merge

INSTALL.rst

@@ -210,6 +210,12 @@ Zlib
    make
    make install
 
+With Debian or Ubuntu, you can use
+
+.. code:: bash
+
+   sudo apt install zlib1g-dev
+
 
 
 OCaml
@@ -217,6 +223,13 @@ OCaml
 
 *OCaml* is a general purpose programming language with an emphasis on expressiveness and safety.
 
+* The following packages are required (Debian or Ubuntu):
+
+  .. code:: bash
+
+    sudo apt install libncurses5-dev pkg-config libgmp3-dev m4
+
+
 * Download the installer of the OPAM package manager here :
   `<https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh>`_
   and move it in the :file:`${QP_ROOT}/external` directory

REPLACE

@@ -183,3 +183,17 @@ qp_name save_one_body_dm -r save_one_e_dm
 qp_name ezfio_set_aux_quantities_data_one_e_alpha_dm_mo -r ezfio_set_aux_quantities_data_one_e_dm_alpha_mo
 qp_name ezfio_set_aux_quantities_data_one_e_beta_dm_mo -r ezfio_set_aux_quantities_data_one_e_dm_beta_mo
 qp_name two_electron_energy -r two_e_energy
+qp_name do_mono_excitation -r do_single_excitation
+qp_name get_mono_excitation -r get_single_excitation
+qp_name get_mono_excitation_from_fock -r get_single_excitation_from_fock
+qp_name is_connected_to_by_mono -r is_connected_to_by_single
+qp_name connected_to_ref_by_mono -r connected_to_ref_by_single
+qp_name mono_excitation_wee -r single_excitation_wee
+qp_name get_mono_excitation_spin
+qp_name get_mono_excitation_spin -r get_single_excitation_spin
+qp_name get_excitation_degree_vector_mono -r get_excitation_degree_vector_single
+qp_name get_excitation_degree_vector_mono_or_exchange -r get_excitation_degree_vector_single_or_exchange_or_exchange
+qp_name get_excitation_degree_vector_single_or_exchange_or_exchange -r get_excitation_degree_vector_single_or_exchange
+qp_name get_excitation_degree_vector_mono_or_exchange_verbose -r get_excitation_degree_vector_single_or_exchange_verbose
+qp_name i_h_j_mono_spin -r i_h_j_single_spin
+qp_name i_Wee_j_mono -r i_Wee_j_single

TODO

@@ -49,8 +49,6 @@ Refaire les benchmarks
 # Documentation de qpsh
 
 # Documentation de /etc
-# Extrapolation qui prend aussi en compe la variance? a tester
-Parler dans le papier de rPT2
 
 # Toto
 Re-design de qp command
@@ -58,3 +56,5 @@ Re-design de qp command
 Doc: plugins et qp_plugins
 
 Ajouter les symetries dans devel
+
+Compiler ezfio avec openmp

bin/qp_export_as_tgz

@@ -154,7 +154,7 @@ for i in ${FORTRAN_EXEC} ; do
 done > ${QPACKAGE_STATIC}/data/executables
 
 mkdir --parents -- ${QPACKAGE_STATIC}/src/bitmask
-cp ${QP_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/bitmask
+cp ${QP_ROOT}/src/bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/bitmask
 
 
 echo "Copying dynamic libraries"
@@ -179,7 +179,7 @@ if [[ $? -ne 0 ]] ; then
   exit 1
 fi
 
-cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} \
+cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*,gfortran*,quad*} \
    ${QPACKAGE_STATIC}/lib/
 
 #

config/gfortran.cfg

@@ -35,7 +35,7 @@ OPENMP  : 1          ; Append OpenMP flags
 #                           -ffast-math and the Fortran-specific
 #                           -fno-protect-parens and -fstack-arrays.
 [OPT]
-FCFLAGS : -Ofast -msse4.2
+FCFLAGS : -Ofast -march=native
 
 # Profiling flags
 #################

configure

@@ -353,23 +353,24 @@ EOF
 
 
 done
-        
+
+source quantum_package.rc
 
 NINJA=$(find_exe ninja)
 if [[ ${NINJA} = $(not_found) ]] ; then
-        error "Ninja is not installed."
+        error "Ninja (ninja) is not installed."
         fail
 fi
 
 IRPF90=$(find_exe irpf90)
 if [[ ${IRPF90} = $(not_found) ]] ; then
-        error "IRPf90 is not installed."
+        error "IRPf90 (irpf90) is not installed."
         fail
 fi
 
 ZEROMQ=$(find_lib -lzmq)
 if [[ ${ZEROMQ} = $(not_found) ]] ; then
-        error "ZeroMQ is not installed."
+        error "ZeroMQ (zeromq) is not installed."
         fail
 fi
 
@@ -387,31 +388,31 @@ fi
 
 OCAML=$(find_exe ocaml)
 if [[ ${OCAML} = $(not_found) ]] ; then
-        error "OCaml compiler is not installed."
+        error "OCaml (ocaml) compiler is not installed."
         fail
 fi
 
 EZFIO=$(find_dir "${QP_ROOT}"/external/ezfio)
 if [[ ${EZFIO} = $(not_found) ]] ; then
-        error "EZFIO is not installed."
+        error "EZFIO (ezfio) is not installed."
         fail
 fi
 
 ZLIB=$(find_lib -lz)
 if [[ ${ZLIB} = $(not_found) ]] ; then
-        error "Zlib is not installed."
+        error "Zlib (zlib) is not installed."
         fail
 fi
 
 DOCOPT=$(find_python_lib docopt)
 if [[ ${DOCOPT} = $(not_found) ]] ; then
-        error "docopt is not installed."
+        error "docopt (docopt) is not installed."
         fail
 fi
 
 RESULTSFILE=$(find_python_lib resultsFile)
 if [[ ${RESULTSFILE} = $(not_found) ]] ; then
-        error "resultsFile is not installed."
+        error "resultsFile (resultsFile) is not installed."
         fail
 fi
 

docs/source/_static/links.rst

@@ -12,7 +12,6 @@
 .. _Irene: http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm
 .. _IRPF90: http://irpf90.ups-tlse.fr
 .. _LAPACK: http://www.netlib.org/lapack/
-.. _Molden: http://cheminf.cmbi.ru.nl/molden/
 .. _NECI: https://github.com/ghb24/NECI_STABLE
 .. _Ninja: https://ninja-build.org/
 .. _NWChem: http://www.nwchem-sw.org/
@@ -53,12 +52,15 @@
 .. |CIPSI| replace:: :abbr:`CIPSI (Configuration Interaction using a Perturbative Selection)`
 .. |CI| replace:: :abbr:`CI (Configuration Interaction)`
 .. |CISD| replace:: :abbr:`CISD (Configuration Interaction with Single and Double Excitations)`
+.. |CASSCF| replace:: |CAS| - |SCF|
 .. |CIS| replace:: :abbr:`CIS (Configuration Interaction with Single Excitations)`
-.. |DFT| replace:: :abbr:`DFT (Density Functional Theory)`
 .. |DDCI| replace:: :abbr:`DDCI (Difference Dedicated Configuration Interaction)`
+.. |DFT| replace:: :abbr:`DFT (Density Functional Theory)`
 .. |DIIS| replace:: :abbr:`DIIS (Direct Inversion of the Iterative Subspace)`
+.. |FCIQMC| replace:: |FCI| - |QMC|
 .. |FCI| replace:: :abbr:`FCI (Full Configuration Interaction)`
 .. |HF| replace:: :abbr:`HF (Hartree-Fock)`
+.. |KS-DFT| replace:: :abbr:`KS-DFT (Kohn-Sham Density Functional Theory)`
 .. |MO| replace:: :abbr:`MO (Molecular Orbital)`
 .. |MOs| replace:: :abbr:`MOs (Molecular Orbitals)`
 .. |MP2| replace:: :abbr:`MP2 (Moller-Plesset second order perturbative correction)`
@@ -67,15 +69,13 @@
 .. |MRPT| replace:: :abbr:`MRPT (Multi-Reference Perturbation Theory)`
 .. |PT2| replace:: :abbr:`PT2 (Second order perturbative correction)`
 .. |QMC| replace:: :abbr:`QMC (Quantum Monte Carlo)`
+.. |ROHF| replace:: :abbr:`ROHF (Restricted Open-Shell Hartree-Fock)`
+.. |RSDFT| replace:: :abbr:`RSDFT (Range Separated Density Functional Theory)`
+.. |RSH| replace:: :abbr:`RSH (Range Separated Hybrids)`
 .. |rst| replace:: :abbr:`RST (ReStructured Text)`
 .. |SCF| replace:: :abbr:`SCF (Self Consistent Field)`
-.. |RSH| replace:: :abbr:`RSH (Range Separated Hybrids)`
-.. |RSDFT| replace:: :abbr:`RSDFT (Range Separated Density Functional Theory)`
-.. |KS-DFT| replace:: :abbr:`KS-DFT (Kohn-Sham Density Functional Theory)`
 .. |sCI| replace:: :abbr:`sCI (Selected-CI)`
 .. |WFT| replace:: :abbr:`WFT (Wave Function Theory)`
-.. |CASSCF| replace:: |CAS| - |SCF|
-.. |FCIQMC| replace:: |FCI| - |QMC|
 
 .. |kalpha| replace:: :math:`|\alpha \rangle`
 .. |H| replace:: :math:`\hat H`

docs/source/conf.py

@@ -171,7 +171,7 @@ for f in os.listdir("users_guide"):
 
 for f in os.listdir("programs"):
   name = f.split('.')[0]
-  if name not in []:
+  if name not in [""]:
     filename = os.path.join("programs",name)
     man_pages.append( (filename, name, qpdoc, [author], 1) )
 

docs/source/intro/selected_ci.rst

@@ -55,8 +55,6 @@ Simple Algorithm
 
 .. |SetDI| replace:: `\{|D_I\rangle\}^{(n)}`
 .. |Psi_n| replace:: `|\Psi^{(n)}\rangle`
-.. |H| replace:: `\hat H`
-.. |kalpha| replace:: `|\alpha\rangle`
 .. |kalpha_star| replace:: `\{ |\alpha \rangle \}_\star ^{(n)}`
 .. |ealpha| replace:: `e_\alpha`
 .. |EPT| replace:: `E_\text{PT2}`

docs/source/modules/ao_basis.rst

@@ -23,9 +23,13 @@ The |AO| coefficients are normalized as:
 
   {\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c  e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2 dr}
 
-Warning: `ao_coef` contains the |AO| coefficients given in input. These do not
+
-include the normalization constant of the |AO|. The `ao_coef_normalized` provider includes
+.. warning::
-this normalization factor.
+
+  `ao_coef` contains the |AO| coefficients given in input. These do not
+  include the normalization constant of the |AO|. The `ao_coef_normalized`
+  provider includes this normalization factor.
+
 
 The |AOs| are also sorted by increasing exponent to accelerate the calculation of
 the two electron integrals.
@@ -1076,7 +1080,7 @@ Subroutines / functions
         double precision function ao_value(i,r)
 
 
-    return the value of the ith ao at point r
+    Returns the value of the i-th ao at point $\textbf{r}$
 
     Needs:
 
@@ -1101,9 +1105,12 @@ Subroutines / functions
         subroutine give_all_aos_and_grad_and_lapl_at_r(r,aos_array,aos_grad_array,aos_lapl_array)
 
 
-    input      : r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    input  : r(1) ==> r(1) = x, r(2) = y, r(3) = z
-    output     : aos_array(i) = ao(i) evaluated at r
+    
-               : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r
+    output :
+    
+    * aos_array(i) = ao(i) evaluated at $\textbf{r}$
+    * aos_grad_array(1,i) = $\nabla_x$ of the ao(i) evaluated at $\textbf{r}$
 
     Needs:
 
@@ -1138,9 +1145,13 @@ Subroutines / functions
         subroutine give_all_aos_and_grad_at_r(r,aos_array,aos_grad_array)
 
 
-    input      : r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    input : r(1) ==> r(1) = x, r(2) = y, r(3) = z
-    output     : aos_array(i) = ao(i) evaluated at r
+    
-               : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r
+    output :
+    
+    * aos_array(i) = ao(i) evaluated at ro
+    * aos_grad_array(1,i) = gradient X of the ao(i) evaluated at $\textbf{r}$
+    
 
     Needs:
 
@@ -1175,8 +1186,9 @@ Subroutines / functions
         subroutine give_all_aos_at_r(r,aos_array)
 
 
-    input : r == r(1) = x and so on
+    input  : r == r(1) = x and so on
-    aos_array(i) = aos(i) evaluated in r
+    
+    output : aos_array(i) = aos(i) evaluated in $\textbf{r}$
 
     Needs:
 
@@ -1211,7 +1223,7 @@ Subroutines / functions
         subroutine give_all_aos_at_r_old(r,aos_array)
 
 
-    gives the values of aos at a given point r
+    Gives the values of |AOs| at a given point $\textbf{r}$
 
     Needs:
 
@@ -1231,7 +1243,8 @@ Subroutines / functions
         double precision function primitive_value(i,j,r)
 
 
-    return the value of the jth primitive of ith ao at point r WITHOUT THE COEF
+    Returns the value of the j-th primitive of the i-th |AO| at point $\textbf{r}
+    **without the coefficient**
 
     Needs:
 

docs/source/modules/ao_one_e_ints.rst

@@ -232,8 +232,10 @@ Providers
 
     Second derivative matrix elements in the |AO| basis.
     
-    :math:`{\tt ao\_deriv2\_x} =
+    .. math::
-     \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle`
+    
+      {\tt ao\_deriv2\_x} =
+      \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
     
 
     Needs:
@@ -271,8 +273,10 @@ Providers
 
     Second derivative matrix elements in the |AO| basis.
     
-    :math:`{\tt ao\_deriv2\_x} =
+    .. math::
-     \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle`
+    
+      {\tt ao\_deriv2\_x} =
+      \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
     
 
     Needs:
@@ -310,8 +314,10 @@ Providers
 
     Second derivative matrix elements in the |AO| basis.
     
-    :math:`{\tt ao\_deriv2\_x} =
+    .. math::
-     \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle`
+    
+      {\tt ao\_deriv2\_x} =
+      \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
     
 
     Needs:
@@ -642,7 +648,8 @@ Providers
 
     Kinetic energy integrals in the |AO| basis.
     
-    :math:`\langle \chi_i |\hat{T}| \chi_j \rangle`
+    :math:`\langle \chi_i |\hat{T}| \chi_j \rangle` 
+    
 
     Needs:
 
@@ -1331,7 +1338,8 @@ Providers
       power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in)
 
 
-    Returns the explicit polynomial in terms of the $t$ variable of the following polynomial:
+    Returns the explicit polynomial in terms of the $t$ variable of the
+    following polynomial:
     
     $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$.
 
@@ -1355,7 +1363,8 @@ Providers
       power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in,p,p_inv,p_inv_2,p_new,P_center)
 
 
-    Returns the explicit polynomial in terms of the $t$ variable of the following polynomial:
+    Returns the explicit polynomial in terms of the $t$ variable of the
+    following polynomial:
     
     $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$.
 
@@ -1724,7 +1733,7 @@ Subroutines / functions
 
 
     Subroutine that returns all integrals over $r$ of type
-    $\frac{ \erf(\mu * |r-R_C|) }{ |r-R_C| }$
+    $\frac{ \erf(\mu * | r - R_C | ) }{ | r - R_C | }$
 
     Needs:
 
@@ -1812,8 +1821,12 @@ Subroutines / functions
 
 
     Computes the following integral :
-    $\int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 )
+    
-     \frac{\erf(\mu |r-R_C|)}{|r-R_c|}$.
+    .. math::
+    
+      \int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 )
+      \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$.
+    
 
     Calls:
 
@@ -1834,7 +1847,7 @@ Subroutines / functions
 
 
     Computes the following integral :
-    $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu |r-R_C|)}{|r-R_C|}$.
+    $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$.
 
