From 0bfc60ee93f08314dc8703fb1b11542f5bcc0be5 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 16 Jan 2019 14:59:22 +0100
Subject: [PATCH] creating doc for programs

---
 docs/source/conf.py                          |   6 +
 docs/source/programs/cis.rst                 |  42 +++++++
 docs/source/programs/cisd.rst                |  38 ++++++
 docs/source/programs/diagonalize_h.rst       |  16 +++
 docs/source/programs/fci.rst                 |  50 ++++++++
 docs/source/programs/fcidump.rst             |  22 ++++
 docs/source/programs/four_idx_transform.rst  |  16 +++
 docs/source/programs/ks_scf.rst              |  12 ++
 docs/source/programs/molden.rst              |  12 ++
 docs/source/programs/print_e_conv.rst        |  18 +++
 docs/source/programs/print_wf.rst            |  18 +++
 docs/source/programs/pt2.rst                 |  18 +++
 docs/source/programs/rs_ks_scf.rst           |  12 ++
 docs/source/programs/save_natorb.rst         |  20 ++++
 docs/source/programs/save_one_e_dm.rst       |  16 +++
 docs/source/programs/save_ortho_mos.rst      |  18 +++
 docs/source/programs/scf.rst                 |  18 +++
 docs/source/programs/write_integrals_erf.rst |  12 ++
 man/cis.1                                    |  71 ++++++++++++
 man/cisd.1                                   |  67 +++++++++++
 man/diagonalize_h.1                          |  49 ++++++++
 man/fci.1                                    |  77 +++++++++++++
 man/fcidump.1                                |  57 +++++++++
 man/four_idx_transform.1                     |  49 ++++++++
 man/ks_scf.1                                 |  42 +++++++
 man/molden.1                                 |  42 +++++++
 man/print_e_conv.1                           |  53 +++++++++
 man/print_wf.1                               |  51 ++++++++
 man/printing.1                               |  83 +++++++++++++
 man/pt2.1                                    |  51 ++++++++
 man/qp_update.1                              |  51 ++++++++
 man/qpsh.1                                   | 115 +++++++++++++++++++
 man/rs_ks_scf.1                              |  42 +++++++
 man/save_natorb.1                            |  53 +++++++++
 man/save_one_e_dm.1                          |  49 ++++++++
 man/save_ortho_mos.1                         |  51 ++++++++
 man/scf.1                                    |  51 ++++++++
 man/write_integrals_erf.1                    |  42 +++++++
 38 files changed, 1510 insertions(+)
 create mode 100644 docs/source/programs/cis.rst
 create mode 100644 docs/source/programs/cisd.rst
 create mode 100644 docs/source/programs/diagonalize_h.rst
 create mode 100644 docs/source/programs/fci.rst
 create mode 100644 docs/source/programs/fcidump.rst
 create mode 100644 docs/source/programs/four_idx_transform.rst
 create mode 100644 docs/source/programs/ks_scf.rst
 create mode 100644 docs/source/programs/molden.rst
 create mode 100644 docs/source/programs/print_e_conv.rst
 create mode 100644 docs/source/programs/print_wf.rst
 create mode 100644 docs/source/programs/pt2.rst
 create mode 100644 docs/source/programs/rs_ks_scf.rst
 create mode 100644 docs/source/programs/save_natorb.rst
 create mode 100644 docs/source/programs/save_one_e_dm.rst
 create mode 100644 docs/source/programs/save_ortho_mos.rst
 create mode 100644 docs/source/programs/scf.rst
 create mode 100644 docs/source/programs/write_integrals_erf.rst
 create mode 100644 man/cis.1
 create mode 100644 man/cisd.1
 create mode 100644 man/diagonalize_h.1
 create mode 100644 man/fci.1
 create mode 100644 man/fcidump.1
 create mode 100644 man/four_idx_transform.1
 create mode 100644 man/ks_scf.1
 create mode 100644 man/molden.1
 create mode 100644 man/print_e_conv.1
 create mode 100644 man/print_wf.1
 create mode 100644 man/printing.1
 create mode 100644 man/pt2.1
 create mode 100644 man/qp_update.1
 create mode 100644 man/qpsh.1
 create mode 100644 man/rs_ks_scf.1
 create mode 100644 man/save_natorb.1
 create mode 100644 man/save_one_e_dm.1
 create mode 100644 man/save_ortho_mos.1
 create mode 100644 man/scf.1
 create mode 100644 man/write_integrals_erf.1

diff --git a/docs/source/conf.py b/docs/source/conf.py
index edd568a6..914e55a6 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -166,6 +166,12 @@ for f in os.listdir("users_guide"):
     filename = os.path.join("users_guide",name)
     man_pages.append( (filename, name, qpdoc, [author], 1) )
 
+for f in os.listdir("programs"):
+  name = f.split('.')[0]
+  if name not in []:
+    filename = os.path.join("programs",name)
+    man_pages.append( (filename, name, qpdoc, [author], 1) )
+
 
 # -- Options for Texinfo output ----------------------------------------------
 
diff --git a/docs/source/programs/cis.rst b/docs/source/programs/cis.rst
new file mode 100644
index 00000000..9f378b6c
--- /dev/null
+++ b/docs/source/programs/cis.rst
@@ -0,0 +1,42 @@
+.. _.cis.: 
+ 
+.. program:: cis 
+ 
+=== 
+cis 
+=== 
+ 
+ 
+
+
+ Configuration Interaction with Single excitations. 
