Merge branch 'master' of github.com:scemama/quantum_package

Conflicts:
	scripts/compilation/qp_create_ninja.py

.travis.yml

@@ -1,4 +1,8 @@
 sudo: true
+#
+#cache:
+#  directories:
+#  - $HOME/.opam/
 
 language: python
 python:
@@ -12,6 +16,7 @@ before_script:
 script: 
   - ./configure  --production ./config/gfortran.cfg
   - source ./quantum_package.rc
+  - qp_install_module.py install Full_CI Hartree_Fock
   - ninja
   - cd ocaml ; make ; cd -
   - cd testing_no_regression ; ./unit_test.py

COMPILE_RUN.md

@@ -1,38 +0,0 @@
-# Compile
-
-We need to create the file which contains all the tree dependencies for the
-binaries.  It's not a Makefile, but a Ninja file (so don't type `make` is
-hopeless, type `ninja` instead).
-
-The script to create the dependency file (aka `build.ninja`) is
-`qp_create_ninja.py`.
-
-## What utilization of the code will you do?
-
-* If you only want the binaries (for production workflow) use the flag
-  `--production` in when calling this script. It's quicker 
-* Else if you are a developer and you want to be able to compile specific
-  modules use: `--development`. It will create for you the `build.ninja` in each
-  module
-
-## Compilation Flags
-
-You need to specify all the flags useful for the compilation:  like the
-optimization flags, the Lapack libary, etc.  ``$QP_ROOT/config`` contains
-``ifort.cfg`` and ``gfortran.cfg`` containing the compiler flags that will be
-used.  You can edit these files to modify the compiling options. 
-
-## Example to create the Ninja file
-
-`qp_create_ninja.py create --production $QP_ROOT/config/ifort.cfg`
-
-## Compiling
-
-Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja`
-elsewhere). The compilation will take approximately 3 min.
-
-If you have set the `--developement` flag in a specific module you can go in
-the corresponding module directory and run `ninja` to build only this module.
-You can type `ninja all` in a module for compiling all the submodule
-
-Finally, go in `$QP_ROOT/ocaml` and type `make`

INSTALL.md

@@ -1,85 +0,0 @@
-# Installation
-
-## Requirements
-
-* curl
-* m4
-* GNU make
-* Fortran compiler (ifort or gfortran are tested)
-* Python >= 2.6
-* Bash
-* Patch (for opam)
-
-## Optional
-
-* graphviz
-
-
-## Standard installation
-
-1) `./setup_environment.sh`
-
-This command will download and install all the requirements.
-Installing OCaml and the Core library may take somme time
-(up to 20min on an old machine).
-
-2) `source quantum_package.rc`
-
-This file contains all the environement variables neeeded by the quantum package
-both to compile and run. This should also be done before running calculations.
-
-3) `cp ./src/Makefile.config.gfortran  ./src/Makefile.config`
-
-Create the ``Makefile.config`` which contains all the flags needed by the compiler.
-The is also an example for the Intel Compiler (`Makefile.config.ifort`).
-Edit this file and tune the flags as you want.
-
-4) `make build`
-
-It will compile all the executables and tools. 
-
-5) `make binary`
-
-Optional. It will build a `tar.gz` file containing everything needed to run the quantum package on a
-machine where you can't compile.
-
-
-## Installing behind a firewall
-
-1) Download `tsocks`:
-
-    wget http://sourceforge.net/projects/tsocks/files/latest/download
-    mv download tsocks.tar.gz
-
-2) Tranfer `tsocks.tar.gz` on the remote host
-
-3) Configure `tsocks` with the proper directory for the `tsocks.conf` file:
-
-    tar -zxvf tsocks.tar.gz
-    cd tsocks-*
-    ./configure --with-conf=${PWD}/tsocks.conf
-
-4) Create the `tsocks.conf` file with the following content:
-
-    server = 127.0.0.1
-    server_port = 10000
-
-5) Create the tsocks library:
-
-    make
-
-6) Add the `libtsocks.so` to the `LD_PRELOAD` environment variable:
-
-    export LD_PRELOAD="${PWD}/libtsocks.so.1.8"
-
-7) Create a custom curl command to set the tsocks option: open a file named
-   `curl`, which is accessible from your `PATH` environment variable before the
-   real `curl` command, and fill this file with:
-
-    #!/bin/bash
-    /usr/bin/curl --socks5 127.0.0.1:10000 $@
-
-8) Start a tsocks ssh tunnel:
-
-    ssh -fN -D 10000 user@external-server.com
-