     Needs:
 

docs/source/modules/ao_two_e_erf_ints.rst

@@ -587,11 +587,13 @@ Subroutines / functions
         double precision function ERI_erf(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z)
 
 
-    ATOMIC PRIMTIVE two-electron integral between the 4 primitives ::
+    Atomic primtive two-electron integral between the 4 primitives :
-           primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
+    
-           primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
+    * primitive 1 : $x_1^{a_x} y_1^{a_y} z_1^{a_z} \exp(-\alpha * r1^2)$
-           primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
+    * primitive 2 : $x_1^{b_x} y_1^{b_y} z_1^{b_z} \exp(- \beta * r1^2)$
-           primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
+    * primitive 3 : $x_2^{c_x} y_2^{c_y} z_2^{c_z} \exp(-\delta * r2^2)$
+    * primitive 4 : $x_2^{d_x} y_2^{d_y} z_2^{d_z} \exp(-\gamma * r2^2)$
+    
 
     Needs:
 
@@ -776,9 +778,11 @@ Subroutines / functions
         subroutine integrale_new_erf(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt)
 
 
-    calculate the integral of the polynom ::
+    Calculate the integral of the polynomial :
-            I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
+    
-    between ( 0 ; 1)
+    $I_x1(a_x+b_x, c_x+d_x,p,q) \, I_x1(a_y+b_y, c_y+d_y,p,q) \, I_x1(a_z+b_z, c_z+d_z,p,q)$
+    
+    between $( 0 ; 1)$
 
     Needs:
 

docs/source/modules/ao_two_e_ints.rst

@@ -362,7 +362,7 @@ Providers
         recursive subroutine I_x1_pol_mult_a1(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
 
 
-    recursive function involved in the two-electron integral
+    Recursive function involved in the two-electron integral
 
     Called by:
 
@@ -392,7 +392,7 @@ Providers
         recursive subroutine I_x1_pol_mult_a2(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
 
 
-    recursive function involved in the two-electron integral
+    Recursive function involved in the two-electron integral
 
     Called by:
 
@@ -422,7 +422,7 @@ Providers
         recursive subroutine I_x1_pol_mult_recurs(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
 
 
-    recursive function involved in the two-electron integral
+    Recursive function involved in the two-electron integral
 
     Called by:
 
@@ -487,7 +487,7 @@ Providers
         recursive subroutine I_x2_pol_mult(c,B_10,B_01,B_00,C_00,D_00,d,nd,dim)
 
 
-    recursive function involved in the two-electron integral
+    Recursive function involved in the two-electron integral
 
     Called by:
 
@@ -1027,7 +1027,8 @@ Subroutines / functions
 
     subroutine that returns the explicit polynom in term of the "t"
     variable of the following polynomw :
-            I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
+    
+    $I_{x_1}(a_x,d_x,p,q) \, I_{x_1}(a_y,d_y,p,q) \ I_{x_1}(a_z,d_z,p,q)$
 
     Called by:
 
@@ -1055,7 +1056,7 @@ Subroutines / functions
         subroutine I_x1_pol_mult(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
 
 
-    recursive function involved in the two-electron integral
+    Recursive function involved in the two-electron integral
 
     Called by:
 
@@ -1119,9 +1120,10 @@ Subroutines / functions
         subroutine integrale_new(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt)
 
 
-    calculate the integral of the polynom ::
+    Calculates the integral of the polynomial :
-            I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
+    
-    between ( 0 ; 1)
+    $I_{x_1}(a_x+b_x,c_x+d_x,p,q) \, I_{x_1}(a_y+b_y,c_y+d_y,p,q) \, I_{x_1}(a_z+b_z,c_z+d_z,p,q)$
+    in $( 0 ; 1)$
 
     Needs:
 
@@ -1186,8 +1188,9 @@ Subroutines / functions
 
 
     Returns the upper boundary of the degree of the polynomial involved in the
-    bielctronic integral :
+    two-electron integral :
-          Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
+    
+    $I_x(a_x,b_x,c_x,d_x) \, I_y(a_y,b_y,c_y,d_y) \, I_z(a_z,b_z,c_z,d_z)$
 
  
 .. c:function:: push_integrals:

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
+* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which
-  one-body alpha and beta densities which are necessary read from the EZFIO
+  are the one-body alpha and beta densities which are necessary read from the
-  folder.
+  |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/cipsi.rst

@@ -49,7 +49,7 @@ By default, the program will stop when more than one million determinants have
 been selected, or when the |PT2| energy is below :math:`10^{-4}`.
 
 The variational and |PT2| energies of the iterations are stored in the
-|EZFIO| database, in the :ref:`iterations` module.
+|EZFIO| database, in the :ref:`module_iterations` module.
 
 
 
@@ -180,55 +180,6 @@ Providers
 
 
  
-.. c:function:: pt2_collector:
-
-
-    File : :file:`cipsi/pt2_stoch_routines.irp.f`
-
-    .. code:: fortran
-
-        subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
-  variance, norm, b, N_)
-
-
-
-    Needs:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:data:`pt2_j`
-       * :c:data:`pt2_stoch_istate`
-       * :c:data:`n_states`
-       * :c:data:`pt2_f`
-       * :c:data:`pt2_w`
-       * :c:data:`n_det_generators`
-       * :c:data:`pt2_n_teeth`
-       * :c:data:`pt2_u`
-
-    Called by:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:func:`zmq_pt2`
-
-    Calls:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:func:`add_to_selection_buffer`
-       * :c:func:`check_mem`
-       * :c:func:`create_selection_buffer`
-       * :c:func:`delete_selection_buffer`
-       * :c:func:`end_zmq_to_qp_run_socket`
-       * :c:func:`pull_pt2_results`
-       * :c:func:`sleep`
-       * :c:func:`sort_selection_buffer`
-       * :c:func:`wall_time`
-
- 
 .. c:var:: pt2_cw
 
 
@@ -311,7 +262,6 @@ Providers
        * :c:data:`n_core_orb`
        * :c:data:`n_det_generators`
        * :c:data:`n_det_selectors`
-       * :c:data:`n_states`
        * :c:data:`psi_det_sorted_gen`
 
 
@@ -455,7 +405,6 @@ Providers
        * :c:data:`n_core_orb`
        * :c:data:`n_det_generators`
        * :c:data:`n_det_selectors`
-       * :c:data:`n_states`
        * :c:data:`psi_det_sorted_gen`
 
 
@@ -1164,6 +1113,54 @@ Subroutines / functions
        * :c:func:`run_slave_cipsi`
 
  
+.. c:function:: pt2_collector:
+
+
+    File : :file:`cipsi/pt2_stoch_routines.irp.f`
+
+    .. code:: fortran
+
+        subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, variance, norm, b, N_)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_j`
+       * :c:data:`pt2_stoch_istate`
+       * :c:data:`n_states`
+       * :c:data:`pt2_f`
+       * :c:data:`pt2_w`
+       * :c:data:`n_det_generators`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_u`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`zmq_pt2`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`add_to_selection_buffer`
+       * :c:func:`check_mem`
+       * :c:func:`create_selection_buffer`
+       * :c:func:`delete_selection_buffer`
+       * :c:func:`end_zmq_to_qp_run_socket`
+       * :c:func:`pull_pt2_results`
+       * :c:func:`sleep`
+       * :c:func:`sort_selection_buffer`
+       * :c:func:`wall_time`
+
+ 
 .. c:function:: pt2_find_sample:
 
 
@@ -1633,21 +1630,31 @@ Subroutines / functions
     .. hlist::
        :columns: 3
 
+       * :c:data:`pt2_stoch_istate`
+       * :c:data:`psi_det`
+       * :c:data:`zmq_state`
        * :c:data:`psi_coef`
        * :c:data:`mpi_rank`
-       * :c:data:`zmq_state`
-       * :c:data:`state_average_weight`
        * :c:data:`mpi_master`
-       * :c:data:`pt2_stoch_istate`
-       * :c:data:`n_states`
        * :c:data:`n_det`
-       * :c:data:`pt2_e0_denominator`
-       * :c:data:`n_det_selectors`
-       * :c:data:`n_det_generators`
-       * :c:data:`psi_det`
-       * :c:data:`n_states_diag`
        * :c:data:`zmq_context`
+       * :c:data:`n_det_selectors`
+       * :c:data:`psi_occ_pattern_hii`
+       * :c:data:`state_average_weight`
+       * :c:data:`mo_num`
+       * :c:data:`nthreads_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`pt2_e0_denominator`
+       * :c:data:`qp_max_mem`
+       * :c:data:`n_states_diag`
+       * :c:data:`s2_eig`
        * :c:data:`threshold_generators`
+       * :c:data:`det_to_occ_pattern`
+       * :c:data:`n_states`
+       * :c:data:`pt2_f`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_int`
+       * :c:data:`psi_det_hii`
 
     Called by:
 
@@ -1661,9 +1668,11 @@ Subroutines / functions
     .. hlist::
        :columns: 3
 
+       * :c:func:`check_mem`
        * :c:func:`davidson_slave_tcp`
        * :c:func:`mpi_print`
        * :c:func:`omp_set_nested`
+       * :c:func:`resident_memory`
        * :c:func:`run_pt2_slave`
        * :c:func:`run_selection_slave`
        * :c:func:`sleep`
@@ -1832,13 +1841,12 @@ Subroutines / functions
        * :c:data:`n_states`
        * :c:data:`n_det`
        * :c:data:`psi_bilinear_matrix_transp_values`
-       * :c:data:`elec_alpha_num`
+       * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`n_det_selectors`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`n_int`
        * :c:data:`psi_det_generators`
-       * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`psi_det_alpha_unique`
        * :c:data:`psi_det_sorted`
        * :c:data:`psi_det_sorted`
@@ -1859,7 +1867,6 @@ Subroutines / functions
 
        * :c:func:`apply_hole`
        * :c:func:`bitstring_to_list_ab`
-       * :c:func:`check_mem`
        * :c:func:`fill_buffer_double`
        * :c:func:`get_excitation_degree_spin`
        * :c:func:`isort`
@@ -2103,14 +2110,15 @@ Subroutines / functions
        * :c:data:`pt2_stoch_istate`
        * :c:data:`psi_selectors`
        * :c:data:`psi_bilinear_matrix_values`
-       * :c:data:`psi_det_alpha_unique`
+       * :c:data:`psi_occ_pattern_hii`
        * :c:data:`pt2_e0_denominator`
        * :c:data:`pt2_n_teeth`
        * :c:data:`psi_selectors_coef_transp`
        * :c:data:`n_det`
+       * :c:data:`mo_two_e_integrals_in_map`
        * :c:data:`s2_eig`
        * :c:data:`pt2_j`
-       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`psi_det_alpha_unique`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`state_average_weight`
        * :c:data:`mo_num`
@@ -2119,16 +2127,18 @@ Subroutines / functions
        * :c:data:`mo_one_e_integrals`
        * :c:data:`elec_alpha_num`
        * :c:data:`nproc`
+       * :c:data:`qp_max_mem`
        * :c:data:`psi_bilinear_matrix_columns_loc`
        * :c:data:`threshold_generators`
        * :c:data:`psi_det_beta_unique`
-       * :c:data:`qp_max_mem`
+       * :c:data:`det_to_occ_pattern`
        * :c:data:`psi_bilinear_matrix_transp_rows_loc`
        * :c:data:`n_states`
        * :c:data:`pt2_f`
        * :c:data:`n_det_generators`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`n_int`
+       * :c:data:`psi_det_hii`
        * :c:data:`pt2_j`
        * :c:data:`psi_det_sorted`
        * :c:data:`pt2_w`

docs/source/modules/cis.rst

@@ -8,34 +8,39 @@
 cis
 ===
 
-This module contains a CIS program.
+This module contains a |CIS| program.
 
 The user point of view
 ----------------------
 
-The :command:`cis` program performs the CI of the ROHF-like + all single excitations on top of it.
+The :ref:`cis` program performs the CI to obtain the ROHF reference + all
-This program can be very useful to :
+single excitations on top of it. This program can be very useful to:
 
-* **Ground state calculations**: generate a guess for the ground state wave function if one is not sure that the :c:func:`scf` program gave the lowest SCF solution. In combination with :c:func:`save_natorb` it can produce new |MOs| in order to reperform an :c:func:`scf` optimization.
+* **Ground state calculations**: generate a guess for the ground state wave
+  function if one is not sure that the :ref:`scf` program gave the lowest |SCF|
+  solution. In combination with :ref:`save_natorb` it can produce new |MOs| in
+  order to reperform an :ref:`scf` optimization.
 
-* **Excited states calculations**: generate guess for all the :option:`determinants n_states` wave functions, that will be used by the :c:func:`fci` program.
+* **Excited states calculations**: generate guesses for all the
+  :option:`determinants n_states` wave functions, that will be used by the
+  :ref:`fci` program.
 
 
 The main keywords/options to be used are:
 
-* :option:`determinants n_states` : number of states to consider for the |CIS| calculation
+* :option:`determinants n_states`: number of states to consider for the |CIS| calculation
 
-* :option:`determinants s2_eig` : force all states to have the desired value of :math:`S^2`
+* :option:`determinants s2_eig`: force all states to have the desired value of |S^2|
 
-* :option:`determinants expected_s2` : desired value of :math:`S^2`
+* :option:`determinants expected_s2`: desired value of |S^2|
 
 
 
 
-The programmer point of view
+The programmer's point of view
-----------------------------
+------------------------------
 
-This module have been built by setting the following rules:
+This module was built by setting the following rules:
 
 * The only generator determinant is the Hartree-Fock (single-reference method)
 * All generated singly excited determinants are included in the wave function (no perturbative

docs/source/modules/davidson.rst

@@ -9,15 +9,22 @@ davidson
 ========
 
 Abstract module for Davidson's diagonalization.
-It contains everything required for the Davidson algorithm, dressed or not. If
+It contains everything required for the Davidson algorithm, dressed or
-a dressing is used, the dressing column should be defined and the
+not. If a dressing is used, the dressing column should be defined and
-:ref:`davidson_dressed` module should be used. If no dressing is required,
+the :ref:`module_davidson_dressed` module should be used. If no dressing
-the :ref:`davidson` module should be used, and it has a default zero dressing vector.
+is required, the :ref:`module_davidson` module should be used, and it
+has a default zero dressing vector.
 
 The important providers for that module are:
 
-# `psi_energy` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the Hamiltonian, dressed or not. It uses the general subroutine `u_0_H_u_0`.
+#. :c:data:`psi_energy` which is the expectation value over the wave
-# `psi_energy_two_e` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the standard two-electrons coulomb operator. It uses the general routine `u_0_H_u_0_two_e`.
+   function (:c:data:`psi_det`, :c:data:`psi_coef`) of the Hamiltonian,
+   dressed or not. It uses the general subroutine :c:func:`u_0_H_u_0`.
+
+#. :c:data:`psi_energy_two_e` which is the expectation value over the
+   wave function (:c:data:`psi_det`, :c:data:`psi_coef`) of the standard
+   two-electron Coulomb operator. It uses the general routine
+   :c:func:`u_0_H_u_0_two_e`.
  