+
+ This program takes a reference Slater determinant of ROHF-like occupancy, and performs all single excitations on top of it. Disregarding spatial symmetry, it computes the `n_states` lowest eigenstates of that CI matrix. (see :option:`determinants n_states`) 
+
+ This program can be useful in many cases: 
+
+ # Ground state calculation 
+
+ To be sure to have the lowest |SCF| solution, perform an :ref:`.scf.` (see the :ref:`hartree_fock` module), then a :ref:`.cis.`, save the natural orbitals (see :ref:`.save_natorb.`) and re-run an :ref:`.scf.` optimization from this |MO| guess. 
+
+ 
+
+ # Excited states calculations 
+
+ The lowest excited states are much likely to be dominated by single-excitations. Therefore, running a :ref:`cis/cis` will save the `n_states` lowest states within the |CIS| space in the |EZFIO| directory, which can afterwards be used as guess wave functions for a further multi-state |FCI| calculation if :option:`determinants read_wf` is set to |true| before running the :ref:`fci/fci` executable. 
+
+ If :option:`determinants s2_eig` is set to |true|, the |CIS| will only retain states having the expected |S^2| value (see :option:`determinants expected_s2`). Otherwise, the |CIS| will take the lowest :option:`determinants n_states`, whatever multiplicity they are. 
+
+ # Note 
+
+ To discard some orbitals, use the :ref:`qp_set_mo_class` command to specify: 
+
+ * *core* orbitals which will be always doubly occupied 
+
+ * *act* orbitals where an electron can be either excited from or to 
+
+ * *del* orbitals which will be never occupied 
+
+ 
+ 
+File: :file:`cis/cis.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/cisd.rst b/docs/source/programs/cisd.rst
new file mode 100644
index 00000000..3370bc5a
--- /dev/null
+++ b/docs/source/programs/cisd.rst
@@ -0,0 +1,38 @@
+.. _.cisd.: 
+ 
+.. program:: cisd 
+ 
+==== 
+cisd 
+==== 
+ 
+ 
+Configuration Interaction with Single and Double excitations. 
+
+ This program takes a reference Slater determinant of ROHF-like occupancy, 
+
+ and performs all single and double excitations on top of it, disregarding spatial symmetry and compute the "n_states" lowest eigenstates of that CI matrix (see :option:`determinants n_states`). 
+
+ This program can be useful in many cases: 
+
+ * 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 orbitals as a guess for the :c:func:`scf`. 
+
+ 
+
+ 
+
+ * 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 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 having the good value :math:`S^2` value (see :option:`determinants expected_s2` and :option:`determinants s2_eig`). If "s2_eig" = False, it will take the lowest n_states, whatever multiplicity they are. 
+
+ 
+
+ 
+
+ Note: if you would like to discard some orbitals, use :ref:`qp_set_mo_class` to specify: 
+
+ * "core" orbitals which will be always doubly occupied 
+
+ * "act" orbitals where an electron can be either excited from or to 
+
+ * "del" orbitals which will be never occupied 
+ 
+File: :file:`cisd/cisd.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/diagonalize_h.rst b/docs/source/programs/diagonalize_h.rst
new file mode 100644
index 00000000..bc79f115
--- /dev/null
+++ b/docs/source/programs/diagonalize_h.rst
@@ -0,0 +1,16 @@
+.. _.diagonalize_h.: 
+ 
+.. program:: diagonalize_h 
+ 
+============= 
+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. 
+
+ If :option:`determinants s2_eig` = True, it will retain only states 
+
+ which corresponds to the desired value of :option:`determinants expected_s2`. 
