Merge branch 'develop' of https://github.com/QuantumPackage/qp2 into develop

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.
+
  
  
  

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`
 
  
  

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 

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: 
  

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: 
  

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: 
  

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: 
  

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: 
  

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: 
  

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: 
  

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.
 

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

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

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:

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

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

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

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

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

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

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.
+

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

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`
 

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
 

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.

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

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

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'

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

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

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