to + ! * **Excited states calculations**: the lowest excited states are much likely to ! be dominanted by single- or double-excitations. ! Therefore, running a :c:func:`cisd` will save the "n_states" lowest states within ! the CISD space - ! in the EZFIO folder, which can afterward be used as guess wave functions + ! in the |EZFIO| directory, which can afterward be used as guess wave functions ! for a further multi-state fci calculation if you specify "read_wf" = True ! before running the fci executable (see :option:`determinants read_wf`). ! Also, if you specify "s2_eig" = True, the cisd will only retain states diff --git a/src/density_for_dft/README.rst b/src/density_for_dft/README.rst index 278a27ef..612d236e 100644 --- a/src/density_for_dft/README.rst +++ b/src/density_for_dft/README.rst @@ -3,10 +3,14 @@ density_for_dft =============== -This module defines the *provider* of the density used for the DFT related calculations. -This definition is done through the keyword :option:`density_for_dft density_for_dft`. -The density can be: +This module defines the *provider* of the density used for the |DFT| related +calculations. This definition is done through the keyword +:option:`density_for_dft density_for_dft`. The density can be: -* WFT : the density is computed with a potentially multi determinant wave function (see variables `psi_det` and `psi_det`)# input_density : the density is set to a density previously stored in the |EZFIO| folder (see ``aux_quantities``) -* damping_rs_dft : the density is damped between the input_density and the WFT density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` +* `WFT`: the density is computed with a potentially multi determinant wave + function (see variables `psi_det` and `psi_det`)# input_density: the density + is set to a density previously stored in the |EZFIO| directory (see + ``aux_quantities``) +* `damping_rs_dft`: the density is damped between the input_density and the WFT + density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` diff --git a/src/determinants/example.irp.f b/src/determinants/example.irp.f index c8571995..97bc5388 100644 --- a/src/determinants/example.irp.f +++ b/src/determinants/example.irp.f @@ -105,7 +105,7 @@ subroutine example_determinants_psi_det END_DOC read_wf = .True. touch read_wf - ! you force the wave function to be set to the one in the EZFIO folder + ! you force the wave function to be set to the one in the EZFIO directory call routine_example_psi_det end diff --git a/src/fci/pt2.irp.f b/src/fci/pt2.irp.f index 4a555d69..45860fb5 100644 --- a/src/fci/pt2.irp.f +++ b/src/fci/pt2.irp.f @@ -1,13 +1,18 @@ program pt2 implicit none BEGIN_DOC - ! Second order perturbative correction to the wave function contained in the EZFIO directory. + ! Second order perturbative correction to the wave function contained + ! in the |EZFIO| directory. ! - ! This programs runs the stochastic PT2 correction on all "n_states" wave function stored in the EZFIO folder (see :option:`determinant n_states`). + ! This programs runs the stochastic |PT2| correction on all + ! :option:`determinants n_states` wave functions stored in the |EZFIO| + ! directory. ! - ! The option for the PT2 correction are the "pt2_relative_error" which is the relative stochastic + ! The main option for the |PT2| correction is the + ! :option:`perturbation pt2_relative_error` which is the relative + ! stochastic error on the |PT2| to reach before stopping the + ! sampling. ! - ! error on the PT2 to reach before stopping the stochastic sampling. (see :option:`perturbation pt2_relative_error`) END_DOC if (.not. is_zmq_slave) then read_wf = .True. diff --git a/src/tools/diagonalize_h.irp.f b/src/tools/diagonalize_h.irp.f index 5b3cbdf5..c9ae2033 100644 --- a/src/tools/diagonalize_h.irp.f +++ b/src/tools/diagonalize_h.irp.f @@ -1,11 +1,14 @@ program diagonalize_h implicit none BEGIN_DOC -! Program that extracts the :option:`determinants n_states` lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. +! Program that extracts the :option:`determinants n_states` lowest +! states of the Hamiltonian within the set of Slater determinants stored +! in the |EZFIO| directory. ! -! If :option:`determinants s2_eig` = True, it will retain only states +! If :option:`determinants s2_eig` = |true|, it will retain only states +! which correspond to the desired value of +! :option:`determinants expected_s2`. ! -! which corresponds to the desired value of :option:`determinants expected_s2`. END_DOC read_wf = .True. touch read_wf diff --git a/src/tools/fcidump.irp.f b/src/tools/fcidump.irp.f index f979ac1a..bf4d07fb 100644 --- a/src/tools/fcidump.irp.f +++ b/src/tools/fcidump.irp.f @@ -1,17 +1,22 @@ program fcidump implicit none BEGIN_DOC -! Produce a regular FCIDUMP file from the |MOs| stored in the |EZFIO| folder. +! Produce a regular `FCIDUMP` file from the |MOs| stored in the |EZFIO| +! directory. ! -! To specify an active space, the class of the mos have to set in the |EZFIO| folder (see :ref:`qp_set_mo_class`). +! To specify an active space, the class of the |MOs| have to set in the +! |EZFIO| directory (see :ref:`qp_set_mo_class`). ! -! The fcidump program supports 3 types of MO_class : +! The :ref:`fcidump` program supports 3 types of |MO| classes : ! -! * the "core" orbitals which are always doubly occupied in the calculation +! * the *core* orbitals which are always doubly occupied in the +! calculation ! -! * the "del" orbitals that are never occupied in the calculation +! * the *deleted* orbitals that are never occupied in the calculation +! +! * the *active* orbitals that are occupied with a varying number of +! electrons ! -! * the "act" orbitals that will be occupied by a varying number of electrons END_DOC character*(128) :: output integer :: i_unit_output,getUnitAndOpen diff --git a/src/tools/four_idx_transform.irp.f b/src/tools/four_idx_transform.irp.f index 45198770..92e87cad 100644 --- a/src/tools/four_idx_transform.irp.f +++ b/src/tools/four_idx_transform.irp.f @@ -1,11 +1,15 @@ program four_idx_transform implicit none BEGIN_DOC -! 4-index transformation of two-electron integrals from |AO| to |MO| integrals. +! 4-index transformation of two-electron integrals from |AO| to |MO| +! integrals. ! -! This program will compute the two-electron integrals on the |MO| basis and store it into the |EZFIO| folder. +! This program will compute the two-electron integrals on the |MO| basis +! and store it into the |EZFIO| directory. +! +! This program can be useful if the AO --> MO transformation is an +! expensive step by itself. ! -! This program can be useful if the AO --> MO transformation is an expensive step by itself. END_DOC io_mo_two_e_integrals = 'Write' diff --git a/src/tools/print_wf.irp.f b/src/tools/print_wf.irp.f index 2a8335fc..01fc8948 100644 --- a/src/tools/print_wf.irp.f +++ b/src/tools/print_wf.irp.f @@ -1,17 +1,20 @@ program print_wf implicit none BEGIN_DOC - ! Print the ground state wave function stored in the |EZFIO| folder in the intermediate normalization. + ! Print the ground state wave function stored in the |EZFIO| directory + ! in the intermediate normalization. ! - ! It also prints a lot of information regarding the excitation operators from the reference determinant + ! It also prints a lot of information regarding the excitation + ! operators from the reference determinant ! and a first-order + ! perturbative analysis of the wave function. ! - ! and a first-order perturbative analysis of the wave function. - ! - ! If the wave function strongly deviates from the first-order analysis, something funny is going on :) + ! If the wave function strongly deviates from the first-order analysis, + ! something funny is going on :) END_DOC - ! this has to be done in order to be sure that N_det, psi_det and psi_coef are the wave function stored in the EZFIO folder + ! this has to be done in order to be sure that N_det, psi_det and + ! psi_coef are the wave function stored in the |EZFIO| directory. read_wf = .True. touch read_wf call routine diff --git a/src/tools/save_natorb.irp.f b/src/tools/save_natorb.irp.f index e18309ba..88b28f06 100644 --- a/src/tools/save_natorb.irp.f +++ b/src/tools/save_natorb.irp.f @@ -1,15 +1,16 @@ program save_natorb implicit none BEGIN_DOC -! Save natural MOs into the EZFIO +! Save natural |MOs| into the |EZFIO|. ! -! This program reads the wave function stored in the EZFIO folder, +! This program reads the wave function stored in the |EZFIO| directory, +! extracts the corresponding natural orbitals and setd them as the new +! |MOs|. ! -! extracts the corresponding natural orbitals and set them as the new MOs -! -! If this is a multi-state calculation, the density matrix that produces the natural orbitals -! -! is obtained from a state-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). +! If this is a multi-state calculation, the density matrix that produces +! the natural orbitals is obtained from an average of the density +! matrices of each state with the corresponding +! :option:`determinants state_average_weight` END_DOC read_wf = .True. touch read_wf diff --git a/src/tools/save_one_e_dm.irp.f b/src/tools/save_one_e_dm.irp.f index 9bfa6717..e850131e 100644 --- a/src/tools/save_one_e_dm.irp.f +++ b/src/tools/save_one_e_dm.irp.f @@ -1,13 +1,16 @@ program save_one_e_dm implicit none BEGIN_DOC -! 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. +! Program that computes the one body density on the |MO| basis +! for $\alpha$ and $\beta$ electrons from the wave function +! stored in the |EZFIO| directory, and then saves it into the +! :ref:`module_aux_quantities`. ! -! Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. -! -! This can be used to perform damping on the density in RS-DFT calculation (see the density_for_dft module). +! Then, the global variable :option:`aux_quantities data_one_e_dm_alpha_mo` +! and :option:`aux_quantities data_one_e_dm_beta_mo` will automatically +! read this density in the next calculation. This can be used to perform +! damping on the density in |RSDFT| calculations (see +! :ref:`module_density_for_dft`). END_DOC read_wf = .True. touch read_wf