+ 
+File: :file:`tools/diagonalize_h.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/fci.rst b/docs/source/programs/fci.rst
new file mode 100644
index 00000000..46e12bfd
--- /dev/null
+++ b/docs/source/programs/fci.rst
@@ -0,0 +1,50 @@
+.. _.fci.: 
+ 
+.. program:: fci 
+ 
+=== 
+fci 
+=== 
+ 
+ 
+Selected Full Configuration Interaction with stochastic selection and PT2 . 
+
+ This program performs a CIPSI-like selected CI using a stochastic scheme for both 
+
+ the selection of the important Slater determinants and the computation of the PT2 correction. 
+
+ This CIPSI-like algorithm will be performed for the "n_states" lowest states of the variational space (see :option:`determinants n_det_max`) 
+
+ The fci program will stop when reaching at least one the two following conditions: 
+
+ * number of Slater determinant > "n_det_max" (see :option:`determinants n_det_max`) 
+
+ * |PT2| < "pt2_max" (see :option:`perturbation pt2_max`) 
+
+ 
+
+ The following other options can be of interest: 
+
+ If "read_wf" = False, it starts with a ROHF-like Slater determinant as a guess wave function. 
+
+ If "read_wf" = True , it starts with the wave function(s) stored in the EZFIO folder as guess wave function(s). 
+
+ (see :option:`determinants read_wf`) 
+
+ If "s2_eig" = True, it will systematically add all necessary Slater determinants in order 
+
+ to have a pure spin wave function with an :math:`S^2` value corresponding to "expected_s2". 
+
+ (see :option:`determinants s2_eig` and :option:`determinants expected_s2`) 
+
+ 
+
+ 
+
+ 
+
+ For excited states calculations, it is recommended to start with a :c:func:`cis` or :c:func:`cisd` guess wave functions 
+
+ for the "n_states", and to set "s2_eig" = True. 
+ 
+File: :file:`fci/fci.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/fcidump.rst b/docs/source/programs/fcidump.rst
new file mode 100644
index 00000000..a91a79f5
--- /dev/null
+++ b/docs/source/programs/fcidump.rst
@@ -0,0 +1,22 @@
+.. _.fcidump.: 
+ 
+.. program:: fcidump 
+ 
+======= 
+fcidump 
+======= 
+ 
+ 
+Produce a regular FCIDUMP file from the |MOs| stored in the |EZFIO| folder. 
+
+ To specify an active space, the class of the mos have to set in the |EZFIO| folder (see :ref:`qp_set_mo_class`). 
+
+ The fcidump program supports 3 types of MO_class : 
+
+ * the "core" orbitals which are always doubly occupied in the calculation 
+
+ * the "del" orbitals that are never occupied in the calculation 
+
+ * the "act" orbitals that will be occupied by a varying number of electrons 
+ 
+File: :file:`tools/fcidump.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/four_idx_transform.rst b/docs/source/programs/four_idx_transform.rst
new file mode 100644
index 00000000..78afec89
--- /dev/null
+++ b/docs/source/programs/four_idx_transform.rst
@@ -0,0 +1,16 @@
+.. _.four_idx_transform.: 
+ 
+.. program:: four_idx_transform 
+ 
+================== 
+four_idx_transform 
+================== 
+ 
+ 
+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 can be useful if the AO --> MO transformation is an expensive step by itself. 
+ 
+File: :file:`tools/four_idx_transform.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/ks_scf.rst b/docs/source/programs/ks_scf.rst
new file mode 100644
index 00000000..454e82d3
--- /dev/null
+++ b/docs/source/programs/ks_scf.rst
@@ -0,0 +1,12 @@
+.. _.ks_scf.: 
+ 
+.. program:: ks_scf 
+ 
+====== 
+ks_scf 
+====== 
+ 
+ 
+Produce `Kohn_Sham` MO orbital output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ output: kohn_sham.energy optional: mo_basis.mo_coef 
+ 
+File: :file:`kohn_sham/ks_scf.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/molden.rst b/docs/source/programs/molden.rst
new file mode 100644
index 00000000..e45959c6
--- /dev/null
+++ b/docs/source/programs/molden.rst
@@ -0,0 +1,12 @@
+.. _.molden.: 
+ 
+.. program:: molden 
+ 
+====== 
+molden 
+====== 
+ 
+ 
+Produce a Molden file 
+ 
+File: :file:`tools/molden.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/print_e_conv.rst b/docs/source/programs/print_e_conv.rst
new file mode 100644
index 00000000..26e7d257
--- /dev/null
+++ b/docs/source/programs/print_e_conv.rst
@@ -0,0 +1,18 @@
+.. _.print_e_conv.: 
+ 
+.. program:: print_e_conv 
+ 
+============ 
+print_e_conv 
+============ 
+ 
+ 
+program that prints in a human readable format the convergence of the CIPSI algorithm. 