  
  
@@ -40,7 +47,7 @@ EZFIO parameters
  
     Number of micro-iterations before re-contracting
  
-    Default: 8
+    Default: 15
  
 .. option:: state_following
  
@@ -585,7 +592,6 @@ Subroutines / functions
        * :c:data:`psi_det_beta_unique`
        * :c:data:`only_expected_s2`
        * :c:data:`distributed_davidson`
-       * :c:data:`n_states`
        * :c:data:`n_int`
 
     Called by:
@@ -626,7 +632,6 @@ Subroutines / functions
     .. hlist::
        :columns: 3
 
-       * :c:data:`n_states_diag`
        * :c:data:`nthreads_davidson`
 
  
@@ -682,7 +687,6 @@ Subroutines / functions
     .. hlist::
        :columns: 3
 
-       * :c:data:`n_states_diag`
        * :c:data:`nthreads_davidson`
 
  
@@ -696,7 +700,7 @@ Subroutines / functions
         subroutine davidson_pull_results(zmq_socket_pull, v_t, s_t, imin, imax, task_id)
 
 
-    Pull the results of $H|U \rangle$ on the master.
+    Pull the results of $H | U \rangle$ on the master.
 
     Needs:
 
@@ -724,7 +728,7 @@ Subroutines / functions
         subroutine davidson_push_results(zmq_socket_push, v_t, s_t, imin, imax, task_id)
 
 
-    Push the results of $H|U \rangle$ from a worker to the master.
+    Push the results of $H | U \rangle$ from a worker to the master.
 
     Needs:
 
@@ -850,6 +854,7 @@ Subroutines / functions
        :columns: 3
 
        * :c:data:`psi_det_beta_unique`
+       * :c:data:`mpi_rank`
        * :c:data:`psi_bilinear_matrix_order_transp_reverse`
        * :c:data:`psi_det_alpha_unique`
        * :c:data:`mpi_initialized`
@@ -858,6 +863,7 @@ Subroutines / functions
        * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`nproc`
        * :c:data:`ref_bitmask_energy`
+       * :c:data:`n_states_diag`
        * :c:data:`psi_bilinear_matrix_columns_loc`
 
     Called by:
@@ -874,7 +880,6 @@ Subroutines / functions
 
        * :c:func:`davidson_push_results`
        * :c:func:`h_s2_u_0_nstates_openmp_work`
-       * :c:func:`sleep`
 
  
 .. c:function:: diagonalize_ci:
@@ -934,7 +939,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp(v_0,s_0,u_0,N_st,sze)
 
 
-    Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$.
+    Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2  | u_0\rangle$.
     
     Assumes that the determinants are in psi_det
     
@@ -977,7 +982,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$
+    Computes $v_t = H | u_t\rangle$ and $s_t = S^2  | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1020,7 +1025,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work_1(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1072,7 +1077,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work_2(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1124,7 +1129,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work_3(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1176,7 +1181,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work_4(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1228,7 +1233,7 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_openmp_work_N_int(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1280,13 +1285,13 @@ Subroutines / functions
         subroutine H_S2_u_0_nstates_zmq(v_0,s_0,u_0,N_st,sze)
 
 
-    Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$
+    Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2  | u_0\rangle$
     
     n : number of determinants
     
-    H_jj : array of $\langle j|H|j \rangle$
+    H_jj : array of $\langle j | H | j \rangle$
     
-    S2_jj : array of $\langle j|S^2|j \rangle$
+    S2_jj : array of $\langle j | S^2 | j \rangle$
 
     Needs:
 
@@ -1303,7 +1308,6 @@ Subroutines / functions
        * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`nproc`
        * :c:data:`ref_bitmask_energy`
-       * :c:data:`n_states_diag`
        * :c:data:`psi_bilinear_matrix_columns_loc`
 
     Called by:
@@ -1327,13 +1331,6 @@ Subroutines / functions
        * :c:func:`new_parallel_job`
        * :c:func:`omp_set_nested`
 
-    Touches:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:data:`n_states_diag`
-
  
 .. c:function:: h_s2_u_0_two_e_nstates_openmp:
 
@@ -1345,7 +1342,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp(v_0,s_0,u_0,N_st,sze)
 
 
-    Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$
+    Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$
     
     Assumes that the determinants are in psi_det
     
@@ -1387,7 +1384,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$
+    Computes $v_t = H | u_t\rangle$ and $s_t = S^2 | u_t\rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1429,7 +1426,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work_1(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2  | u_t \rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1479,7 +1476,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work_2(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2  | u_t \rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1529,7 +1526,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work_3(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2  | u_t \rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1579,7 +1576,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work_4(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2  | u_t \rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1629,7 +1626,7 @@ Subroutines / functions
         subroutine H_S2_u_0_two_e_nstates_openmp_work_N_int(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
 
 
-    Computes $v_t = H|u_t
angle$ and $s_t = S^2 |u_t
angle$
+    Computes $v_t = H | u_t \rangle$ and $s_t = S^2  | u_t \rangle$
     
     Default should be 1,N_det,0,1
 
@@ -1679,9 +1676,9 @@ Subroutines / functions
         subroutine u_0_H_u_0(e_0,s_0,u_0,n,keys_tmp,Nint,N_st,sze)
 
 
-    Computes $E_0 = \frac{\langle u_0|H|u_0 \rangle}{\langle u_0|u_0 \rangle}$
+    Computes $E_0 = \frac{\langle u_0 | H | u_0 \rangle}{\langle u_0 | u_0 \rangle}$
     
-    and      $S_0 = \frac{\langle u_0|S^2|u_0 \rangle}{\langle u_0|u_0 \rangle}$
+    and      $S_0 = \frac{\langle u_0 | S^2 | u_0 \rangle}{\langle u_0 | u_0 \rangle}$
     
     n : number of determinants
     
@@ -1692,7 +1689,6 @@ Subroutines / functions
        :columns: 3
 
        * :c:data:`n_states_diag`
-       * :c:data:`n_states`
        * :c:data:`distributed_davidson`
 
     Called by:
@@ -1710,13 +1706,6 @@ Subroutines / functions
        * :c:func:`h_s2_u_0_nstates_openmp`
        * :c:func:`h_s2_u_0_nstates_zmq`
 
-    Touches:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:data:`n_states_diag`
-
  
 .. c:function:: u_0_h_u_0_two_e:
 
@@ -1728,7 +1717,7 @@ Subroutines / functions
         subroutine u_0_H_u_0_two_e(e_0,u_0,n,keys_tmp,Nint,N_st,sze)
 
 
-    Computes $E_0 = \frac{ \langle u_0|H|u_0\rangle}{\langle u_0|u_0 \rangle}$.
+    Computes $E_0 = \frac{ \langle u_0 | H | u_0\rangle}{\langle u_0 | u_0 \rangle}$.
     
     n : number of determinants
     

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 module defines the *provider* of the density used for the |DFT| related
-This definition is done through the keyword :option:`density_for_dft density_for_dft`.
+calculations.  This definition is done through the keyword
-The density can be:
+: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``)
+* `WFT`: the density is computed with a potentially multi determinant wave
-* 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`
+  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/modules/determinants.rst

@@ -13,15 +13,15 @@ Contains everything for the computation of the Hamiltonian matrix elements in th
 The main providers for this module are:
 
 * :option:`determinants n_states`: number of states to be computed
-* `psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|.
+* :c:data:`psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|.
-* `psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants.
+* :c:data:`psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants.
 
 The main routines for this module are:
 
-* `i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants.
+* :c:func:`i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants.
-* `i_H_j_s2`: computes the Hamiltonian and (:math:`S^2`) matrix element between two arbitrary Slater determinants.
+* :c:func:`i_H_j_s2`: computes the Hamiltonian and (|S^2|) matrix element between two arbitrary Slater determinants.
-* `i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor.
+* :c:func:`i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor.
-* `i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants.
+* :c:func:`i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants.
 
 
 For an example of how to use these routines and providers, take a look at :file:`example.irp.f`.
@@ -81,12 +81,12 @@ EZFIO parameters
  
 .. option:: n_int
  
-    Number of integers required to represent bitstrings (set in module :ref:`bitmask`)
+    Number of integers required to represent bitstrings (set in module :ref:`module_bitmask`)
  
  
 .. option:: bit_kind
  
-    (set in module :ref:`bitmask`)
+    (set in module :ref:`module_bitmask`)
  
  
 .. option:: mo_label

docs/source/modules/dft_utils_in_r.rst

@@ -769,13 +769,19 @@ Subroutines / functions
         subroutine density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array)
 
 
-    input      : r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    input:
-    output     : dm_a = alpha density evaluated at r
+    
-               : dm_b = beta  density evaluated at r
+    * r(1) ==> r(1) = x, r(2) = y, r(3) = z
-               : aos_array(i) = ao(i) evaluated at r
+    
-               : grad_dm_a(1) = X gradient of the alpha density evaluated in r
+    output:
-               : grad_dm_a(1) = X gradient of the beta  density evaluated in r
+    
-               : grad_aos_array(1) = X gradient of the aos(i) evaluated at r
+    * dm_a = alpha density evaluated at r
+    * dm_b = beta  density evaluated at r
+    * aos_array(i) = ao(i) evaluated at r
+    * grad_dm_a(1) = X gradient of the alpha density evaluated in r
+    * grad_dm_a(1) = X gradient of the beta  density evaluated in r
+    * grad_aos_array(1) = X gradient of the aos(i) evaluated at r
+    
 
     Needs:
 

docs/source/modules/fci.rst

@@ -15,43 +15,52 @@ fci
 The user point of view
 ----------------------
 
-* :c:func:`fci` performs |CIPSI| calculations using a stochastic scheme for both the selection and the |PT2| contribution,
+* :ref:`fci` performs |CIPSI| calculations using a stochastic scheme for both
-* :c:func:`pt2` computes the |PT2| contribution using the wave function stored in the |EZFIO|
+  the selection and the |PT2| contribution,
-  database.
+
+* :ref:`pt2` computes the |PT2| contribution using the wave function stored in
+  the |EZFIO| database.
 
 
 The main keywords/options for this module are:
 
-* :option:`determinants n_det_max` : maximum number of Slater determinants in the CIPSI wave function. The :command:`fci` program will stop when the size of the CIPSI wave function will exceed :option:`determinants n_det_max`.
+* :option:`determinants n_det_max` : maximum number of Slater determinants in
+  the |CIPSI| wave function. The :ref:`fci` program will stop when the size of
+  the |CIPSI| wave function will exceed :option:`determinants n_det_max`.
 
-* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the CIPSI calculation. Once the |PT2| :math:`<` :option:`perturbation pt2_max`, the CIPSI calculation stops.
+* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the
+  |CIPSI| calculation. Once the abs(|PT2|) :math:`<` :option:`perturbation pt2_max`,
+  the |CIPSI| calculation stops.
 
-* :option:`determinants n_states` : number of states to consider in the CIPSI calculation.
+* :option:`determinants n_states` : number of states to consider in the |CIPSI|
+  calculation.
 
-* :option:`determinants read_wf` : if False, starts with a ROHF-like determinant, if True, starts with the current wave function(s) stored in the |EZFIO| folder.
+* :option:`determinants read_wf` : if |false|, starts with a |ROHF|-like
+  determinant, if |true|, starts with the current wave function(s) stored in
+  the |EZFIO| directory.
 
 .. note::
-   For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd`
+   For a multi-state calculation, it is recommended to start with :ref:`cis`
-   wave functions as a guess.
+   or :ref:`cisd` wave functions as a guess.
 
-* :option:`determinants s2_eig` : if True, systematically add all the determinants needed to have a pure value of :math:`S^2`. Also, if True, it tracks only the states having the good :option:`determinants expected_s2`.
+* :option:`determinants expected_s2` : expected value of |S^2| for the
+  desired spin multiplicity.
 
-.. note::
+* :option:`determinants s2_eig` : if |true|, systematically add all the
-   For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd`
+  determinants needed to have a pure value of |S^2|. Also, if |true|, it
-   wave functions as a guess.
+  tracks only the states having the good :option:`determinants expected_s2`.
-
-* :option:`determinants expected_s2` : expected value of :math:`S^2` for the desired spin multiplicity.
 
 
 
-The programmer point of view
-----------------------------
 
-This module have been created with the :ref:`cipsi` module.
+The programmer's point of view
+------------------------------
+
+This module was created with the :ref:`module_cipsi` module.
 
 .. seealso::
 
-    The documentation of the :ref:`cipsi` module.
+    The documentation of the :ref:`module_cipsi` module.
 
 
  

docs/source/modules/hartree_fock.rst

@@ -14,9 +14,9 @@ calculations (the spatial part of the |MOs| is common for alpha and beta
 spinorbitals).
 
 The Hartree-Fock algorithm is a |SCF| and therefore is based on the
-:ref:`module_scf_utils`` module. 
+:ref:`module_scf_utils` module. 
 
-The Fock matrix is defined in :file:`hartree_fock fock_matrix_hf.irp.f`.
+The Fock matrix is defined in :file:`fock_matrix_hf.irp.f`.
 
 
 

docs/source/modules/mo_basis.rst

@@ -562,9 +562,9 @@ Subroutines / functions
 
     Rotates the j-th |MO| with the k-th |MO| to give two new |MOs| that are
     
-    * $+ = \frac{1}{\sqrt{2}} (|j\rangle + |k\rangle)$
+    * $+ = \frac{1}{\sqrt{2}} ( | j\rangle +  | k\rangle)$
     
-    * $- = \frac{1}{\sqrt{2}} (|j\rangle - |k\rangle)$
+    * $- = \frac{1}{\sqrt{2}} ( | j\rangle -  | k\rangle)$
     
     by convention, the '+' |MO| is in the lowest  index (min(j,k))
     by convention, the '-' |MO| is in the highest index (max(j,k))

docs/source/modules/perturbation.rst

@@ -106,39 +106,6 @@ EZFIO parameters
 Providers 
 --------- 
  
-.. c:function:: fill_h_apply_buffer_selection:
-
-
-    File : :file:`perturbation/selection.irp.f`
-
-    .. code:: fortran
-
-        subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, &
-   N_st,Nint,iproc,select_max_out)
-
-
-    Fill the H_apply buffer with determiants for the selection
-
-    Needs:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:data:`selection_criterion`
-       * :c:data:`h_apply_buffer_allocated`
-       * :c:data:`n_det`
-       * :c:data:`n_int`
-
-    Calls:
-
-    .. hlist::
-       :columns: 3
-
-       * :c:func:`omp_set_lock`
-       * :c:func:`omp_unset_lock`
-       * :c:func:`resize_h_apply_buffer`
-
- 
 .. c:var:: h0_type
 
 
@@ -253,6 +220,38 @@ Providers
 Subroutines / functions 
 ----------------------- 
  
+.. c:function:: fill_h_apply_buffer_selection:
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, N_st,Nint,iproc,select_max_out)
+
+
+    Fill the H_apply buffer with determiants for the selection
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`selection_criterion`
+       * :c:data:`h_apply_buffer_allocated`
+       * :c:data:`n_det`
+       * :c:data:`n_int`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`omp_set_lock`
+       * :c:func:`omp_unset_lock`
+       * :c:func:`resize_h_apply_buffer`
+
+ 
 .. c:function:: perturb_buffer_by_mono_dummy:
 
 
@@ -263,7 +262,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -298,7 +297,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -333,7 +332,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -368,7 +367,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -403,7 +402,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -438,7 +437,7 @@ Subroutines / functions
         subroutine perturb_buffer_by_mono_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -473,7 +472,7 @@ Subroutines / functions
         subroutine perturb_buffer_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -509,7 +508,7 @@ Subroutines / functions
         subroutine perturb_buffer_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -545,7 +544,7 @@ Subroutines / functions
         subroutine perturb_buffer_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -581,7 +580,7 @@ Subroutines / functions
         subroutine perturb_buffer_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -617,7 +616,7 @@ Subroutines / functions
         subroutine perturb_buffer_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:
@@ -653,7 +652,7 @@ Subroutines / functions
         subroutine perturb_buffer_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
 
 
-     Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
+    Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
     routine.
 