README.md

@@ -1,10 +1,161 @@
 Quantum package
 ===============
+
 [![Build Status](https://travis-ci.org/LCPQ/quantum_package.svg?branch=master)](https://travis-ci.org/LCPQ/quantum_package)
 
-[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/LCPQ/quantum_package?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/LCPQ/quantum_package?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
-Set of quantum chemistry programs and libraries.
+Set of quantum chemistry programs and libraries. 
+(under GNU GENERAL PUBLIC LICENSE v2)
 
-For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or the [Install](INSTALL.md) file.
+For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or bellow for the installation instruction.
+
+# Installation
+
+## Requirements
+* Fortran compiler (`ifort` and `gfortran` are tested)
+* Python >= 2.6
+* GNU make
+* Bash
+
+## Standard installation
+
+### 1) Configure
+
+    $ ./configure <config_file> (--production | --development)
+
+For example you can type `./configure config/gfortran.cfg --production`
+
+This command have to purpose :
+
+ - Download and install all the requirements.
+   Installing OCaml and the Core library may take somme time (up to 20min on an old machine).
+ - And create the file which contains all the tree dependencies for the binaries.  
+   It's not a Makefile, but a Ninja file (so don't type `make` is hopeless, type `ninja` instead)
+
+####Compilation Flags (`<config_file>`)
+
+`<config_file>` is the path to the file who contain all the flags useful for the compilation:  like the optimization flags, the Lapack libary, etc.  We have two default configure file in  ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``.  You can edit these files to modify the compiling options. 
+
+#### What utilization of the code will you do?
+
+* If you only want the binaries (for production workflow) use the flag
+  `--production` in when calling this script. It's quicker 
+* Else if you are a developer and you want to be able to compile specific modules use: `--development`. It will create for you the `build.ninja` in each module
+
+### 2) Set environment variable
+ 
+    source quantum_package.rc
+This file contains all the environment variables needed by the quantum package both to compile and run. This should also be done before running calculations.
+
+### Optional) Add some new module
+
+      Usage: qp_install_module.py list (--installed|--avalaible-local|--avalaible-remote)
+       qp_install_module.py install <name>...
+       qp_install_module.py create -n <name> [<children_module>...]
+       qp_install_module.py download -n <name> [<path_folder>...]
+
+ For exemple you can type :
+`qp_install_module.py install Full_CI`
+
+### 3) Compiling the fortran
+
+    ninja 
+Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja`
+elsewhere). The compilation will take approximately 3 min.
+
+If you have set the `--developement` flag in a specific module you can go in
+the corresponding module directory and run `ninja` to build only this module.
+You can type `ninja all` in a module for compiling all the submodule
+
+
+### 4) Compiling the OCaml
+
+    cd ocaml ; make ; cd -
+
+### 5) Testing if all is ok
+
+    cd testing_no_regression ; ./unit_test.py
+
+## Installing behind a firewall !
+
+1) Download `tsocks`:
+
+    wget http://sourceforge.net/projects/tsocks/files/latest/download
+    mv download tsocks.tar.gz
+
+2) Tranfer `tsocks.tar.gz` on the remote host
+
+3) Configure `tsocks` with the proper directory for the `tsocks.conf` file:
+
+    tar -zxvf tsocks.tar.gz
+    cd tsocks-*
+    ./configure --with-conf=${PWD}/tsocks.conf
+
+4) Create the `tsocks.conf` file with the following content:
+
+    server = 127.0.0.1
+    server_port = 10000
+
+5) Create the tsocks library:
+
+    make
+
+6) Add the `libtsocks.so` to the `LD_PRELOAD` environment variable:
+
+    export LD_PRELOAD="${PWD}/libtsocks.so.1.8"
+
+7) Create a custom curl command to set the tsocks option: open a file named
+   `curl`, which is accessible from your `PATH` environment variable before the
+   real `curl` command, and fill this file with:
+
+    #!/bin/bash
+    /usr/bin/curl --socks5 127.0.0.1:10000 $@
+
+8) Start a tsocks ssh tunnel:
+
+    ssh -fN -D 10000 user@external-server.com
+
+# Note on EZFIO.cfg
+
+##Format specification :
+
+```
+Required:
+    [<provider_name>]   The name of the provider in irp.f90 and in the EZFIO lib
+    doc:<str>           The plain text documentation
+    type:<str>          A Fancy_type supported by the ocaml.
+                            type `ei_handler.py get_supported_type` for a list
+    interface:<str>     The interface is list of string sepeared by ","  who can containt :
+                          - ezfio (if you only whant the ezfiolib)
+                          - provider (if you want the provider)
+                          - ocaml (if you want the ocaml gestion)
+Optional:
+    default: <str>      The default value needed,
+                            if 'ocaml' is in interface list.
+                           ! No list is allowed for now !
+    size: <str>         The size information.
+                            (by default is one)
+                            Example : 1, =sum(ao_num); (ao_num,3)
+    ezfio_name: <str>   The name for the EZFIO lib
+                             (by default is <provider_name>)
+    ezfio_dir: <str>    Will be the folder of EZFIO.
+                              (by default is <module_lower>)
+```
+
+##Example of EZFIO.cfg:
+
+```
+[thresh_SCF]
+doc: Threshold on the convergence of the Hartree Fock energy
+type: Threshold
+default: 1.e-10
+interface: provider,ezfio,ocaml
+size: 1
+
+[energy]
+type: Strictly_negative_float
+doc: Calculated HF energy
+interface: ezfio
+```