+
+ for all istate, this program produces 
+
+ * a file "EZFIO.istate.conv" containing the variational and var+PT2 energies as a function of N_det 
+
+ * for istate > 1, a file EZFIO.istate.delta_e.conv containing the energy difference (both var and var+PT2) with the ground state as a function of N_det 
+ 
+File: :file:`tools/print_e_conv.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/print_wf.rst b/docs/source/programs/print_wf.rst
new file mode 100644
index 00000000..a69e71d6
--- /dev/null
+++ b/docs/source/programs/print_wf.rst
@@ -0,0 +1,18 @@
+.. _.print_wf.: 
+ 
+.. program:: print_wf 
+ 
+======== 
+print_wf 
+======== 
+ 
+ 
+Print the ground state wave function stored in the |EZFIO| folder in the intermediate normalization. 
+
+ 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. 
+
+ If the wave function strongly deviates from the first-order analysis, something funny is going on :) 
+ 
+File: :file:`tools/print_wf.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/pt2.rst b/docs/source/programs/pt2.rst
new file mode 100644
index 00000000..21730691
--- /dev/null
+++ b/docs/source/programs/pt2.rst
@@ -0,0 +1,18 @@
+.. _.pt2.: 
+ 
+.. program:: pt2 
+ 
+=== 
+pt2 
+=== 
+ 
+ 
+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`). 
+
+ The option for the PT2 correction are the "pt2_relative_error" which is the relative stochastic 
+
+ error on the PT2 to reach before stopping the stochastic sampling. (see :option:`perturbation pt2_relative_error`) 
+ 
+File: :file:`fci/pt2.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/rs_ks_scf.rst b/docs/source/programs/rs_ks_scf.rst
new file mode 100644
index 00000000..30c34037
--- /dev/null
+++ b/docs/source/programs/rs_ks_scf.rst
@@ -0,0 +1,12 @@
+.. _.rs_ks_scf.: 
+ 
+.. program:: rs_ks_scf 
+ 
+========= 
+rs_ks_scf 
+========= 
+ 
+ 
+Produce `Range_separated_Kohn_Sham` MO orbital output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ output: kohn_sham.energy optional: mo_basis.mo_coef 
+ 
+File: :file:`kohn_sham_rs/rs_ks_scf.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/save_natorb.rst b/docs/source/programs/save_natorb.rst
new file mode 100644
index 00000000..ff3dfc92
--- /dev/null
+++ b/docs/source/programs/save_natorb.rst
@@ -0,0 +1,20 @@
+.. _.save_natorb.: 
+ 
+.. program:: save_natorb 
+ 
+=========== 
+save_natorb 
+=========== 
+ 
+ 
+Save natural MOs into the EZFIO 
+
+ This program reads the wave function stored in the EZFIO folder, 
+
+ 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). 
+ 
+File: :file:`tools/save_natorb.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/save_one_e_dm.rst b/docs/source/programs/save_one_e_dm.rst
new file mode 100644
index 00000000..54925686
--- /dev/null
+++ b/docs/source/programs/save_one_e_dm.rst
@@ -0,0 +1,16 @@
+.. _.save_one_e_dm.: 
+ 
+.. program:: save_one_e_dm 
+ 
+============= 
+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. 
+
+ 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). 
+ 
+File: :file:`tools/save_one_e_dm.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/save_ortho_mos.rst b/docs/source/programs/save_ortho_mos.rst
new file mode 100644
index 00000000..60e0205e
--- /dev/null
+++ b/docs/source/programs/save_ortho_mos.rst
@@ -0,0 +1,18 @@
+.. _.save_ortho_mos.: 
+ 
+.. program:: save_ortho_mos 
+ 
+============== 
+save_ortho_mos 
+============== 
+ 
+ 
+Save orthonormalized MOs in the EZFIO. 
+
+ This program reads the current MOs, computes the corresponding overlap matrix in the MO basis 
+
+ and perform a Lowdin orthonormalization : :math:`MO_{new} = S^{-1/2} MO_{guess}`. 
+
+ Thanks to the Lowdin orthonormalization, the new MOs are the most similar to the guess MOs. 
