Mega cleaning.

.gitignore

@@ -1,11 +1,15 @@
 quantum_package.rc
-EZFIO
-irpf90
-EMSL_Basis
+EZFIO/
+irpf90/
+EMSL_Basis/
+ninja/
 bin/
 *.log
 quantum_package_static.tar.gz
 resultsFile
 opam_installer.sh
 *.mod
-*.p
+*.p
+build.ninja
+.ninja_log
+.ninja_deps

.travis.yml

@@ -12,9 +12,7 @@ before_script:
 script: 
   - ./setup_environment.sh --robot 
   - source ./quantum_package.rc
-  - cp ./src/Makefile.config.gfortran  ./src/Makefile.config
-  - ./scripts/compilation/create_ninja_build.py ./config/gfortran_example.cfg > build.ninja
-  - ./ninja/ninja -v
-  - ei_handler.py ocaml_global
+  - ./scripts/compilation/create_ninja_build.py --production ./config/gfortran_example.cfg
+  - ./ninja/ninja
   - cd ocaml ; make ; cd -
   - ./tests/unit_test/unit_test.py

Compile.md

@@ -0,0 +1,13 @@
+``$QPACKAGE_ROOT/config`` contains ``ifort.cfg`` and ``gfortran.cfg`` files which
+have the compiler flags that will be used to compile the code. You can edit these
+files to modify the compiling options (This configuration file is parsed by
+``read_compilation_cfg.py``).
+
+To create the Ninja file ::
+
+  create_ninja_build.py --production $QPACKAGE_ROOT/config/ifort.cfg
+
+
+To compile, run ::
+
+  $QPACKAGE_ROOT/ninja/ninja

ocaml/.gitignore

@@ -0,0 +1,51 @@
+cd .gitignore
+ezfio.ml
+Qptypes.ml
+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
+qp_set_mo_class.native
+test_atom.byte
+test_basis.byte
+test_bitlist.byte
+test_determinants.byte
+test_elements.byte
+test_excitation.byte
+test_gto.byte
+test_mo_label.byte
+test_molecule.byte
+test_point3d.byte
+test_atom
+test_basis
+test_bitlist
+test_determinants
+test_elements
+test_excitation
+test_gto
+test_mo_label
+test_molecule
+test_point3d
+qp_basis_clean
+qp_create_ezfio_from_xyz
+qp_edit
+qp_print
+qp_run
+qp_set_ddci
+qp_set_mo_class
+qp_edit.ml
+Input_pseudo.ml
+Input_integrals_bielec.ml
+Input_hartree_fock.ml
+Input_perturbation.ml
+Input_determinants.ml
+Input_properties.ml
+Input_cas_sd.ml
+Input_cisd_sc2_selected.ml
+Input_full_ci.ml
+Input_mrcc.ml
+Input_auto_generated.ml

scripts/compilation/.gitignore

@@ -0,0 +1 @@
+*.pyc

scripts/compilation/create_ninja_build.py

@@ -11,7 +11,7 @@ from os.path import join
 from collections import namedtuple
 
 try:
-    from module_handler import file_dependancy
+    from module_handler import file_dependency
     from module_handler import get_dict_module_boss, get_dict_genealogy_desc
     from read_compilation_cfg import get_compilation_option
     from docopt import docopt
@@ -309,7 +309,7 @@ def get_l_irp_for_module(path_module_abs):
     return dump
 
 
-def get_irp_dependancy(d_info_module):
+def get_irp_dependency(d_info_module):
     """
     For a module return all the irp.f90 file who depend
     """
@@ -345,7 +345,7 @@ def ninja_irpf90_make_rule():
                 "   command = {0}".format(" ; ".join(l_cmd)),
                 "   pool = irp_pool",
                 "   generator = 1",
-                "   description = Create the irp tree for $module"
+                "   description = Create the IRP_Tree for $module"
                 ""]
 
     return l_string
@@ -355,7 +355,7 @@ def ninja_irpf90_make_build(path_module,
                             l_needed_molule,
                             d_irp):
     """
-    Creatre the dependancy for a irpf90.make
+    Creatre the dependency for a irpf90.make
     We need all the symklink and all the irp.f
     """
     # ~#~#~#~#~#~ #
@@ -381,7 +381,7 @@ def ninja_irpf90_make_build(path_module,
     # N i n j a _ b u i l d #
     # ~#~#~#~#~#~#~#~#~#~#~ #
 
