Merge pull request #19 from LCPQ/master

Correct gfortran

.travis.yml

@@ -10,7 +10,7 @@ before_script:
   - sudo apt-get install graphviz
 
 script: 
-  - ./configure.py  --production ./config/gfortran.cfg
+  - ./configure  --production ./config/gfortran.cfg
   - source ./quantum_package.rc
   - ninja
   - cd ocaml ; make ; cd -

config/gfortran.cfg

@@ -29,21 +29,20 @@ OPENMP  : 1          ; Append OpenMP flags
 # Optimization flags
 ####################
 #
-# -march=native           : Compile a binary optimized for the current architecture
 # -Ofast                  : Disregard strict standards compliance. Enables all -O3 optimizations.
 #                           It also enables optimizations that are not valid
 #                           for all standard-compliant programs.  It turns on
 #                           -ffast-math and the Fortran-specific
 #                           -fno-protect-parens and -fstack-arrays.
 [OPT]
-FCFLAGS : -Ofast -march=native 
+FCFLAGS : -Ofast 
 
 # Profiling flags
 #################
 #
 [PROFILE]
 FC      : -p -g
-FCFLAGS : -Ofast -march=native 
+FCFLAGS : -Ofast 
 
 # Debugging flags
 #################

configure

@@ -4,14 +4,22 @@
 
 Usage: configure <config_file> (--production | --development)
 
+
 Options:
-    config_file   A config file will all the information for the compilation
+
-                    (Fortran Compiler, FLag, ...)
+    config_file   A config file with all the information for the compilation
-   --production   You cannot compile only one module with this flag.
+                  Example config_files are given in config/
-                    but the compilation will be lighting fast
+
+   --production   You can only compile all the modules with this flag,
+                  but the compilation will be lighting fast
+
    --development  It will create a build.ninja for each directory
-                    who containt a binary, than you can compile then
+                  who contains a binary, than you can compile then
-                    individualy if you want
+                  individualy if you want
+
+Example:
+
+    ./configure config/gfortran.cfg --production
 
 """
 
@@ -37,6 +45,8 @@ QP_ROOT = os.getcwd()
 QP_ROOT_BIN = join(QP_ROOT, "bin")
 QP_ROOT_INSTALL = join(QP_ROOT, "install")
 
+os.environ["PATH"] = os.environ["PATH"] + ":"+QP_ROOT_BIN
+
 d_dependency = {
     "ocaml": ["m4", "curl", "zlib", "patch", "gcc"],
     "m4": ["make"],
@@ -62,7 +72,7 @@ path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"}
 
 ocaml = Info(
     url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh',
-    description=' ocaml (it will take some time roughly 20min)',
+    description=' Ocaml, Opam and the Core library (it will take some time roughly 20min)',
     default_path=join(QP_ROOT_BIN, "opam"))
 
 m4 = Info(
@@ -87,12 +97,12 @@ path = Info(
 
 irpf90 = Info(
     url='{head}/LCPQ/irpf90/{tail}'.format(**path_github),
-    description=' irpf90',
+    description=' IRPF90',
     default_path=join(QP_ROOT_BIN, "irpf90"))
 
 docopt = Info(
     url='{head}/docopt/docopt/{tail}'.format(**path_github),
-    description=' docop',
+    description=' docopt',
     default_path=join(QP_ROOT_INSTALL, "docopt"))
 
 resultsFile = Info(
@@ -108,7 +118,7 @@ ninja = Info(
 emsl = Info(
     url='{head}/LCPQ/EMSL_Basis_Set_Exchange_Local/{tail}'.format(**
                                                                   path_github),
-    description=' emsl',
+    description=' EMSL basis set library',
     default_path=join(QP_ROOT_INSTALL, "emsl"))
 
 ezfio = Info(
@@ -178,7 +188,7 @@ def checking(d_dependency):
             print "To old version (need >2.5). Abort"
             sys.exit(1)
 
-    def check_availabiliy(binary):
+    def check_availability(binary):
         """
         If avalabie return the path who can can't find the
         binary else return 0
@@ -228,7 +238,7 @@ def checking(d_dependency):
     for i in d_dependency.keys():
         print "Checking {0:>{1}}...".format(i, length),
 
-        r = check_availabiliy(i)
+        r = check_availability(i)
         if r:
             print "[  OK  ] ( {0} )".format(r.strip())
             l_installed[i] = r.strip()
@@ -289,7 +299,7 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
     d_print = {
         "install_ninja": "Install ninja...",
         "build": "Creating build.ninja...",
-        "install": "Installing the dependancy through ninja..."
+        "install": "Installing the dependency through ninja..."
     }
 
     length = max(map(len, d_print.values()))
@@ -339,15 +349,15 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
                     ""]
 
         # Build to install
-        l_dependancy = [d_info[i].default_path for i in d_dependency[need]
+        l_dependency = [d_info[i].default_path for i in d_dependency[need]
                         if i in l_install_descendant]
-        str_dependancy = " ".join(l_dependancy)
+        str_dependency = " ".join(l_dependency)
 
         rule = "install" if need != "ocaml" else "install_verbose"
 
         l_build += ["build {0}: {1} {2} {3}".format(default_path, rule,
                                                     archive_path,
-                                                    str_dependancy),
+                                                    str_dependency),
                     "   target = {0}".format(need),
                     "   descr = {0}".format(descr), ""]
 

doc/code_architecture/Script.md

@@ -12,7 +12,7 @@ For more information you can type `ei_handler.py -h`
 # `module_handler.py`
 
 This script in located in `$QP_ROOT/scripts/module/`.
-It provide all the resource related to the tree dependancy of the modules.
+It provide all the resource related to the tree dependency of the modules.
 If more useful as a librairy than a cli.
 