     Needs:

docs/source/modules/scf_utils.rst

@@ -192,11 +192,11 @@ Providers
 
     .. code:: fortran
 
-        subroutine extrapolate_Fock_matrix(      &
+        subroutine extrapolate_Fock_matrix(               &
-  error_matrix_DIIS,Fock_matrix_DIIS,    &
+           error_matrix_DIIS,Fock_matrix_DIIS,    &
-  Fock_matrix_AO_,size_Fock_matrix_AO,   &
+           Fock_matrix_AO_,size_Fock_matrix_AO,   &
-  iteration_SCF,dim_DIIS                 &
+           iteration_SCF,dim_DIIS                 &
-)
+           )
 
 
     Compute the extrapolated Fock matrix using the DIIS procedure

docs/source/modules/selectors_cassd.rst

@@ -9,5 +9,5 @@ selectors_cassd
 ===============
 
 Selectors for |CAS-SD| calculations. The selectors are defined as first the
-generators from :ref:`Generators_CAS`, and then the rest of the wave function.
+generators from :ref:`module_generators_cas`, and then the rest of the wave function.
  

docs/source/modules/utils.rst

@@ -855,8 +855,8 @@ Subroutines / functions
        * :c:func:`remove_duplicates_in_selection_buffer`
        * :c:func:`run_cipsi`
        * :c:func:`run_pt2_slave`
+       * :c:func:`run_slave_main`
        * :c:func:`run_stochastic_cipsi`
-       * :c:func:`select_singles_and_doubles`
        * :c:func:`selection_collector`
        * :c:func:`sort_selection_buffer`
        * :c:func:`testteethbuilding`
@@ -2651,6 +2651,7 @@ Subroutines / functions
        * :c:func:`check_mem`
        * :c:func:`davidson_diag_hjj_sjj`
        * :c:func:`print_memory_usage`
+       * :c:func:`run_slave_main`
        * :c:func:`zmq_pt2`
 
     Calls:

docs/source/programmers_guide/conventions.rst

@@ -107,7 +107,7 @@ Only standard Fortran is allowed : Intel or GNU extensions are forbidden.
 The name of a program should be the same as the name of the file. For example,
 for the :ref:`fci` program, we have
 
-.. code-block:: fortan
+.. code-block:: fortran
 
    program fci
 

docs/source/programmers_guide/ezfio.rst

@@ -8,7 +8,7 @@ EZFIO.cfg
 
 The simplest way to add control parameters in the |EZFIO| directory is to create a
 :file:`EZFIO.cfg` file in the module. An example can be found in existing modules
-such as :ref:`hartree_fock`::
+such as :ref:`module_hartree_fock`::
 
    [max_dim_diis]
    type: integer
@@ -92,7 +92,7 @@ Optional
 
 It is possible to directly add to the current module |EZFIO| configuration
 files, named with the ``.ezfio_config`` suffix. An example is in the
-:ref:`bitmask` module. 
+:ref:`module_bitmask` module. 
 
 .. code:: text
 

docs/source/programmers_guide/index_providers.rst

@@ -226,7 +226,6 @@ Index of Providers
 * :c:data:`ezfio_work_dir` 
 * :c:data:`fact_inv` 
 * :c:data:`file_lock` 
-* :c:data:`fill_h_apply_buffer_selection` 
 * :c:data:`final_grid_points` 
 * :c:data:`final_weight_at_r` 
 * :c:data:`final_weight_at_r_vector` 
@@ -606,7 +605,6 @@ Index of Providers
 * :c:data:`psi_selectors_coef_transp` 
 * :c:data:`psi_selectors_diag_h_mat` 
 * :c:data:`psi_selectors_size` 
-* :c:data:`pt2_collector` 
 * :c:data:`pt2_cw` 
 * :c:data:`pt2_e0_denominator` 
 * :c:data:`pt2_f` 
@@ -907,6 +905,7 @@ Index of Subroutines/Functions
 * :c:func:`fcidump` 
 * :c:func:`fill_buffer_double` 
 * :c:func:`fill_h_apply_buffer_no_selection` 
+* :c:func:`fill_h_apply_buffer_selection` 
 * :c:func:`filter_connected` 
 * :c:func:`filter_connected_i_h_psi0` 
 * :c:func:`filter_not_connected` 
@@ -1198,6 +1197,7 @@ Index of Subroutines/Functions
 * :c:func:`provide_all_mo_integrals_erf` 
 * :c:func:`provide_everything` 
 * :c:func:`pt2` 
+* :c:func:`pt2_collector` 
 * :c:func:`pt2_dummy` 
 * :c:func:`pt2_epstein_nesbet` 
 * :c:func:`pt2_epstein_nesbet_2x2` 

docs/source/programs/cis.rst

@@ -20,25 +20,22 @@ cis
  This program can be useful in many cases: 
   
   
- Ground state calculation 
+ 1. Ground state calculation 
- ------------------------ 
   
- To be sure to have the lowest |SCF| solution, perform an :ref:`scf` 
+    To be sure to have the lowest |SCF| solution, perform an :ref:`scf` 
- (see the :ref:`hartree_fock` module), then a :ref:`cis`, save 
+    (see the :ref:`module_hartree_fock` module), then a :ref:`cis`, save the 
- the natural orbitals (see :ref:`save_natorb`) and re-run an 
+    natural orbitals (see :ref:`save_natorb`) and re-run an :ref:`scf` 
- :ref:`scf` optimization from this |MO| guess. 
+    optimization from this |MO| guess. 
   
   
- Excited states calculations 
+ 2. Excited states calculations 
- --------------------------- 
   
- The lowest excited states are much likely to be dominated by 
+    The lowest excited states are much likely to be dominated by 
- single-excitations. Therefore, running a :ref:`cis` will save 
+    single-excitations. Therefore, running a :ref:`cis` will save the 
- the `n_states` lowest states within the |CIS| space in the |EZFIO| 
+    `n_states` lowest states within the |CIS| space in the |EZFIO| 
- directory, which can afterwards be used as guess wave functions for 
+    directory, which can afterwards be used as guess wave functions for 
- a further multi-state |FCI| calculation if :option:`determinants read_wf` 
+    a further multi-state |FCI| calculation if :option:`determinants 
- is set to |true| before running the :ref:`fci` 
+    read_wf` is set to |true| before running the :ref:`fci` executable. 
- executable. 
   
   
  If :option:`determinants s2_eig` is set to |true|, the |CIS| 

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 
@@ -50,6 +50,7 @@ cisd
    * "act" orbitals where an electron can be either excited from or to 
   
    * "del" orbitals which will be never occupied 
+  
  
  Needs: 
  

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/fci.rst

@@ -21,7 +21,7 @@ fci
  conditions: 
   
  * number of Slater determinants > :option:`determinants n_det_max` 
- * |PT2| < :option:`perturbation pt2_max` 
+ * abs(|PT2|) less than :option:`perturbation pt2_max` 
   
  The following other options can be of interest: 
   
@@ -38,7 +38,7 @@ fci
    :option:`determinants expected_s2`. 
   
  For excited states calculations, it is recommended to start with 
- :ref:`.cis.` or :ref:`.cisd.` guess wave functions, eventually in 
+ :ref:`cis` or :ref:`cisd` guess wave functions, eventually in 
  a restricted set of |MOs|, and to set :option:`determinants s2_eig` 
  to |true|. 
   

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/molden.rst

@@ -9,7 +9,7 @@ molden
  
  
  
- Produce a Molden file 
+ Produces a Molden file 
  
  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 an average of the density 
- If this is a multi-state calculation, the density matrix that produces the natural orbitals 
+ matrices of each state with the corresponding 
-  
+ :option:`determinants state_average_weight` 
- 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). 
  
  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 
+ Program that computes the one body density on the |MO| basis 
- from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities. 
+ 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. 
+ 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 
- This can be used to perform damping on the density in RS-DFT calculation (see the density_for_dft module). 
+ 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/programs/write_integrals_erf.rst

@@ -9,7 +9,8 @@ write_integrals_erf
  
  
  
- Saves the two-electron integrals with the :math:`erf(\mu r_{12})/r_{12}` oprerator into the EZFIO folder 
+ Saves the two-electron integrals with the $erf(\mu r_{12})/r_{12}$ 
+ oprerator into the EZFIO directory. 
  
  Needs: 
  

docs/source/users_guide/interfaces.rst

@@ -15,7 +15,7 @@ A few interfaces to external codes are available.
 |qp| -> \* 
 ----------
 
-`Molden`_
+`Molden <http://cheminf.cmbi.ru.nl/molden>`_
   3D plots of Molecular Orbitals
 
 FCIDUMP 

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.
 

docs/source/users_guide/qp_reset.rst

@@ -0,0 +1,32 @@
+.. _qp_reset:
+
+========
+qp_reset
+========
+
+.. program:: qp_reset
+
+This command resets parts of the |EZFIO| directory.
+
+
+Usage
+-----
+
+.. code:: bash
+
+  qp_reset [-adhm] EZFIO_DIR
+
+.. option:: -a, --all
+
+  Reset to the state in which the directory is after after running :ref:`qp_create_ezfio`.
+
+.. option:: -d, --dets
+
+  Deletes the determinants and CI coefficients.
+
+.. option:: -m, --mos
+
+  Deletes the |MOs|, and consequently the determinants and CI coefficients.
+
+
+

docs/source/users_guide/qpsh.rst

@@ -95,7 +95,7 @@ Running programs
 
      qp (run|srun|mpirun) [options] <program>
 
-  Runs :ref:`qp_run`, :ref:`qp_srun`, or :ref:`qp_mpirun` using the current 
+  Runs :ref:`qp_run`, :command:`qp_srun`, or :command:`qp_mpirun` using the current 
   |EZFIO| directory.
 
 .. option:: stop

docs/source/users_guide/quickstart.rst

@@ -74,7 +74,8 @@ The expected energy is ``-92.827856698`` au.
 
 .. seealso:: 
 
-    The documentation of the :ref:`hartree_fock` module and that of the :c:func:`scf` program.
+    The documentation of the :ref:`module_hartree_fock` module and that of the
+    :ref:`scf` program.
 
 This creates the |MOs| in the |EZFIO| database that will be used to
 perform any other post-SCF method. The |qp| does not handle symmetry and
@@ -138,7 +139,7 @@ The estimated |FCI| energy of HCN is ``-93.0501`` au.
 
 .. seealso:: 
 
-    The documentation of the :ref:`fci` module and that of the :c:func:`fci` program.
+    The documentation of the :ref:`module_fci` module and that of the :ref:`fci` program.
 
 
 ---------------------------

etc/paths.rc

@@ -32,7 +32,8 @@ export PYTHONPATH=$(qp_prepend_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PY
 
 export PATH=$(qp_prepend_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)
 
-export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
+export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib)
+
 
 export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
 

man/cis.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CIS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "CIS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 cis \-  | Quantum Package >
 .
@@ -40,19 +40,24 @@ 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:
+.INDENT 0.0
+.IP 1. 3
+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
+(see the module_hartree_fock module), then a \fI\%cis\fP, save the
-the natural orbitals (see save_natorb) and re\-run an
+natural orbitals (see save_natorb) and re\-run an scf
-scf optimization from this MO guess.
+optimization from this MO guess.
+.IP 2. 3
+Excited states calculations
 .sp
 The lowest excited states are much likely to be dominated by
-single\-excitations. Therefore, running a \fI\%cis\fP will save
+single\-excitations. Therefore, running a \fI\%cis\fP will save the
-the \fIn_states\fP lowest states within the CIS space in the \fI\%EZFIO\fP
+\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
+a further multi\-state FCI calculation if \fBdeterminants
-is set to \fBtrue\fP before running the fci
+read_wf\fP is set to \fBtrue\fP before running the fci executable.
-executable.
+.UNINDENT
 .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

man/cisd.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CISD" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "CISD" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 cisd \-  | Quantum Package >
 .
@@ -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/configure.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CONFIGURE" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "CONFIGURE" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 configure \-  | Quantum Package >
 .

man/diagonalize_h.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "DIAGONALIZE_H" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "DIAGONALIZE_H" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 diagonalize_h \-  | Quantum Package >
 .
@@ -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
+If \fBdeterminants s2_eig\fP = \fBtrue\fP, it will retain only states
-.sp
+which correspond to the desired value of
-which corresponds to the desired value of \fBdeterminants expected_s2\fP\&.
+\fBdeterminants expected_s2\fP\&.
 .sp
 Needs:
 .INDENT 0.0

man/excited_states.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "EXCITED_STATES" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "EXCITED_STATES" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 excited_states \-  | Quantum Package >
 .

man/fci.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FCI" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "FCI" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 fci \-  | Quantum Package >
 .
@@ -46,7 +46,7 @@ conditions:
 .IP \(bu 2
 number of Slater determinants > \fBdeterminants n_det_max\fP
 .IP \(bu 2
-PT2 < \fBperturbation pt2_max\fP
+abs(PT2) less than \fBperturbation pt2_max\fP
 .UNINDENT
 .sp
 The following other options can be of interest:
@@ -66,7 +66,7 @@ function with an \ewidehat{S^2} value corresponding to
 .UNINDENT
 .sp
 For excited states calculations, it is recommended to start with
-\&.cis. or \&.cisd. guess wave functions, eventually in
+cis or cisd guess wave functions, eventually in
 a restricted set of MOs, and to set \fBdeterminants s2_eig\fP
 to \fBtrue\fP\&.
 .sp

man/fcidump.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FCIDUMP" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "FCIDUMP" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 fcidump \-  | Quantum Package >
 .
@@ -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

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FOUR_IDX_TRANSFORM" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "FOUR_IDX_TRANSFORM" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 four_idx_transform \-  | Quantum Package >
 .
@@ -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/interfaces.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "INTERFACES" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "INTERFACES" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 interfaces \-  | Quantum Package >
 .

man/ks_scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "KS_SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "KS_SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 ks_scf \-  | Quantum Package >
 .

man/molden.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "MOLDEN" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "MOLDEN" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 molden \-  | Quantum Package >
 .
@@ -32,7 +32,7 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
 ..
 .INDENT 0.0
 .INDENT 3.5
-Produce a Molden file
+Produces a Molden file
 .sp
 Needs:
 .INDENT 0.0

man/natural_orbitals.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "NATURAL_ORBITALS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "NATURAL_ORBITALS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 natural_orbitals \-  | Quantum Package >
 .

man/plugins.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PLUGINS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "PLUGINS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 plugins \-  | Quantum Package >
 .

man/print_e_conv.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINT_E_CONV" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "PRINT_E_CONV" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 print_e_conv \-  | Quantum Package >
 .

man/print_wf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINT_WF" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "PRINT_WF" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 print_wf \-  | Quantum Package >
 .
@@ -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.
+If the wave function strongly deviates from the first\-order analysis,
-.sp
+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

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINTING" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "PRINTING" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 printing \-  | Quantum Package >
 .
@@ -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

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PT2" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "PT2" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 pt2 \-  | Quantum Package >
 .
@@ -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
+The main option for the PT2 correction is the
-.sp
+\fBperturbation pt2_relative_error\fP which is the relative
-error on the PT2 to reach before stopping the stochastic sampling. (see \fBperturbation pt2_relative_error\fP)
+stochastic error on the PT2 to reach before stopping the
+sampling.
 .sp
 Needs:
 .INDENT 0.0

man/qp_convert_output_to_ezfio.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_convert_output_to_ezfio \-  | Quantum Package >
 .