ocaml/.gitignore

@@ -38,12 +38,12 @@ qp_print
 qp_run
 qp_set_ddci
 qp_set_mo_class
-Input_determinants.ml
-Input_hartree_fock.ml
-Input_integrals_bielec.ml
-Input_perturbation.ml
-Input_properties.ml
 Input_pseudo.ml
+Input_integrals_bielec.ml
+Input_hartree_fock.ml
+Input_perturbation.ml
+Input_determinants.ml
+Input_properties.ml
 qp_edit.ml
 qp_edit
 qp_edit.native

plugins/CAS_SD/EZFIO.cfg

@@ -1,10 +1,10 @@
 [energy]
 type: double precision
 doc: "Calculated CAS-SD energy"
-interface: output
+interface: ezfio
 
 [energy_pt2]
 type: double precision
 doc: "Calculated selected CAS-SD energy with PT2 correction"
-interface: output
+interface: ezfio
 

plugins/CID_selected/README.rst

@@ -33,120 +33,120 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2047>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6631>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1529>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6113>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1852>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6436>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2811>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5103>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3575>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5867>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3057>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5349>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3380>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5672>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2293>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4585>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2616>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4908>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5867>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4339>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5349>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3821>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5672>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4144>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3575>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4585>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3057>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4908>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3380>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4339>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2811>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3821>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2293>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4144>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2616>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6631>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2047>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6113>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1529>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6436>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1852>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD_SC2_selected/EZFIO.cfg

@@ -1,10 +1,10 @@
 [energy]
 type: double precision
 doc: Calculated CISD_SC2 energy of ground_state
-interface: output
+interface: ezfio
 
 [energy_pt2]
 type: double precision
 doc: Calculated CISD_SC2 energy+pt2 of ground_state
-interface: output
+interface: ezfio
 

plugins/CISD_selected/README.rst

@@ -33,120 +33,120 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2047>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6631>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1529>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6113>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1852>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6436>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2811>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5103>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3575>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5867>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3057>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5349>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3380>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5672>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2293>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4585>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2616>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4908>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5867>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4339>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5349>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3821>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5672>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4144>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3575>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4585>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3057>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4908>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3380>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4339>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2811>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3821>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2293>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4144>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2616>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6631>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2047>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6113>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1529>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6436>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1852>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/DDCI_selected/EZFIO.cfg

@@ -1,4 +1,4 @@
 [energy]
 type: double precision
 doc: "Calculated CAS-SD energy"
-interface: output
+interface: ezfio

plugins/Full_CI/EZFIO.cfg

@@ -1,10 +1,10 @@
 [energy]
 type: double precision
 doc: Calculated Selected FCI energy
-interface: output
+interface: ezfio
 
 [energy_pt2]
 type: double precision
 doc: Calculated FCI energy + PT2
-interface: output
+interface: ezfio