+ 
+File: :file:`tools/save_ortho_mos.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/scf.rst b/docs/source/programs/scf.rst
new file mode 100644
index 00000000..0533bc81
--- /dev/null
+++ b/docs/source/programs/scf.rst
@@ -0,0 +1,18 @@
+.. _.scf.: 
+ 
+.. program:: scf 
+ 
+=== 
+scf 
+=== 
+ 
+ 
+Produce `Hartree_Fock` |MOs| 
+
+ output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ 
+
+ output: hartree_fock.energy 
+
+ optional: mo_basis.mo_coef 
+ 
+File: :file:`hartree_fock/scf.irp.f`
\ No newline at end of file
diff --git a/docs/source/programs/write_integrals_erf.rst b/docs/source/programs/write_integrals_erf.rst
new file mode 100644
index 00000000..cfbdf345
--- /dev/null
+++ b/docs/source/programs/write_integrals_erf.rst
@@ -0,0 +1,12 @@
+.. _.write_integrals_erf.: 
+ 
+.. program:: write_integrals_erf 
+ 
+=================== 
+write_integrals_erf 
+=================== 
+ 
+ 
+Saves the two-electron integrals with the :math:`erf(\mu r_{12})/r_{12}` oprerator into the EZFIO folder 
+ 
+File: :file:`tools/write_integrals_erf.irp.f`
\ No newline at end of file
diff --git a/man/cis.1 b/man/cis.1
new file mode 100644
index 00000000..1b39338e
--- /dev/null
+++ b/man/cis.1
@@ -0,0 +1,71 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "CIS" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+cis \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.INDENT 0.0
+.INDENT 3.5
+Configuration Interaction with Single excitations.
+.sp
+This program takes a reference Slater determinant of ROHF\-like occupancy, and performs all single excitations on top of it. Disregarding spatial symmetry, it computes the \fIn_states\fP lowest eigenstates of that CI matrix. (see \fBdeterminants n_states\fP)
+.sp
+This program can be useful in many cases:
+.sp
+# Ground state calculation
+.sp
+To be sure to have the lowest SCF solution, perform an \&.scf. (see the hartree_fock module), then a \fI\%cis\fP, save the natural orbitals (see \&.save_natorb.) and re\-run an \&.scf. optimization from this MO guess.
+.sp
+# Excited states calculations
+.sp
+The lowest excited states are much likely to be dominated by single\-excitations. Therefore, running a cis/cis will save the \fIn_states\fP lowest states within the CIS space in the \fI\%EZFIO\fP directory, which can afterwards be used as guess wave functions for a further multi\-state FCI calculation if \fBdeterminants read_wf\fP is set to \fBtrue\fP before running the fci/fci executable.
+.sp
+If \fBdeterminants s2_eig\fP is set to \fBtrue\fP, the CIS will only retain states having the expected \ewidehat{S^2} value (see \fBdeterminants expected_s2\fP). Otherwise, the CIS will take the lowest \fBdeterminants n_states\fP, whatever multiplicity they are.
+.sp
+# Note
+.sp
+To discard some orbitals, use the qp_set_mo_class command to specify:
+.INDENT 0.0
+.IP \(bu 2
+\fIcore\fP orbitals which will be always doubly occupied
+.IP \(bu 2
+\fIact\fP orbitals where an electron can be either excited from or to
+.IP \(bu 2
+\fIdel\fP orbitals which will be never occupied
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBcis/cis.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/cisd.1 b/man/cisd.1
new file mode 100644
index 00000000..d4d9cf71
--- /dev/null
+++ b/man/cisd.1
@@ -0,0 +1,67 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "CISD" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+cisd \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Configuration Interaction with Single and Double excitations.
+.INDENT 0.0
+.INDENT 3.5
+This program takes a reference Slater determinant of ROHF\-like occupancy,
+.sp
+and performs all single and double excitations on top of it, disregarding spatial symmetry and compute the “n_states” lowest eigenstates of that CI matrix (see \fBdeterminants n_states\fP).
+.sp
+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 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 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 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 having the good value S^2 value (see \fBdeterminants expected_s2\fP and \fBdeterminants s2_eig\fP). If “s2_eig” = False, it will take the lowest n_states, whatever multiplicity they are.