man/qp_create_ezfio_from_xyz.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_create_ezfio_from_xyz \-  | Quantum Package >
 .

man/qp_edit.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_EDIT" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_EDIT" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_edit \-  | Quantum Package >
 .

man/qp_export_as_tgz.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_EXPORT_AS_TGZ" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_EXPORT_AS_TGZ" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_export_as_tgz \-  | Quantum Package >
 .

man/qp_plugins.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_PLUGINS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_PLUGINS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_plugins \-  | Quantum Package >
 .

man/qp_reset.1

@@ -0,0 +1,66 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "QP_RESET" "1" "Jan 29, 2019" "2.0" "Quantum Package"
+.SH NAME
+qp_reset \-  | 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 resets parts of the \fI\%EZFIO\fP directory.
+.SH USAGE
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_reset [\-adhm] EZFIO_DIR
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-a, \-\-all
+Reset to the state in which the directory is after after running qp_create_ezfio\&.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-d, \-\-dets
+Deletes the determinants and CI coefficients.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-m, \-\-mos
+Deletes the MOs, and consequently the determinants and CI coefficients.
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2019, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.

man/qp_run.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_RUN" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_RUN" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_run \-  | Quantum Package >
 .

man/qp_set_frozen_core.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_SET_FROZEN_CORE" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_SET_FROZEN_CORE" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_set_frozen_core \-  | Quantum Package >
 .

man/qp_set_mo_class.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_SET_MO_CLASS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_SET_MO_CLASS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_set_mo_class \-  | Quantum Package >
 .

man/qp_stop.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_STOP" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_STOP" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_stop \-  | Quantum Package >
 .

man/qp_update.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_UPDATE" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QP_UPDATE" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_update \-  | Quantum Package >
 .

man/qpsh.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QPSH" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "QPSH" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 qpsh \-  | Quantum Package >
 .
@@ -153,7 +153,7 @@ qp (run|srun|mpirun) [options] <program>
 .UNINDENT
 .UNINDENT
 .sp
-Runs qp_run, qp_srun, or qp_mpirun using the current
+Runs qp_run, \fBqp_srun\fP, or \fBqp_mpirun\fP using the current
 \fI\%EZFIO\fP directory.
 .UNINDENT
 .INDENT 0.0

man/rs_ks_scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "RS_KS_SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "RS_KS_SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 rs_ks_scf \-  | Quantum Package >
 .

man/save_natorb.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_NATORB" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "SAVE_NATORB" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_natorb \-  | Quantum Package >
 .
@@ -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
+If this is a multi\-state calculation, the density matrix that produces
-.sp
+the natural orbitals is obtained from an average of the density
-If this is a multi\-state calculation, the density matrix that produces the natural orbitals
+matrices of each state with the corresponding
-.sp
+\fBdeterminants state_average_weight\fP
-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).
 .sp
 Needs:
 .INDENT 0.0

man/save_one_e_dm.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_ONE_E_DM" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "SAVE_ONE_E_DM" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_one_e_dm \-  | Quantum Package >
 .
@@ -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
+Program that computes the one body density on the MO basis
-from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities.
+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.
+Then, the global variable \fBaux_quantities data_one_e_dm_alpha_mo\fP
-.sp
+and \fBaux_quantities data_one_e_dm_beta_mo\fP will automatically
-This can be used to perform damping on the density in RS\-DFT calculation (see the density_for_dft module).
+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

man/save_ortho_mos.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_ORTHO_MOS" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "SAVE_ORTHO_MOS" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_ortho_mos \-  | Quantum Package >
 .

man/scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 scf \-  | Quantum Package >
 .

man/write_integrals_erf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "WRITE_INTEGRALS_ERF" "1" "Jan 25, 2019" "2.0" "Quantum Package"
+.TH "WRITE_INTEGRALS_ERF" "1" "Jan 29, 2019" "2.0" "Quantum Package"
 .SH NAME
 write_integrals_erf \-  | Quantum Package >
 .
@@ -32,7 +32,8 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
 ..
 .INDENT 0.0
 .INDENT 3.5
-Saves the two\-electron integrals with the erf(\emu r_{12})/r_{12} oprerator into the EZFIO folder
+Saves the two\-electron integrals with the $erf(mu r_{12})/r_{12}$
+oprerator into the EZFIO directory.
 .sp
 Needs:
 .INDENT 0.0

ocaml/TaskServer.ml

@@ -50,7 +50,7 @@ let zmq_context =
   Zmq.Context.create ()
 
 let () =
-  Zmq.Context.set_io_threads zmq_context 8
+  Zmq.Context.set_io_threads zmq_context 16
 
 
 let bind_socket ~socket_type ~socket ~port =

src/ao_basis/README.rst

@@ -17,9 +17,13 @@ The |AO| coefficients are normalized as:
 
   {\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c  e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2 dr}
 
-Warning: `ao_coef` contains the |AO| coefficients given in input. These do not
+
-include the normalization constant of the |AO|. The `ao_coef_normalized` provider includes
+.. warning::
-this normalization factor.
+
+  `ao_coef` contains the |AO| coefficients given in input. These do not
+  include the normalization constant of the |AO|. The `ao_coef_normalized`
+  provider includes this normalization factor.
+
 
 The |AOs| are also sorted by increasing exponent to accelerate the calculation of
 the two electron integrals.

src/ao_basis/aos_value.irp.f

@@ -1,7 +1,7 @@
 double precision function ao_value(i,r)
  implicit none
  BEGIN_DOC
-! return the value of the ith ao at point r
+! Returns the value of the i-th ao at point $\textbf{r}$
  END_DOC
  double precision, intent(in) :: r(3)
  integer, intent(in) :: i
@@ -35,7 +35,8 @@ end
 double precision function primitive_value(i,j,r)
  implicit none
  BEGIN_DOC
-! return the value of the jth primitive of ith ao at point r WITHOUT THE COEF
+! Returns the value of the j-th primitive of the i-th |AO| at point $\textbf{r}
+! **without the coefficient**
  END_DOC
  double precision, intent(in) :: r(3)
  integer, intent(in) :: i,j
@@ -68,8 +69,9 @@ end
 subroutine give_all_aos_at_r(r,aos_array)
  implicit none
  BEGIN_dOC
-! input : r == r(1) = x and so on
+! input  : r == r(1) = x and so on
-! aos_array(i) = aos(i) evaluated in r
+!
+! output : aos_array(i) = aos(i) evaluated in $\textbf{r}$
  END_DOC
  double precision, intent(in) :: r(3)
  double precision, intent(out):: aos_array(ao_num)
@@ -106,9 +108,13 @@ end
 subroutine give_all_aos_and_grad_at_r(r,aos_array,aos_grad_array)
  implicit none
  BEGIN_DOC
-! input      : r(1) ==> r(1) = x, r(2) = y, r(3) = z
+! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z
-! output     : aos_array(i) = ao(i) evaluated at r
+!
-!            : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r
+! output : 
+!
+! * aos_array(i) = ao(i) evaluated at ro
+! * aos_grad_array(1,i) = gradient X of the ao(i) evaluated at $\textbf{r}$
+!
  END_DOC
  double precision, intent(in) :: r(3)
  double precision, intent(out) :: aos_array(ao_num)
@@ -172,9 +178,12 @@ end
 subroutine give_all_aos_and_grad_and_lapl_at_r(r,aos_array,aos_grad_array,aos_lapl_array)
  implicit none
  BEGIN_DOC
-! input      : r(1) ==> r(1) = x, r(2) = y, r(3) = z
+! input  : r(1) ==> r(1) = x, r(2) = y, r(3) = z
-! output     : aos_array(i) = ao(i) evaluated at r
+!
-!            : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r
+! output :
+!
+! * aos_array(i) = ao(i) evaluated at $\textbf{r}$
+! * aos_grad_array(1,i) = $\nabla_x$ of the ao(i) evaluated at $\textbf{r}$
  END_DOC
  double precision, intent(in) :: r(3)
  double precision, intent(out) :: aos_array(ao_num)

src/ao_one_e_ints/kin_ao_ints.irp.f

@@ -5,8 +5,10 @@
   BEGIN_DOC
   ! Second derivative matrix elements in the |AO| basis.
   !
-  ! :math:`{\tt ao\_deriv2\_x} =
+  ! .. math::
-  !  \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle`
+  !
+  !   {\tt ao\_deriv2\_x} =
+  !   \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
   !
   END_DOC
   integer :: i,j,n,l
@@ -122,7 +124,8 @@ BEGIN_PROVIDER [double precision, ao_kinetic_integrals, (ao_num,ao_num)]
   BEGIN_DOC
   ! Kinetic energy integrals in the |AO| basis.
   !
-  ! :math:`\langle \chi_i |\hat{T}| \chi_j \rangle`
+  ! $\langle \chi_i |\hat{T}| \chi_j \rangle$
+  !
   END_DOC
   integer                        :: i,j,k,l
 

src/ao_one_e_ints/pot_ao_erf_ints.irp.f

@@ -2,7 +2,7 @@ subroutine give_all_erf_kl_ao(integrals_ao,mu_in,C_center)
   implicit none
   BEGIN_DOC
   ! Subroutine that returns all integrals over $r$ of type
-  ! $\frac{ \erf(\mu * |r-R_C|) }{ |r-R_C| }$
+  ! $\frac{ \erf(\mu * | r - R_C | ) }{ | r - R_C | }$
   END_DOC
   double precision, intent(in)   :: mu_in,C_center(3)
   double precision, intent(out)  :: integrals_ao(ao_num,ao_num)
@@ -20,7 +20,7 @@ double precision function NAI_pol_mult_erf_ao(i_ao,j_ao,mu_in,C_center)
   implicit none
   BEGIN_DOC
   ! Computes the following integral :
-  ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu |r-R_C|)}{|r-R_C|}$.
+  ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$.
   END_DOC
   integer, intent(in)            :: i_ao,j_ao
   double precision, intent(in)   :: mu_in, C_center(3)
@@ -51,8 +51,12 @@ end
 double precision function NAI_pol_mult_erf(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in,mu_in)
   BEGIN_DOC
   ! Computes the following integral :
-  ! $\int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 )
+  !
-  !  \frac{\erf(\mu |r-R_C|)}{|r-R_c|}$.
+  ! .. math::
+  ! 
+  !   \int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 )
+  !   \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$.
+  !
   END_DOC
 
   implicit none
@@ -126,7 +130,8 @@ end
 subroutine give_polynomial_mult_center_one_e_erf_opt(A_center,B_center,alpha,beta,&
       power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in,p,p_inv,p_inv_2,p_new,P_center)
   BEGIN_DOC
-  ! Returns the explicit polynomial in terms of the $t$ variable of the following polynomial:
+  ! Returns the explicit polynomial in terms of the $t$ variable of the
+  ! following polynomial:
   !
   ! $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$.
   END_DOC
@@ -244,7 +249,8 @@ end
 subroutine give_polynomial_mult_center_one_e_erf(A_center,B_center,alpha,beta,&
       power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in)
   BEGIN_DOC
-  ! Returns the explicit polynomial in terms of the $t$ variable of the following polynomial:
+  ! Returns the explicit polynomial in terms of the $t$ variable of the 
+  ! following polynomial:
   !
   ! $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$.
   END_DOC
@@ -262,7 +268,6 @@ subroutine give_polynomial_mult_center_one_e_erf(A_center,B_center,alpha,beta,&
   double precision               :: accu,  pq_inv, p10_1, p10_2, p01_1, p01_2
   double precision               :: p,P_center(3),rho,p_inv,p_inv_2
   accu = 0.d0
-  !COMPTEUR irp_rdtsc1 = irp_rdtsc()
   ASSERT (n_pt_in > 1)
   p = alpha+beta
   p_inv = 1.d0/p

src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f

@@ -458,11 +458,13 @@ end
 double precision function ERI_erf(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z)
   implicit none
   BEGIN_DOC
-  !  ATOMIC PRIMTIVE two-electron integral between the 4 primitives ::
+  ! Atomic primtive two-electron integral between the 4 primitives :
-  !         primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
+  !
-  !         primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
+  ! * primitive 1 : $x_1^{a_x} y_1^{a_y} z_1^{a_z} \exp(-\alpha * r1^2)$
-  !         primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
+  ! * primitive 2 : $x_1^{b_x} y_1^{b_y} z_1^{b_z} \exp(- \beta * r1^2)$
-  !         primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
+  ! * primitive 3 : $x_2^{c_x} y_2^{c_y} z_2^{c_z} \exp(-\delta * r2^2)$
+  ! * primitive 4 : $x_2^{d_x} y_2^{d_y} z_2^{d_z} \exp(-\gamma * r2^2)$
+  !
   END_DOC
   double precision, intent(in)   :: delta,gama,alpha,beta
   integer, intent(in)            :: a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z
@@ -517,9 +519,11 @@ end
 
 subroutine integrale_new_erf(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt)
   BEGIN_DOC
-  ! calculate the integral of the polynom ::
+  ! Calculate the integral of the polynomial :
-  !         I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
+  !
-  ! between ( 0 ; 1)
+  ! $I_x1(a_x+b_x, c_x+d_x,p,q) \, I_x1(a_y+b_y, c_y+d_y,p,q) \, I_x1(a_z+b_z, c_z+d_z,p,q)$
+  !
+  ! between $( 0 ; 1)$
   END_DOC
 
 

src/ao_two_e_ints/two_e_integrals.irp.f

@@ -641,9 +641,10 @@ end
 
 subroutine integrale_new(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt)
   BEGIN_DOC
-  ! calculate the integral of the polynom ::
+  ! Calculates the integral of the polynomial :
-  !         I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
+  !
-  ! between ( 0 ; 1)
+  ! $I_{x_1}(a_x+b_x,c_x+d_x,p,q) \, I_{x_1}(a_y+b_y,c_y+d_y,p,q) \, I_{x_1}(a_z+b_z,c_z+d_z,p,q)$
+  ! in $( 0 ; 1)$
   END_DOC
 
 
@@ -775,8 +776,9 @@ integer function n_pt_sup(a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z)
   implicit none
   BEGIN_DOC
   ! Returns the upper boundary of the degree of the polynomial involved in the
-  ! bielctronic integral :
+  ! two-electron integral :
-  !       Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
+  !
+  ! $I_x(a_x,b_x,c_x,d_x) \, I_y(a_y,b_y,c_y,d_y) \, I_z(a_z,b_z,c_z,d_z)$
   END_DOC
   integer                        :: a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z
   n_pt_sup =  shiftl( a_x+b_x+c_x+d_x + a_y+b_y+c_y+d_y + a_z+b_z+c_z+d_z,1 )
@@ -790,7 +792,8 @@ subroutine give_polynom_mult_center_x(P_center,Q_center,a_x,d_x,p,q,n_pt_in,pq_i
   BEGIN_DOC
   ! subroutine that returns the explicit polynom in term of the "t"
   ! variable of the following polynomw :
-  !         I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
+  !
+  ! $I_{x_1}(a_x,d_x,p,q) \, I_{x_1}(a_y,d_y,p,q) \ I_{x_1}(a_z,d_z,p,q)$
   END_DOC
   integer, intent(in)            :: n_pt_in
   integer,intent(out)            :: n_pt_out
@@ -851,7 +854,7 @@ end
 subroutine I_x1_pol_mult(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
   implicit none
   BEGIN_DOC
-  ! recursive function involved in the two-electron integral
+  ! Recursive function involved in the two-electron integral
   END_DOC
   integer , intent(in)           :: n_pt_in
   include 'utils/constants.include.F'
@@ -885,7 +888,7 @@ end
 recursive subroutine I_x1_pol_mult_recurs(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
   implicit none
   BEGIN_DOC
-  ! recursive function involved in the two-electron integral
+  ! Recursive function involved in the two-electron integral
   END_DOC
   integer , intent(in)           :: n_pt_in
   include 'utils/constants.include.F'
@@ -966,7 +969,7 @@ end
 recursive subroutine I_x1_pol_mult_a1(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
   implicit none
   BEGIN_DOC
-  ! recursive function involved in the two-electron integral
+  ! Recursive function involved in the two-electron integral
   END_DOC
   integer , intent(in)           :: n_pt_in
   include 'utils/constants.include.F'
@@ -1017,7 +1020,7 @@ end
 recursive subroutine I_x1_pol_mult_a2(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in)
   implicit none
   BEGIN_DOC
-  ! recursive function involved in the two-electron integral
+  ! Recursive function involved in the two-electron integral
   END_DOC
   integer , intent(in)           :: n_pt_in
   include 'utils/constants.include.F'
@@ -1075,7 +1078,7 @@ end
 recursive subroutine I_x2_pol_mult(c,B_10,B_01,B_00,C_00,D_00,d,nd,dim)
   implicit none
   BEGIN_DOC
-  ! recursive function involved in the two-electron integral
+  ! Recursive function involved in the two-electron integral
   END_DOC
   integer , intent(in)           :: dim
   include 'utils/constants.include.F'

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
+* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which
-  one-body alpha and beta densities which are necessary read from the EZFIO
+  are the one-body alpha and beta densities which are necessary read from the
-  folder.
+  |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/cipsi/README.rst

@@ -43,7 +43,7 @@ By default, the program will stop when more than one million determinants have
 been selected, or when the |PT2| energy is below :math:`10^{-4}`.
 