 It have some usefull property:

install/scripts/install_ocaml.sh

@@ -32,7 +32,10 @@ export LIBRARY_PATH=${QP_ROOT}/lib:${LIBRARY_PATH}
 export C_INCLUDE_PATH=${QP_ROOT}/lib:${C_INCLUDE_PATH}
 source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
 
-${QP_ROOT}/bin/opam install ${PACKAGES} -y -q || exit 1
+
+NCPUs=$(cat /proc/cpuinfo  | grep -i  MHz | wc -l)
+${QP_ROOT}/bin/opam install -j ${NCPUs} ${PACKAGES} -y -q || exit 1
+
 rm -f ../_build/ocaml.log
 exit 0
 

install/scripts/install_zlib.sh

@@ -14,6 +14,8 @@ function _install()
   make install prefix=$QP_ROOT/install/${TARGET} || exit 1
   ln -s -f $QP_ROOT/install/${TARGET}/lib/libz.so $QP_ROOT/lib || exit 1
   ln -s -f $QP_ROOT/install/${TARGET}/lib/libz.a $QP_ROOT/lib || exit 1
+  ln -s -f $QP_ROOT/install/${TARGET}/include/zlib.h $QP_ROOT/lib || exit 1
+  ln -s -f $QP_ROOT/install/${TARGET}/include/zconf.h $QP_ROOT/lib || exit 1
 }
 
 source scripts/build.sh

ocaml/.gitignore

@@ -5,6 +5,7 @@ qptypes_generator.byte
 _build
 qp_basis_clean.native
 qp_create_ezfio_from_xyz.native
+qp_edit.native
 qp_print.native
 qp_run.native
 qp_set_ddci.native
@@ -32,6 +33,7 @@ test_molecule
 test_point3d
 qp_basis_clean
 qp_create_ezfio_from_xyz
+qp_edit
 qp_print
 qp_run
 qp_set_ddci

ocaml/Makefile

@@ -72,7 +72,7 @@ Qptypes.ml: qptypes_generator.byte
 	./qptypes_generator.byte > Qptypes.ml
 
 ${QP_ROOT}/install/EZFIO/Ocaml/ezfio.ml: 
-	$(MAKE) -C ${QP_ROOT}/install/src ezfio
+	$(NINJA) -C ${QP_ROOT}/install/EZFIO
 
 Input_auto_generated.ml qp_edit.ml:
 	ei_handler.py ocaml_global

ocaml/Qpackage.ml

@@ -109,7 +109,11 @@ let get_ezfio_default directory data =
   let dirname = root^"/data/ezfio_defaults/" in
   
   let rec aux = function 
-  | []           -> raise Not_found
+  | []           -> 
+      begin
+        Printf.printf "%s/%s not found\n%!" directory data;
+        raise Not_found
+      end
   | filename :: tail ->
     let filename = 
       dirname^filename

scripts/compilation/qp_create_ninja.py

@@ -38,10 +38,10 @@ header = r"""#
 #
 # https://github.com/LCPQ/quantum_package,
 #
-# Generated automatically by {0}.".format(__file__)
+# Generated automatically by {0}
 #
 #
-"""
+""".format(__file__)
 
 #  __
 # /__ |  _  |_   _. |       _. ._ o  _. |_  |  _   _

src/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#L6631>`_
+`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>`_
   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#L6113>`_
+`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>`_
   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#L6436>`_
+`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>`_
   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#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet <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_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5867>`_
+`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>`_
   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#L5349>`_
+`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>`_
   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#L5672>`_
+`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>`_
   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#L4585>`_
+`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>`_
   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#L4908>`_
+`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>`_
   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#L4339>`_
+`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>`_
   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#L3821>`_
+`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>`_
   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#L4144>`_
+`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>`_
   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#L3575>`_
+`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>`_
   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#L3057>`_
+`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>`_
   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#L3380>`_
+`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>`_
   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#L2811>`_
+`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>`_
   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#L2293>`_
+`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>`_
   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#L2616>`_
+`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>`_
   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#L2047>`_
+`h_apply_cisd_selection_h_core <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_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1529>`_
+`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>`_
   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#L1852>`_
+`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>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

src/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#L6631>`_
+`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>`_
   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#L6113>`_
+`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>`_
   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#L6436>`_
+`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>`_
   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#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet <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_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5867>`_
+`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>`_
   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#L5349>`_
+`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>`_
   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#L5672>`_
+`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>`_
   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#L4585>`_
+`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>`_
   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#L4908>`_
+`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>`_
   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#L4339>`_
+`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>`_
   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#L3821>`_
+`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>`_
   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#L4144>`_
+`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>`_
   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#L3575>`_
+`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>`_
   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#L3057>`_
+`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>`_
   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#L3380>`_
+`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>`_
   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#L2811>`_
+`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>`_
   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#L2293>`_
+`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>`_
   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#L2616>`_
+`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>`_
   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#L2047>`_
+`h_apply_cisd_selection_h_core <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_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1529>`_
+`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>`_
   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#L1852>`_
+`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>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

src/Hartree_Fock/EZFIO.cfg

@@ -20,8 +20,3 @@ default: Huckel
 type: double precision
 doc: Calculated HF energy
 interface: output
-
-[energy_sdfsdf]
-type: double precision
-doc: Calculated HF energy
-interface: output