+.UNINDENT
+.sp
+Note: if you would like to discard some orbitals, use qp_set_mo_class to specify:
+.INDENT 0.0
+.IP \(bu 2
+“core” orbitals which will be always doubly occupied
+.IP \(bu 2
+“act” orbitals where an electron can be either excited from or to
+.IP \(bu 2
+“del” orbitals which will be never occupied
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBcisd/cisd.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/diagonalize_h.1 b/man/diagonalize_h.1
new file mode 100644
index 00000000..1b8cc7f8
--- /dev/null
+++ b/man/diagonalize_h.1
@@ -0,0 +1,49 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "DIAGONALIZE_H" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+diagonalize_h \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Program that extracts the \fBdeterminants n_states\fP lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder.
+.INDENT 0.0
+.INDENT 3.5
+If \fBdeterminants s2_eig\fP = True, it will retain only states
+.sp
+which corresponds to the desired value of \fBdeterminants expected_s2\fP\&.
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/diagonalize_h.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/fci.1 b/man/fci.1
new file mode 100644
index 00000000..c67e069c
--- /dev/null
+++ b/man/fci.1
@@ -0,0 +1,77 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "FCI" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+fci \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Selected Full Configuration Interaction with stochastic selection and PT2 .
+.INDENT 0.0
+.INDENT 3.5
+This program performs a CIPSI\-like selected CI using a stochastic scheme for both
+.sp
+the selection of the important Slater determinants and the computation of the PT2 correction.
+.sp
+This CIPSI\-like algorithm will be performed for the “n_states” lowest states of the variational space (see \fBdeterminants n_det_max\fP)
+.sp
+The fci program will stop when reaching at least one the two following conditions:
+.INDENT 0.0
+.IP \(bu 2
+number of Slater determinant > “n_det_max” (see \fBdeterminants n_det_max\fP)
+.IP \(bu 2
+PT2 < “pt2_max” (see \fBperturbation pt2_max\fP)
+.UNINDENT
+.sp
+The following other options can be of interest:
+.sp
+If “read_wf” = False, it starts with a ROHF\-like Slater determinant as a guess wave function.
+.sp
+If “read_wf” = True , it starts with the wave function(s) stored in the EZFIO folder as guess wave function(s).
+.sp
+(see \fBdeterminants read_wf\fP)
+.sp
+If “s2_eig” = True, it will systematically add all necessary Slater determinants in order
+.sp
+to have a pure spin wave function with an S^2 value corresponding to “expected_s2”.
+.sp
+(see \fBdeterminants s2_eig\fP and \fBdeterminants expected_s2\fP)
+.sp
+For excited states calculations, it is recommended to start with a \fBcis()\fP or \fBcisd()\fP guess wave functions
+.sp
+for the “n_states”, and to set “s2_eig” = True.
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBfci/fci.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/fcidump.1 b/man/fcidump.1
new file mode 100644
index 00000000..7f1ba044
--- /dev/null
+++ b/man/fcidump.1
@@ -0,0 +1,57 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "FCIDUMP" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+fcidump \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Produce a regular FCIDUMP file from the MOs stored in the \fI\%EZFIO\fP folder.
+.INDENT 0.0
+.INDENT 3.5
+To specify an active space, the class of the mos have to set in the \fI\%EZFIO\fP folder (see qp_set_mo_class).
+.sp
+The fcidump program supports 3 types of MO_class :
+.INDENT 0.0
+.IP \(bu 2
+the “core” orbitals which are always doubly occupied in the calculation
+.IP \(bu 2
+the “del” orbitals that are never occupied in the calculation
+.IP \(bu 2
+the “act” orbitals that will be occupied by a varying number of electrons
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/fcidump.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/four_idx_transform.1 b/man/four_idx_transform.1
new file mode 100644
index 00000000..56be245d
--- /dev/null
+++ b/man/four_idx_transform.1
@@ -0,0 +1,49 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "FOUR_IDX_TRANSFORM" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+four_idx_transform \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+4\-index transformation of two\-electron integrals from AO to MO integrals.
+.INDENT 0.0
+.INDENT 3.5
+This program will compute the two\-electron integrals on the MO basis and store it into the \fI\%EZFIO\fP folder.
+.sp
+This program can be useful if the AO –> MO transformation is an expensive step by itself.
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/four_idx_transform.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/ks_scf.1 b/man/ks_scf.1
new file mode 100644
index 00000000..255a970d
--- /dev/null
+++ b/man/ks_scf.1
@@ -0,0 +1,42 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "KS_SCF" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+ks_scf \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Produce \fIKohn_Sham\fP MO orbital output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ output: kohn_sham.energy optional: mo_basis.mo_coef
+.sp
+File: \fBkohn_sham/ks_scf.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/molden.1 b/man/molden.1
new file mode 100644
index 00000000..ebcde5e3
--- /dev/null
+++ b/man/molden.1
@@ -0,0 +1,42 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "MOLDEN" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+molden \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Produce a Molden file
+.sp
+File: \fBtools/molden.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/print_e_conv.1 b/man/print_e_conv.1
new file mode 100644
index 00000000..46e04817
--- /dev/null
+++ b/man/print_e_conv.1
@@ -0,0 +1,53 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "PRINT_E_CONV" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+print_e_conv \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+program that prints in a human readable format the convergence of the CIPSI algorithm.