 The variational and |PT2| energies of the iterations are stored in the
-|EZFIO| database, in the :ref:`iterations` module.
+|EZFIO| database, in the :ref:`module_iterations` module.
 
 
 

src/cipsi/energy.irp.f

@@ -11,9 +11,15 @@ BEGIN_PROVIDER [ double precision, pt2_E0_denominator, (N_states) ]
  BEGIN_DOC
  ! E0 in the denominator of the PT2
  END_DOC
+ integer :: i,j
  if (initialize_pt2_E0_denominator) then
    if (h0_type == "EN") then
      pt2_E0_denominator(1:N_states) = psi_energy(1:N_states)
+   else if (h0_type == "HF") then
+     do i=1,N_states
+       j = maxloc(abs(psi_coef(:,i)),1)
+       pt2_E0_denominator(i) = psi_det_hii(j)
+     enddo
    else if (h0_type == "Barycentric") then
      pt2_E0_denominator(1:N_states) = barycentric_electronic_energy(1:N_states)
    else if (h0_type == "Variance") then
@@ -24,7 +30,9 @@ BEGIN_PROVIDER [ double precision, pt2_E0_denominator, (N_states) ]
      print *,  h0_type, ' not implemented'
      stop
    endif
-  call write_double(6,pt2_E0_denominator(1)+nuclear_repulsion, 'PT2 Energy denominator')
+  do i=1,N_states
+    call write_double(6,pt2_E0_denominator(i)+nuclear_repulsion, 'PT2 Energy denominator')
+  enddo
  else
    pt2_E0_denominator = -huge(1.d0)
  endif

src/cipsi/pt2_stoch_routines.irp.f

@@ -10,13 +10,20 @@ END_PROVIDER
 &BEGIN_PROVIDER [ integer, pt2_n_tasks_max ]
   implicit none
   logical, external :: testTeethBuilding
-  integer :: i
+  integer :: i,j
-  integer :: e
+  pt2_n_tasks_max = elec_beta_num*elec_beta_num + elec_alpha_num*elec_beta_num  - n_core_orb*2 
-  e = elec_num - n_core_orb * 2
+  pt2_n_tasks_max = min(pt2_n_tasks_max,1+N_det_generators/10000)
-  pt2_n_tasks_max = 1+min((e*(e-1))/2, int(dsqrt(dble(N_det_selectors)))/4)
+  call write_int(6,pt2_n_tasks_max,'pt2_n_tasks_max')
-  do i=1,N_det_generators
+
-    pt2_F(i) = 1 + int(dble(pt2_n_tasks_max)*maxval(dsqrt(dabs(psi_coef_sorted_gen(i,1:N_states)))))
+  pt2_F(:) = int(sqrt(float(pt2_n_tasks_max)))
+  do i=1,pt2_n_0(1+pt2_N_teeth/4)
+    pt2_F(i) = pt2_n_tasks_max
   enddo
+  do i=1+pt2_n_0(pt2_N_teeth-pt2_N_teeth/4), N_det_generators
+    pt2_F(i) = 1
+  enddo
+
+
 END_PROVIDER
 
  BEGIN_PROVIDER [ integer, pt2_N_teeth ]
@@ -54,17 +61,16 @@ logical function testTeethBuilding(minF, N)
 
   allocate(tilde_w(N_det_generators), tilde_cW(0:N_det_generators))
 
-  do i=1,N_det_generators
-    tilde_w(i)  = psi_coef_sorted_gen(i,pt2_stoch_istate)**2 !+ 1.d-20
-  enddo
-
-  double precision :: norm
   norm = 0.d0
+  double precision :: norm
   do i=N_det_generators,1,-1
-    norm += tilde_w(i)
+    tilde_w(i)  = psi_coef_sorted_gen(i,pt2_stoch_istate) * &
+                  psi_coef_sorted_gen(i,pt2_stoch_istate)
+    norm = norm + tilde_w(i)
   enddo
 
-  tilde_w(:) = tilde_w(:) / norm
+  f = 1.d0/norm
+  tilde_w(:) = tilde_w(:) * f
 
   tilde_cW(0) = -1.d0
   do i=1,N_det_generators
@@ -74,10 +80,14 @@ logical function testTeethBuilding(minF, N)
 
   n0 = 0
   testTeethBuilding = .false.
+  double precision :: f
+  integer :: minFN
+  minFN = N_det_generators - minF * N
+  f = 1.d0/dble(N)
   do
     u0 = tilde_cW(n0)
     r = tilde_cW(n0 + minF)
-    Wt = (1d0 - u0) / dble(N)
+    Wt = (1d0 - u0) * f 
     if (dabs(Wt) <= 1.d-3) then
       return
     endif
@@ -86,7 +96,8 @@ logical function testTeethBuilding(minF, N)
        return
     end if
     n0 += 1
-    if(N_det_generators - n0 < minF * N) then
+!    if(N_det_generators - n0 < minF * N) then
+    if(n0 > minFN) then
       return
     end if
   end do
@@ -103,7 +114,6 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
 
   integer(ZMQ_PTR)               :: zmq_to_qp_run_socket, zmq_socket_pull
   integer, intent(in)            :: N_in
-  integer, external              :: omp_get_thread_num
   double precision, intent(in)   :: relative_error, E(N_states)
   double precision, intent(out)  :: pt2(N_states),error(N_states)
   double precision, intent(out)  :: variance(N_states),norm(N_states)
@@ -111,7 +121,6 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
 
   integer                        :: i, N
 
-  double precision, external     :: omp_get_wtime
   double precision               :: state_average_weight_save(N_states), w(N_states,4)
   integer(ZMQ_PTR), external     :: new_zmq_to_qp_run_socket
   type(selection_buffer)         :: b
@@ -120,7 +129,11 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
   PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
   PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
   PROVIDE psi_bilinear_matrix_transp_order psi_selectors_coef_transp psi_det_sorted
+  PROVIDE psi_det_hii N_generators_bitmask
 
+  if (h0_type == 'SOP') then
+    PROVIDE psi_occ_pattern_hii det_to_occ_pattern
+  endif
 
   if (N_det < max(10,N_states)) then
     pt2=0.d0
@@ -132,6 +145,10 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
 
     N = max(N_in,1) * N_states
     state_average_weight_save(:) = state_average_weight(:)
+    if (int(N,8)*2_8 > huge(1)) then
+      print *,  irp_here, ': integer too large'
+      stop -1
+    endif
     call create_selection_buffer(N, N*2, b)
     ASSERT (associated(b%det))
     ASSERT (associated(b%val))
@@ -244,8 +261,8 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
               + 64.d0*pt2_n_tasks_max           & ! task
               + 3.d0*pt2_n_tasks_max*N_states   & ! pt2, variance, norm
               + 1.d0*pt2_n_tasks_max            & ! i_generator, subset
-              + 2.d0*(N_int*2.d0*N_in + N_in)   & ! selection buffers
+              + 1.d0*(N_int*2.d0*ii+ ii)        & ! selection buffer
-              + 1.d0*(N_int*2.d0*N_in + N_in)   & ! sort/merge selection buffers
+              + 1.d0*(N_int*2.d0*ii+ ii)        & ! sort selection buffer
               + 2.0d0*(ii)                      & ! preinteresting, interesting,
                                                   ! prefullinteresting, fullinteresting
               + 2.0d0*(N_int*2*ii)              & ! minilist, fullminilist
@@ -275,6 +292,7 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
       print '(A)', ' Samples        Energy        Stat. Err     Variance          Norm          Seconds      '
       print '(A)', '========== ================= =========== =============== =============== ================='
 
+      PROVIDE global_selection_buffer 
       !$OMP PARALLEL DEFAULT(shared) NUM_THREADS(nproc_target+1)            &
           !$OMP  PRIVATE(i)
       i = omp_get_thread_num()
@@ -322,12 +340,12 @@ subroutine pt2_slave_inproc(i)
   implicit none
   integer, intent(in)            :: i
 
+  PROVIDE global_selection_buffer 
   call run_pt2_slave(1,i,pt2_e0_denominator)
 end
 
 
-subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
+subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, variance, norm, b, N_)
-  variance, norm, b, N_)
   use f77_zmq
   use selection_types
   use bitmasks
@@ -347,7 +365,8 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
   double precision, allocatable      :: nI(:,:), nI_task(:,:), T3(:)
   integer(ZMQ_PTR),external      :: new_zmq_to_qp_run_socket
   integer(ZMQ_PTR)               :: zmq_to_qp_run_socket
-  integer, external :: zmq_delete_tasks
+  integer, external :: zmq_delete_tasks_async_send
+  integer, external :: zmq_delete_tasks_async_recv
   integer, external :: zmq_abort
   integer, external :: pt2_find_sample_lr
 
@@ -355,13 +374,12 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
   integer, allocatable :: task_id(:)
   integer, allocatable :: index(:)
 
-  double precision, external :: omp_get_wtime
   double precision :: v, x, x2, x3, avg, avg2, avg3, eqt, E0, v0, n0
   double precision :: time, time1, time0
 
   integer, allocatable :: f(:)
   logical, allocatable :: d(:)
-  logical :: do_exit, stop_now
+  logical :: do_exit, stop_now, sending
   logical, external :: qp_stop
   type(selection_buffer) :: b2
 
@@ -369,6 +387,8 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
   double precision :: rss
   double precision, external :: memory_of_double, memory_of_int
 
+  sending =.False.
+
   rss  = memory_of_int(pt2_n_tasks_max*2+N_det_generators*2)
   rss += memory_of_double(N_states*N_det_generators)*3.d0
   rss += memory_of_double(N_states*pt2_n_tasks_max)*3.d0
@@ -444,6 +464,7 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
       ! Add Stochastic part
       c = pt2_R(n)
       if(c > 0) then
+!print *,  'c>0'
         x  = 0d0
         x2 = 0d0
         x3 = 0d0
@@ -470,6 +491,7 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
         pt2(pt2_stoch_istate) = avg
         variance(pt2_stoch_istate) = avg2
         norm(pt2_stoch_istate) = avg3
+        call wall_time(time)
         ! 1/(N-1.5) : see  Brugger, The American Statistician (23) 4 p. 32 (1969)
         if(c > 2) then
           eqt = dabs((S2(t) / c) - (S(t)/c)**2) ! dabs for numerical stability
@@ -490,30 +512,36 @@ subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error,  &
             endif
           endif
         endif
-        call wall_time(time)
       end if
       n += 1
     else if(more == 0) then
       exit
     else
       call pull_pt2_results(zmq_socket_pull, index, eI_task, vI_task, nI_task, task_id, n_tasks, b2)
-      if (zmq_delete_tasks(zmq_to_qp_run_socket,zmq_socket_pull,task_id,n_tasks,more) == -1) then
+      if (zmq_delete_tasks_async_send(zmq_to_qp_run_socket,task_id,n_tasks,sending) == -1) then
-          stop 'Unable to delete tasks'
+          stop 'PT2: Unable to delete tasks (send)'
       endif
       do i=1,n_tasks
-        eI(:, index(i)) += eI_task(:,i)
+        eI(1:N_states, index(i)) += eI_task(1:N_states,i)
-        vI(:, index(i)) += vI_task(:,i)
+        vI(1:N_states, index(i)) += vI_task(1:N_states,i)
-        nI(:, index(i)) += nI_task(:,i)
+        nI(1:N_states, index(i)) += nI_task(1:N_states,i)
         f(index(i)) -= 1
       end do
       do i=1, b2%cur
-        call add_to_selection_buffer(b, b2%det(1,1,i), b2%val(i))
+        ! We assume the pulled buffer is sorted
         if (b2%val(i) > b%mini) exit
+        call add_to_selection_buffer(b, b2%det(1,1,i), b2%val(i))
       end do
+      if (zmq_delete_tasks_async_recv(zmq_to_qp_run_socket,more,sending) == -1) then
+          stop 'PT2: Unable to delete tasks (recv)'
+      endif
     end if
   end do
+!print *,  'deleting b2'
   call delete_selection_buffer(b2)
+!print *,  'sorting b'
   call sort_selection_buffer(b)
+!print *,  'done'
   call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
 
 end subroutine

src/cipsi/run_pt2_slave.irp.f

@@ -1,7 +1,46 @@
+ use omp_lib 
+ use selection_types
+ use f77_zmq
+BEGIN_PROVIDER [ integer(omp_lock_kind), global_selection_buffer_lock ]
+ use omp_lib 
+ implicit none
+ BEGIN_DOC
+ ! Global buffer for the OpenMP selection
+ END_DOC
+ call omp_init_lock(global_selection_buffer_lock)
+END_PROVIDER
+
+BEGIN_PROVIDER [ type(selection_buffer), global_selection_buffer ]
+ use omp_lib 
+ implicit none
+ BEGIN_DOC
+ ! Global buffer for the OpenMP selection
+ END_DOC
+ call omp_set_lock(global_selection_buffer_lock)
+ call delete_selection_buffer(global_selection_buffer)
+ call create_selection_buffer(N_det_generators, 2*N_det_generators, &
+    global_selection_buffer)
+ call omp_unset_lock(global_selection_buffer_lock)
+END_PROVIDER
+
 
 subroutine run_pt2_slave(thread,iproc,energy)
-  use f77_zmq
+ use selection_types
-  use selection_types
+ use f77_zmq
+  implicit none
+
+  double precision, intent(in)    :: energy(N_states_diag)
+  integer,  intent(in)            :: thread, iproc
+  if (N_det > nproc*(elec_alpha_num * (mo_num-elec_alpha_num))**2) then
+    call run_pt2_slave_large(thread,iproc,energy)
+  else
+    call run_pt2_slave_small(thread,iproc,energy)
+  endif
+end
+
+subroutine run_pt2_slave_small(thread,iproc,energy)
+ use selection_types
+ use f77_zmq
   implicit none
 
   double precision, intent(in)    :: energy(N_states_diag)
@@ -18,18 +57,16 @@ subroutine run_pt2_slave(thread,iproc,energy)
   integer(ZMQ_PTR), external     :: new_zmq_push_socket
   integer(ZMQ_PTR)               :: zmq_socket_push
 