+.INDENT 0.0
+.INDENT 3.5
+for all istate, this program produces
+.INDENT 0.0
+.IP \(bu 2
+a file “EZFIO.istate.conv” containing the variational and var+PT2 energies as a function of N_det
+.IP \(bu 2
+for istate > 1, a file EZFIO.istate.delta_e.conv containing the energy difference (both var and var+PT2) with the ground state as a function of N_det
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/print_e_conv.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/print_wf.1 b/man/print_wf.1
new file mode 100644
index 00000000..e8afba16
--- /dev/null
+++ b/man/print_wf.1
@@ -0,0 +1,51 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "PRINT_WF" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+print_wf \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Print the ground state wave function stored in the \fI\%EZFIO\fP folder in the intermediate normalization.
+.INDENT 0.0
+.INDENT 3.5
+It also prints a lot of information regarding the excitation operators from the reference determinant
+.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 :)
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/print_wf.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/printing.1 b/man/printing.1
new file mode 100644
index 00000000..8e66bfea
--- /dev/null
+++ b/man/printing.1
@@ -0,0 +1,83 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "PRINTING" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+printing \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Once obtained the near FCI energy, one can also take a closer look at the wave function stored in the \fI\%EZFIO\fP database.
+If the wave function contains less than 10^4 determinants, you can directly read it with the
+qp_edit command. Just run
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_edit file.ezfio
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+\fBIMPORTANT:\fP
+.INDENT 0.0
+.INDENT 3.5
+The qp_edit mode virtually makes human\-friendly the architecture of the \fI\%EZFIO\fP database
+through \fIvim\fP\-like editor.
+.UNINDENT
+.UNINDENT
+.sp
+Then, look for the word “hand” when you are in the qp_edit mode. If the research is negative,
+then it means that the wave function stored in the \fI\%EZFIO\fP database is too large to be edited
+interactively in qp_edit mode. An alternative is to use the \fBprint_wf\fP command:
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_run print_wf file.ezfio | tee file.ezfio.fci_natorb.wf
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.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 determinants, just change the \fBdeterminants n_det_print_wf\fP keyword using the qp_edit tool.
+.sp
+\fBSEE ALSO:\fP
+.INDENT 0.0
+.INDENT 3.5
+The documentation of the print_wf program.
+.UNINDENT
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/pt2.1 b/man/pt2.1
new file mode 100644
index 00000000..2a9b8fd3
--- /dev/null
+++ b/man/pt2.1
@@ -0,0 +1,51 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "PT2" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+pt2 \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Second order perturbative correction to the wave function contained in the EZFIO directory.
+.INDENT 0.0
+.INDENT 3.5
+This programs runs the stochastic PT2 correction on all “n_states” wave function stored in the EZFIO folder (see \fBdeterminant n_states\fP).
+.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)
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBfci/pt2.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/qp_update.1 b/man/qp_update.1
new file mode 100644
index 00000000..e54e5be5
--- /dev/null
+++ b/man/qp_update.1
@@ -0,0 +1,51 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "QP_UPDATE" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+qp_update \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+This command makes an update of the \fIQuantum Package\fP to the latest stable version.
+.SH USAGE
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_update [\-h]
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/qpsh.1 b/man/qpsh.1
new file mode 100644
index 00000000..8543f069
--- /dev/null
+++ b/man/qpsh.1
@@ -0,0 +1,115 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "QPSH" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+qpsh \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+\fBqpsh\fP is the \fIQuantum Package\fP shell. It is a 
+.nf
+|Bash|
+.fi
+ shell with all
+the required evironment variables loaded, a modified prompt, and the
+qp command.
+.sp
+This command reads the content of the \fI\%EZFIO\fP directory and creates a temporary
+file containing the data.  The data is presented as a \fIReStructured Text\fP (rst)
+document, where each section corresponds to the corresponding \fIQuantum Package\fP module.  The
+content of the file can be modified to change the input parameters.  When the
+text editor is closed, the updated data is saved into the \fI\%EZFIO\fP directory.