-  type(selection_buffer) :: b, b2
+  type(selection_buffer) :: b
   logical :: done, buffer_ready
 
   double precision,allocatable :: pt2(:,:), variance(:,:), norm(:,:)
   integer :: n_tasks, k, N
   integer, allocatable :: i_generator(:), subset(:)
 
-  double precision :: rss
   double precision, external :: memory_of_double, memory_of_int
-  rss  = memory_of_int(pt2_n_tasks_max)*67.d0
+  integer :: bsize ! Size of selection buffers
-  rss += memory_of_double(pt2_n_tasks_max)*(N_states*3)
+!  logical :: sending
-  call check_mem(rss,irp_here)
 
   allocate(task_id(pt2_n_tasks_max), task(pt2_n_tasks_max))
   allocate(pt2(N_states,pt2_n_tasks_max), i_generator(pt2_n_tasks_max), subset(pt2_n_tasks_max))
@@ -50,8 +87,8 @@ subroutine run_pt2_slave(thread,iproc,energy)
   buffer_ready = .False.
   n_tasks = 1
 
+!  sending = .False.
   done = .False.
-  n_tasks = 1
   do while (.not.done)
 
     n_tasks = max(1,n_tasks)
@@ -72,11 +109,11 @@ subroutine run_pt2_slave(thread,iproc,energy)
     enddo
     if (b%N == 0) then
       ! Only first time
-      call create_selection_buffer(N, N*2, b)
+      bsize = min(N, (elec_alpha_num * (mo_num-elec_alpha_num))**2)
-      call create_selection_buffer(N, N*2, b2)
+      call create_selection_buffer(bsize, bsize*2, b)
       buffer_ready = .True.
     else
-      ASSERT (N == b%N)
+      ASSERT (b%N == bsize)
     endif
 
     double precision :: time0, time1
@@ -93,20 +130,19 @@ subroutine run_pt2_slave(thread,iproc,energy)
 !print *,  i_generator(1), time1-time2, n_tasks, pt2_F(i_generator(1))
     enddo
     call wall_time(time1)
-!print *,  i_generator(1), time1-time0, n_tasks
+!print *,  '-->', i_generator(1), time1-time0, n_tasks
 
     integer, external :: tasks_done_to_taskserver
     if (tasks_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id,n_tasks) == -1) then
       done = .true.
     endif
     call sort_selection_buffer(b)
-    call merge_selection_buffers(b,b2)
     call push_pt2_results(zmq_socket_push, i_generator, pt2, variance, norm, b, task_id, n_tasks)
-    b%mini = b2%mini
     b%cur=0
 
-    ! Try to adjust n_tasks around nproc/8 seconds per job
+!    ! Try to adjust n_tasks around nproc/2 seconds per job
-    n_tasks = min(2*n_tasks,int( dble(n_tasks * nproc/8) / (time1 - time0 + 1.d0)))
+!    n_tasks = min(2*n_tasks,int( dble(n_tasks * nproc/2) / (time1 - time0 + 1.d0)))
+    n_tasks = 1
   end do
 
   integer, external :: disconnect_from_taskserver
@@ -120,14 +156,150 @@ subroutine run_pt2_slave(thread,iproc,energy)
   call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
   if (buffer_ready) then
     call delete_selection_buffer(b)
-    call delete_selection_buffer(b2)
   endif
 end subroutine
 
 
+subroutine run_pt2_slave_large(thread,iproc,energy)
+ use selection_types
+ use f77_zmq
+  implicit none
+
+  double precision, intent(in)    :: energy(N_states_diag)
+  integer,  intent(in)            :: thread, iproc
+  integer                         :: rc, i
+
+  integer                        :: worker_id, ctask, ltask
+  character*(512), allocatable   :: task(:)
+  integer, allocatable           :: task_id(:)
+
+  integer(ZMQ_PTR),external      :: new_zmq_to_qp_run_socket
+  integer(ZMQ_PTR)               :: zmq_to_qp_run_socket
+
+  integer(ZMQ_PTR), external     :: new_zmq_push_socket
+  integer(ZMQ_PTR)               :: zmq_socket_push
+
+  type(selection_buffer) :: b
+  logical :: done, buffer_ready
+
+  double precision,allocatable :: pt2(:,:), variance(:,:), norm(:,:)
+  integer :: n_tasks, k, N
+  integer, allocatable :: i_generator(:), subset(:)
+
+  integer :: bsize ! Size of selection buffers
+  logical :: sending
+  PROVIDE global_selection_buffer global_selection_buffer_lock
+
+
+  allocate(task_id(pt2_n_tasks_max), task(pt2_n_tasks_max))
+  allocate(pt2(N_states,pt2_n_tasks_max), i_generator(pt2_n_tasks_max), subset(pt2_n_tasks_max))
+  allocate(variance(N_states,pt2_n_tasks_max))
+  allocate(norm(N_states,pt2_n_tasks_max))
+
+  zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
+
+  integer, external :: connect_to_taskserver
+  if (connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread) == -1) then
+    call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
+    return
+  endif
+
+  zmq_socket_push      = new_zmq_push_socket(thread)
+
+  b%N = 0
+  buffer_ready = .False.
+  n_tasks = 1
+
+  sending = .False.
+  done = .False.
+  do while (.not.done)
+
+    n_tasks = max(1,n_tasks)
+    n_tasks = min(pt2_n_tasks_max,n_tasks)
+
+    integer, external :: get_tasks_from_taskserver
+    if (get_tasks_from_taskserver(zmq_to_qp_run_socket,worker_id, task_id, task, n_tasks) == -1) then
+      exit
+    endif
+    done = task_id(n_tasks) == 0
+    if (done) then
+      n_tasks = n_tasks-1
+    endif
+    if (n_tasks == 0) exit
+
+    do k=1,n_tasks
+      read (task(k),*) subset(k), i_generator(k), N
+    enddo
+    if (b%N == 0) then
+      ! Only first time
+      bsize = min(N, (elec_alpha_num * (mo_num-elec_alpha_num))**2)
+      call create_selection_buffer(bsize, bsize*2, b)
+      buffer_ready = .True.
+    else
+      ASSERT (b%N == bsize)
+    endif
+
+    double precision :: time0, time1
+    call wall_time(time0)
+    do k=1,n_tasks
+        pt2(:,k) = 0.d0
+        variance(:,k) = 0.d0
+        norm(:,k) = 0.d0
+        b%cur = 0
+!double precision :: time2
+!call wall_time(time2)
+        call select_connected(i_generator(k),energy,pt2(1,k),variance(1,k),norm(1,k),b,subset(k),pt2_F(i_generator(k)))
+!call wall_time(time1)
+!print *,  i_generator(1), time1-time2, n_tasks, pt2_F(i_generator(1))
+    enddo
+    call wall_time(time1)
+!print *,  '-->', i_generator(1), time1-time0, n_tasks
+
+    integer, external :: tasks_done_to_taskserver
+    if (tasks_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id,n_tasks) == -1) then
+      done = .true.
+    endif
+    call sort_selection_buffer(b)
+    call push_pt2_results_async_recv(zmq_socket_push,b%mini,sending)
+    call omp_set_lock(global_selection_buffer_lock)
+    global_selection_buffer%mini = b%mini
+    call merge_selection_buffers(b,global_selection_buffer)
+    b%cur=0
+    call omp_unset_lock(global_selection_buffer_lock)
+    if ( iproc == 1 ) then
+      call omp_set_lock(global_selection_buffer_lock)
+      call push_pt2_results_async_send(zmq_socket_push, i_generator, pt2, variance, norm, global_selection_buffer, task_id, n_tasks,sending)
+      global_selection_buffer%cur = 0
+      call omp_unset_lock(global_selection_buffer_lock)
+    else
+      call push_pt2_results_async_send(zmq_socket_push, i_generator, pt2, variance, norm, b, task_id, n_tasks,sending)
+    endif
+
+!    ! Try to adjust n_tasks around nproc/2 seconds per job
+!    n_tasks = min(2*n_tasks,int( dble(n_tasks * nproc/2) / (time1 - time0 + 1.d0)))
+    n_tasks = 1
+  end do
+  call push_pt2_results_async_recv(zmq_socket_push,b%mini,sending)
+
+  integer, external :: disconnect_from_taskserver
+  do i=1,300
+    if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) /= -2) exit
+    call sleep(1)
+    print *,  'Retry disconnect...'
+  end do
+
+  call end_zmq_push_socket(zmq_socket_push,thread)
+  call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
+  if (buffer_ready) then
+    call delete_selection_buffer(b)
+  endif
+  FREE global_selection_buffer
+end subroutine
+
+
 subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task_id, n_tasks)
-  use f77_zmq
+ use selection_types
-  use selection_types
+ use f77_zmq
   implicit none
 
   integer(ZMQ_PTR), intent(in)   :: zmq_socket_push
@@ -136,10 +308,39 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
   double precision, intent(in)   :: norm(N_states,n_tasks)
   integer, intent(in) :: n_tasks, index(n_tasks), task_id(n_tasks)
   type(selection_buffer), intent(inout) :: b
+
+  logical :: sending
+  sending = .False.
+  call push_pt2_results_async_send(zmq_socket_push, index, pt2, variance, norm, b, task_id, n_tasks, sending)
+  call push_pt2_results_async_recv(zmq_socket_push, b%mini, sending)
+end subroutine
+
+
+subroutine push_pt2_results_async_send(zmq_socket_push, index, pt2, variance, norm, b, task_id, n_tasks, sending)
+ use selection_types
+ use f77_zmq
+  implicit none
+
+  integer(ZMQ_PTR), intent(in)   :: zmq_socket_push
+  double precision, intent(in)   :: pt2(N_states,n_tasks)
+  double precision, intent(in)   :: variance(N_states,n_tasks)
+  double precision, intent(in)   :: norm(N_states,n_tasks)
+  integer, intent(in) :: n_tasks, index(n_tasks), task_id(n_tasks)
+  type(selection_buffer), intent(inout) :: b
+  logical, intent(inout) :: sending
   integer :: rc
+  integer*8 :: rc8
+
+  if (sending) then
+    print *,  irp_here, ': sending is true'
+    stop -1
+  endif
+  sending = .True.
 
   rc = f77_zmq_send( zmq_socket_push, n_tasks, 4, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 1
     return
   else if(rc /= 4) then
     stop 'push'
@@ -148,6 +349,8 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
 
   rc = f77_zmq_send( zmq_socket_push, index, 4*n_tasks, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 2
     return
   else if(rc /= 4*n_tasks) then
     stop 'push'
@@ -156,6 +359,8 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
 
   rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states*n_tasks, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 3
     return
   else if(rc /= 8*N_states*n_tasks) then
     stop 'push'
@@ -164,6 +369,8 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
 
   rc = f77_zmq_send( zmq_socket_push, variance, 8*N_states*n_tasks, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 4
     return
   else if(rc /= 8*N_states*n_tasks) then
     stop 'push'
@@ -172,6 +379,8 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
 
   rc = f77_zmq_send( zmq_socket_push, norm, 8*N_states*n_tasks, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 5
     return
   else if(rc /= 8*N_states*n_tasks) then
     stop 'push'
@@ -180,35 +389,71 @@ subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, b, task
 
   rc = f77_zmq_send( zmq_socket_push, task_id, n_tasks*4, ZMQ_SNDMORE)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 6
     return
   else if(rc /= 4*n_tasks) then
     stop 'push'
   endif
 
 
-  rc = f77_zmq_send( zmq_socket_push, b%cur, 4, ZMQ_SNDMORE)
+  if (b%cur == 0) then
-  if (rc == -1) then
+
-    return
+    rc = f77_zmq_send( zmq_socket_push, b%cur, 4, 0)
-  else if(rc /= 4) then
+    if (rc == -1) then
-    stop 'push'
+      print *,  irp_here, ': error sending result'
+      stop 7
+      return
+    else if(rc /= 4) then
+      stop 'push'
+    endif
+
+  else
+
+    rc = f77_zmq_send( zmq_socket_push, b%cur, 4, ZMQ_SNDMORE)
+    if (rc == -1) then
+      print *,  irp_here, ': error sending result'
+      stop 7
+      return
+    else if(rc /= 4) then
+      stop 'push'
+    endif
+
+
+    rc8 = f77_zmq_send8( zmq_socket_push, b%val, 8_8*int(b%cur,8), ZMQ_SNDMORE)
+    if (rc8 == -1_8) then
+      print *,  irp_here, ': error sending result'
+      stop 8
+      return
+    else if(rc8 /= 8_8*int(b%cur,8)) then
+      stop 'push'
+    endif
+
+
+    rc8 = f77_zmq_send8( zmq_socket_push, b%det, int(bit_kind*N_int*2,8)*int(b%cur,8), 0)
+    if (rc8 == -1_8) then
+      print *,  irp_here, ': error sending result'
+      stop 9
+      return
+    else if(rc8 /= int(N_int*2*8,8)*int(b%cur,8)) then
+      stop 'push'
+    endif
+
   endif
 
+end subroutine
 
-  rc = f77_zmq_send( zmq_socket_push, b%val, 8*b%cur, ZMQ_SNDMORE)
+subroutine push_pt2_results_async_recv(zmq_socket_push,mini,sending)
-  if (rc == -1) then
+ use selection_types
-    return
+ use f77_zmq
-  else if(rc /= 8*b%cur) then
+  implicit none
-    stop 'push'
-  endif
 
+  integer(ZMQ_PTR), intent(in)    :: zmq_socket_push
+  double precision, intent(out) :: mini
+  logical, intent(inout) :: sending
+  integer :: rc
 
-  rc = f77_zmq_send( zmq_socket_push, b%det, bit_kind*N_int*2*b%cur, 0)
+  if (.not.sending) return
-  if (rc == -1) then
-    return
-  else if(rc /= N_int*2*8*b%cur) then
-    stop 'push'
-  endif
-
 
 ! Activate is zmq_socket_push is a REQ
 IRP_IF ZMQ_PUSH
@@ -216,19 +461,31 @@ IRP_ELSE
   character*(2) :: ok
   rc = f77_zmq_recv( zmq_socket_push, ok, 2, 0)
   if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 10
     return
   else if ((rc /= 2).and.(ok(1:2) /= 'ok')) then
     print *,  irp_here//': error in receiving ok'
     stop -1
   endif
+  rc = f77_zmq_recv( zmq_socket_push, mini, 8, 0)
+  if (rc == -1) then
+    print *,  irp_here, ': error sending result'
+    stop 11
+    return
+  else if (rc /= 8) then
+    print *,  irp_here//': error in receiving mini' 
+    stop 12
+  endif
 IRP_ENDIF
-
+  sending = .False.
 end subroutine
 
 
+
 subroutine pull_pt2_results(zmq_socket_pull, index, pt2, variance, norm, task_id, n_tasks, b)
-  use f77_zmq
+ use selection_types
-  use selection_types
+ use f77_zmq
   implicit none
   integer(ZMQ_PTR), intent(in)   :: zmq_socket_pull
   double precision, intent(inout) :: pt2(N_states,*)
@@ -238,6 +495,7 @@ subroutine pull_pt2_results(zmq_socket_pull, index, pt2, variance, norm, task_id
   integer, intent(out) :: index(*)
   integer, intent(out) :: n_tasks, task_id(*)
   integer :: rc, rn, i
+  integer*8 :: rc8
 
   rc = f77_zmq_recv( zmq_socket_pull, n_tasks, 4, 0)
   if (rc == -1) then
@@ -295,27 +553,30 @@ subroutine pull_pt2_results(zmq_socket_pull, index, pt2, variance, norm, task_id
     stop 'pull'
   endif
 
-  rc = f77_zmq_recv( zmq_socket_pull, b%val, 8*b%cur, 0)
+  if (b%cur > 0) then
-  if (rc == -1) then
-    n_tasks = 1
-    task_id(1) = 0
-  else if(rc /= 8*b%cur) then
-    stop 'pull'
-  endif
 
-  rc = f77_zmq_recv( zmq_socket_pull, b%det, bit_kind*N_int*2*b%cur, 0)
+    rc8 = f77_zmq_recv8( zmq_socket_pull, b%val, 8_8*int(b%cur,8), 0)
-  if (rc == -1) then
+    if (rc8 == -1_8) then
-    n_tasks = 1
+      n_tasks = 1
-    task_id(1) = 0
+      task_id(1) = 0
-  else if(rc /= N_int*2*8*b%cur) then
+    else if(rc8 /= 8_8*int(b%cur,8)) then
-    stop 'pull'
+      stop 'pull'
-  endif
+    endif
 
+    rc8 = f77_zmq_recv8( zmq_socket_pull, b%det, int(bit_kind*N_int*2,8)*int(b%cur,8), 0)
+    if (rc8 == -1_8) then
+      n_tasks = 1
+      task_id(1) = 0
+    else if(rc8 /= int(N_int*2*8,8)*int(b%cur,8)) then
+      stop 'pull'
+    endif
+
+  endif
 
 ! Activate is zmq_socket_pull is a REP
 IRP_IF ZMQ_PUSH
 IRP_ELSE
-  rc = f77_zmq_send( zmq_socket_pull, 'ok', 2, 0)
+  rc = f77_zmq_send( zmq_socket_pull, 'ok', 2, ZMQ_SNDMORE)
   if (rc == -1) then
     n_tasks = 1
     task_id(1) = 0
@@ -323,6 +584,7 @@ IRP_ELSE
     print *,  irp_here//': error in sending ok'
     stop -1
   endif
+  rc = f77_zmq_send( zmq_socket_pull, b%mini, 8, 0)
 IRP_ENDIF
 
 end subroutine

src/cipsi/run_selection_slave.irp.f

@@ -55,12 +55,13 @@ subroutine run_selection_slave(thread,iproc,energy)
     if (done) then
       ctask = ctask - 1
     else
-      integer :: i_generator, N, subset
+      integer :: i_generator, N, subset, bsize
       read(task,*) subset, i_generator, N
       if(buf%N == 0) then
         ! Only first time
-        call create_selection_buffer(N, N*2, buf)
+        bsize = min(N, (elec_alpha_num * (mo_num-elec_alpha_num))**2)
-        call create_selection_buffer(N, N*2, buf2)
+        call create_selection_buffer(bsize, bsize*2, buf)
+!        call create_selection_buffer(N, N*2, buf2)
         buffer_ready = .True.
       else
         ASSERT (N == buf%N)
@@ -83,9 +84,9 @@ subroutine run_selection_slave(thread,iproc,energy)
       end do
       if(ctask > 0) then
         call sort_selection_buffer(buf)
-        call merge_selection_buffers(buf,buf2)
+!        call merge_selection_buffers(buf,buf2)
         call push_selection_results(zmq_socket_push, pt2, variance, norm, buf, task_id(1), ctask)
-        buf%mini = buf2%mini
+!        buf%mini = buf2%mini
         pt2(:) = 0d0
         variance(:) = 0d0
         norm(:) = 0d0
@@ -108,7 +109,7 @@ subroutine run_selection_slave(thread,iproc,energy)
   call end_zmq_push_socket(zmq_socket_push,thread)
   if (buffer_ready) then
     call delete_selection_buffer(buf)
-    call delete_selection_buffer(buf2)
+!    call delete_selection_buffer(buf2)
   endif
 end subroutine
 

src/cipsi/selection.irp.f

@@ -153,27 +153,11 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
   logical :: monoAdo, monoBdo
   integer :: maskInd
 
-  double precision :: rss
-  double precision, external :: memory_of_double, memory_of_int
-
   PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
   PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
   PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
   PROVIDE psi_bilinear_matrix_transp_order psi_selectors_coef_transp
 
-  ii = min(N_det,(elec_alpha_num*(mo_num-elec_alpha_num))**2)
-  rss = memory_of_double(             &
-            2*N_int*2*ii   &   ! minilist, fullminilist
-          + N_states*mo_num*mo_num    &   ! mat
-        ) + memory_of_int(            &
-          + 2*ii                      &   ! preinteresting, prefullinteresting,
-          + 2*ii                      &   ! interesting, fullinteresting
-          + mo_num*mo_num/2           &   ! banned
-          + mo_num/2                  &   ! bannedOrb
-        )
-
-  call check_mem(rss,irp_here)
-  
   monoAdo = .true.
   monoBdo = .true.
   
@@ -244,7 +228,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
   
   deallocate(exc_degree)
   nmax=k-1
-  
+
   allocate(iorder(nmax))
   do i=1,nmax
     iorder(i) = i
@@ -254,8 +238,8 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
   
   allocate(preinteresting(0:32), prefullinteresting(0:32),     &
       interesting(0:32), fullinteresting(0:32))
-  preinteresting(0) = 0
+  preinteresting(:) = 0
-  prefullinteresting(0) = 0
+  prefullinteresting(:) = 0
   
   do i=1,N_int
     negMask(i,1) = not(psi_det_generators(i,1,i_generator))
@@ -658,13 +642,11 @@ subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, intere
     negMask(i,2) = not(mask(i,2))
   end do
 
-  do i=1, N_sel ! interesting(0)
+  do i=1, N_sel 
-    !i = interesting(ii)
     if (interesting(i) < 0) then
       stop 'prefetch interesting(i) and det(i)'
     endif
 
-
     mobMask(1,1) = iand(negMask(1,1), det(1,1,i))
     mobMask(1,2) = iand(negMask(1,2), det(1,2,i))
     nt = popcnt(mobMask(1, 1)) + popcnt(mobMask(1, 2))
@@ -695,10 +677,10 @@ subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, intere
         end if
     end if
 
-    call bitstring_to_list_in_selection(mobMask(1,1), p(1,1), p(0,1), N_int)
-    call bitstring_to_list_in_selection(mobMask(1,2), p(1,2), p(0,2), N_int)
-
     if (interesting(i) >= i_gen) then
+        call bitstring_to_list_in_selection(mobMask(1,1), p(1,1), p(0,1), N_int)
+        call bitstring_to_list_in_selection(mobMask(1,2), p(1,2), p(0,2), N_int)
+
         perMask(1,1) = iand(mask(1,1), not(det(1,1,i)))
         perMask(1,2) = iand(mask(1,2), not(det(1,2,i)))
         do j=2,N_int
@@ -717,9 +699,14 @@ subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, intere
         else
           call get_d0(det(1,1,i), phasemask, bannedOrb, banned, mat, mask, h, p, sp, psi_selectors_coef_transp(1, interesting(i)))
         end if
-    else
+    else if(nt == 4) then
-        if(nt == 4) call past_d2(banned, p, sp)
+        call bitstring_to_list_in_selection(mobMask(1,1), p(1,1), p(0,1), N_int)
-        if(nt == 3) call past_d1(bannedOrb, p)
+        call bitstring_to_list_in_selection(mobMask(1,2), p(1,2), p(0,2), N_int)
+        call past_d2(banned, p, sp)
+    else if(nt == 3) then
+        call bitstring_to_list_in_selection(mobMask(1,1), p(1,1), p(0,1), N_int)
+        call bitstring_to_list_in_selection(mobMask(1,2), p(1,2), p(0,2), N_int)
+        call past_d1(bannedOrb, p)
     end if
   end do
 
@@ -1279,4 +1266,4 @@ subroutine bitstring_to_list_in_selection( string, list, n_elements, Nint)
   enddo
 
 end
-
+!

src/cipsi/selection_buffer.irp.f

@@ -2,6 +2,10 @@
 subroutine create_selection_buffer(N, siz_, res)
   use selection_types
   implicit none
+  BEGIN_DOC
+! Allocates the memory for a selection buffer.
+! The arrays have dimension siz_ and the maximum number of elements is N
+  END_DOC
 
   integer, intent(in) :: N, siz_
   type(selection_buffer), intent(out) :: res
@@ -33,6 +37,11 @@ subroutine delete_selection_buffer(b)
   if (associated(b%val)) then
     deallocate(b%val)
   endif
+  NULLIFY(b%det)
+  NULLIFY(b%val)
+  b%cur = 0
+  b%mini = 0.d0
+  b%N = 0
 end
 
 
@@ -65,7 +74,7 @@ subroutine merge_selection_buffers(b1, b2)
   type(selection_buffer), intent(inout) :: b2
   integer(bit_kind), pointer     :: detmp(:,:,:)
   double precision, pointer      :: val(:)
-  integer                        :: i, i1, i2, k, nmwen
+  integer                        :: i, i1, i2, k, nmwen, sze
   if (b1%cur == 0) return
   do while (b1%val(b1%cur) > b2%mini)
     b1%cur = b1%cur-1
@@ -76,9 +85,10 @@ subroutine merge_selection_buffers(b1, b2)
   nmwen = min(b1%N, b1%cur+b2%cur)
   double precision :: rss
   double precision, external :: memory_of_double
-  rss = memory_of_double(size(b1%val)) + 2*N_int*memory_of_double(size(b1%det,3))
+  sze = max(size(b1%val), size(b2%val))
+  rss = memory_of_double(sze) + 2*N_int*memory_of_double(sze)
   call check_mem(rss,irp_here)
-  allocate( val(size(b1%val)), detmp(N_int, 2, size(b1%det,3)) )
+  allocate(val(sze), detmp(N_int, 2, sze))
   i1=1
   i2=1
   do i=1,nmwen

src/cipsi/slave_cipsi.irp.f

@@ -53,7 +53,7 @@ subroutine run_slave_main
 
   PROVIDE psi_det psi_coef threshold_generators state_average_weight mpi_master
   PROVIDE zmq_state N_det_selectors pt2_stoch_istate N_det pt2_e0_denominator
-  PROVIDE N_det_generators N_states N_states_diag pt2_e0_denominator
+  PROVIDE N_det_generators N_states N_states_diag pt2_e0_denominator mpi_rank
 
   IRP_IF MPI
     call MPI_BARRIER(MPI_COMM_WORLD, ierr)
@@ -161,18 +161,17 @@ subroutine run_slave_main
         call mpi_print('zmq_get_psi')
       IRP_ENDIF
       if (zmq_get_psi(zmq_to_qp_run_socket,1) == -1) cycle
-      IRP_IF MPI_DEBUG
-        call mpi_print('zmq_get_dvector energy')
-      IRP_ENDIF
-      if (zmq_get_dvector(zmq_to_qp_run_socket,1,'energy',energy,N_states_diag) == -1) cycle
 
       call wall_time(t1)
       call write_double(6,(t1-t0),'Broadcast time')
 
+      !---
       call omp_set_nested(.True.)
       call davidson_slave_tcp(0)
       call omp_set_nested(.False.)
       print *,  mpi_rank, ': Davidson done'
+      !---
+
       IRP_IF MPI
         call MPI_BARRIER(MPI_COMM_WORLD, ierr)
         if (ierr /= MPI_SUCCESS) then
@@ -223,14 +222,6 @@ subroutine run_slave_main
       if (zmq_get_dvector(zmq_to_qp_run_socket,1,'state_average_weight',state_average_weight,N_states) == -1) cycle
       pt2_e0_denominator(1:N_states) = energy(1:N_states)
       SOFT_TOUCH pt2_e0_denominator state_average_weight pt2_stoch_istate threshold_generators
-      if (mpi_master) then
-        print *,  'N_det', N_det
-        print *,  'N_det_generators', N_det_generators
-        print *,  'N_det_selectors', N_det_selectors
-        print *,  'pt2_e0_denominator', pt2_e0_denominator
-        print *,  'pt2_stoch_istate', pt2_stoch_istate
-        print *,  'state_average_weight', state_average_weight
-      endif
 
       call wall_time(t1)
       call write_double(6,(t1-t0),'Broadcast time')
@@ -241,17 +232,78 @@ subroutine run_slave_main
         endif
       IRP_ENDIF
 
+
       IRP_IF MPI_DEBUG
         call mpi_print('Entering OpenMP section')
       IRP_ENDIF
       if (.true.) then
-        !$OMP PARALLEL PRIVATE(i)
+        integer :: nproc_target, ii
-        i = omp_get_thread_num()
+        double precision :: mem_collector, mem, rss
-        call run_pt2_slave(0,i,pt2_e0_denominator)
+
-        !$OMP END PARALLEL
+        call resident_memory(rss)
+
+        nproc_target = nthreads_pt2
+        ii = min(N_det, (elec_alpha_num*(mo_num-elec_alpha_num))**2)
+
+        do
+          mem = rss +                             & !
+                nproc_target * 8.d0 *             & ! bytes
+                ( 0.5d0*pt2_n_tasks_max           & ! task_id
+                + 64.d0*pt2_n_tasks_max           & ! task
+                + 3.d0*pt2_n_tasks_max*N_states   & ! pt2, variance, norm
+                + 1.d0*pt2_n_tasks_max            & ! i_generator, subset
+                + 3.d0*(N_int*2.d0*ii+ ii)        & ! selection buffer
+                + 1.d0*(N_int*2.d0*ii+ ii)        & ! sort selection buffer
+                + 2.0d0*(ii)                      & ! preinteresting, interesting,
+                                                    ! prefullinteresting, fullinteresting
+                + 2.0d0*(N_int*2*ii)              & ! minilist, fullminilist
+                + 1.0d0*(N_states*mo_num*mo_num)  & ! mat
+                ) / 1024.d0**3
+
+          if (nproc_target == 0) then
+            call check_mem(mem,irp_here)
+            nproc_target = 1
+            exit
+          endif
+
+          if (mem+rss < qp_max_mem) then
+            exit
+          endif
+
+          nproc_target = nproc_target - 1
+
+        enddo
+        
+        if (N_det > 100000) then
+
+          if (mpi_master) then
+            print *,  'N_det', N_det
+            print *,  'N_det_generators', N_det_generators
+            print *,  'N_det_selectors', N_det_selectors
+            print *,  'pt2_e0_denominator', pt2_e0_denominator
+            print *,  'pt2_stoch_istate', pt2_stoch_istate
+            print *,  'state_average_weight', state_average_weight
+            print *,  'Number of threads', nproc_target
+          endif
+
+          if (h0_type == 'SOP') then
+            PROVIDE det_to_occ_pattern
+          endif
+
+          PROVIDE global_selection_buffer 
+          if (mpi_master) then
+            print *,  'Running PT2'
+          endif
+          !$OMP PARALLEL PRIVATE(i) NUM_THREADS(nproc_target+1)
+          i = omp_get_thread_num()
+          call run_pt2_slave(0,i,pt2_e0_denominator)
+          !$OMP END PARALLEL
+          FREE state_average_weight
+          print *,  mpi_rank, ': PT2 done'
+          print *,  '-------'
+
+        endif
       endif
-      FREE state_average_weight
-      print *,  mpi_rank, ': PT2 done'
 
       IRP_IF MPI
         call MPI_BARRIER(MPI_COMM_WORLD, ierr)

src/cipsi/stochastic_cipsi.irp.f

@@ -10,7 +10,7 @@ subroutine run_stochastic_cipsi
 
   double precision :: rss
   double precision, external :: memory_of_double
-  PROVIDE H_apply_buffer_allocated
+  PROVIDE H_apply_buffer_allocated N_generators_bitmask
 
   threshold_generators = 1.d0
   SOFT_TOUCH threshold_generators