+.sp
+\fBNOTE:\fP
+.INDENT 0.0
+.INDENT 3.5
+The text editor which will be opened is defined by the \fBEDITOR\fP
+environment variable. If this variable is not set, the \fBvi\fP
+text editor will be used by default.
+.UNINDENT
+.UNINDENT
+.sp
+\fBWARNING:\fP
+.INDENT 0.0
+.INDENT 3.5
+When the wave function is too large (more than 10 000 determinants), the
+determinants are not displayed.
+.UNINDENT
+.UNINDENT
+.SH USAGE
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_edit [\-c] [\-h] [\-n <int>] [\-s <range>] [\-\-] EZFIO_DIR
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-c, \-\-check
+Checks the input data
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-h, \-\-help
+Print the help text and exits
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-n, \-\-ndet=<int>
+Truncates the wavefunction to the target number of determinants
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-s, \-\-state=<range>
+Select the states to extract from the \fI\%EZFIO\fP directory, using the same conventions
+as qp_set_mo_class\&. See example below.
+.UNINDENT
+.SH EXAMPLE
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_edit \-\-state="[1,3\-5]" test.ezfio
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+Removes all states except states 1,3,4 and 5 from \fBtest.ezfio\fP\&.  The
+resulting \fI\%EZFIO\fP directory has 4 states.
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/rs_ks_scf.1 b/man/rs_ks_scf.1
new file mode 100644
index 00000000..7f1ba0ab
--- /dev/null
+++ b/man/rs_ks_scf.1
@@ -0,0 +1,42 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "RS_KS_SCF" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+rs_ks_scf \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Produce \fIRange_separated_Kohn_Sham\fP MO orbital output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ output: kohn_sham.energy optional: mo_basis.mo_coef
+.sp
+File: \fBkohn_sham_rs/rs_ks_scf.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/save_natorb.1 b/man/save_natorb.1
new file mode 100644
index 00000000..2f9b59ca
--- /dev/null
+++ b/man/save_natorb.1
@@ -0,0 +1,53 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SAVE_NATORB" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+save_natorb \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Save natural MOs into the EZFIO
+.INDENT 0.0
+.INDENT 3.5
+This program reads the wave function stored in the EZFIO folder,
+.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).
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/save_natorb.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/save_one_e_dm.1 b/man/save_one_e_dm.1
new file mode 100644
index 00000000..e2cdb4ec
--- /dev/null
+++ b/man/save_one_e_dm.1
@@ -0,0 +1,49 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SAVE_ONE_E_DM" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+save_one_e_dm \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+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.
+.INDENT 0.0
+.INDENT 3.5
+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).
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/save_one_e_dm.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/save_ortho_mos.1 b/man/save_ortho_mos.1
new file mode 100644
index 00000000..54fcc06f
--- /dev/null
+++ b/man/save_ortho_mos.1
@@ -0,0 +1,51 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SAVE_ORTHO_MOS" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+save_ortho_mos \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Save orthonormalized MOs in the EZFIO.
+.INDENT 0.0
+.INDENT 3.5
+This program reads the current MOs, computes the corresponding overlap matrix in the MO basis
+.sp
+and perform a Lowdin orthonormalization : MO_{new} = S^{\-1/2} MO_{guess}\&.
+.sp
+Thanks to the Lowdin orthonormalization, the new MOs are the most similar to the guess MOs.
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBtools/save_ortho_mos.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/scf.1 b/man/scf.1
new file mode 100644
index 00000000..df26847e
--- /dev/null
+++ b/man/scf.1
@@ -0,0 +1,51 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SCF" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+scf \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Produce \fIHartree_Fock\fP MOs
+.INDENT 0.0
+.INDENT 3.5
+output: mo_basis.mo_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+.sp
+output: hartree_fock.energy
+.sp
+optional: mo_basis.mo_coef
+.UNINDENT
+.UNINDENT
+.sp
+File: \fBhartree_fock/scf.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.
diff --git a/man/write_integrals_erf.1 b/man/write_integrals_erf.1
new file mode 100644
index 00000000..06f28c7c
--- /dev/null
+++ b/man/write_integrals_erf.1
@@ -0,0 +1,42 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "WRITE_INTEGRALS_ERF" "1" "Jan 16, 2019" "2.0" "Quantum Package"
+.SH NAME
+write_integrals_erf \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Saves the two\-electron integrals with the erf(\emu r_{12})/r_{12} oprerator into the EZFIO folder
+.sp
+File: \fBtools/write_integrals_erf.irp.f\fP
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2018, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.