-    l_src, l_obj = file_dependancy(path_module.rel)
+    l_src, l_obj = file_dependency(path_module.rel)
     l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule]
 
     l_string = ["build {0}: build_irpf90.ninja {1}".format(str_creation, str_depend),
@@ -411,7 +411,7 @@ def ninja_readme_build(path_module):
     """
     Rule for creation the readme
     """
-    path_irp_man = join(path_module.abs, "IRPF90_man")
+    path_irp_man = join(path_module.abs, "irpf90.make")
     path_readme = join(path_module.abs, "README.rst")
 
     l_string = ["build {0}: build_readme {1}".format(path_readme,
@@ -429,7 +429,7 @@ def ninja_readme_build(path_module):
 #                 /
 def get_program(path_module):
     """
-    Return the list of binary (Path= namedtuple('Path', ['abs', 'rel']) for a module
+    Return the list of binaries (Path= namedtuple('Path', ['abs', 'rel']) for a module
     """
     import subprocess
 
@@ -449,10 +449,10 @@ def get_program(path_module):
             return []
 
 
-def get_dict_binary(mode="development"):
+def get_dict_binaries(mode="development"):
     """
-    Return a dict [module] = list_binary
-    If a the production mode is enable only header module will produce binary
+    Return a dict [module] = list_binaries
+    If a the production mode is enable only header module will produce binaries
 
     Example : The module Full_CI can produce the binary SCF
     so you dont need to use at all the module Hartree-Fock
@@ -460,63 +460,93 @@ def get_dict_binary(mode="development"):
 
     from collections import defaultdict
 
-    d_binary = defaultdict(list)
+    d_binaries = defaultdict(list)
 
-    # Create d_binary
-    # Ake module => binary generated
+    # Create d_binaries
+    # Ake module => binaries generated
     for module in d_genealogy_path.keys():
-        l_binary = get_program(module)
+        l_binaries = get_program(module)
 
-        if l_binary:
-            d_binary[module] += l_binary
+        if l_binaries:
+            d_binaries[module] += l_binaries
 
     if mode == "production":
 
         dict_boss = get_dict_module_boss()
         dict_boss_path = dict_module_genelogy_path(dict_boss)
 
-        d_binary_condensed = defaultdict(list)
-        for module in d_binary:
-            d_binary_condensed[dict_boss_path[module]] += d_binary[module]
+        d_binaries_condensed = defaultdict(list)
+        for module in d_binaries:
+            d_binaries_condensed[dict_boss_path[module]] += d_binaries[module]
 
-        d_binary = d_binary_condensed
+        d_binaries = d_binaries_condensed
 
-    return d_binary
+    return d_binaries
 
 
-def ninja_binary_rule():
+def ninja_binaries_rule():
     """
-    Rule for creating the binary
+    Rule for creating the binaries
     """
 
-    l_cmd = ["cd $module/IRPF90_temp", "ninja -j 1 "]
+    l_cmd = ["cd $module/IRPF90_temp", "ninja"]
 
-    l_string = ["rule build_binary",
+    l_string = ["rule build_binaries",
                 "   command = {0}".format(" ; ".join(l_cmd)),
-                "   description = Create all the binary from $module"
+                "   description = Create all the binaries from $module"
                 ""]
 
     return l_string
 
 
-def ninja_binary_build(path_module, l_children, d_binary):
+def ninja_binaries_build(path_module, l_children, d_binaries):
     """
-    The binary need the EZFIO_LIB, and the irpf90.make (aka build.ninja)
+    The binaries need the EZFIO_LIB, and the irpf90.make (aka build.ninja)
     """
     ninja_module_path = join(path_module.abs, "IRPF90_temp", "build.ninja")
 
-    l_abs_bin = [binary.abs for binary in d_binary[path_module]]
-    l_rel_bin = [binary.rel for binary in d_binary[path_module]]
+    l_abs_bin = [binary.abs for binary in d_binaries[path_module]]
 
-    l_string = ["build {0}: build_binary {1} {2}".format(" ".join(l_abs_bin),
-                                                         EZFIO_LIB,
-                                                         ninja_module_path),
+    l_string = ["build {0}: build_binaries {1} {2}".format(" ".join(l_abs_bin),
+                                                           EZFIO_LIB,
+                                                           ninja_module_path),
                 "   module = {0}".format(path_module.abs),
                 ""]
 
     return l_string
 
 
+# ___
+#  | ._ _   _     _|  _  ._   _  ._   _|  _  ._   _ o  _   _
+#  | | (/_ (/_   (_| (/_ |_) (/_ | | (_| (/_ | | (_ | (/_ _>
+#                        |
+def ninja_dot_tree_rule():
+    """
+    Rule for creating the binaries
+    """
+    l_cmd = ["cd $module", "module_handler.py create_png"]
+
+    l_string = ["rule build_dot_tree",
+                "   command = {0}".format(" ; ".join(l_cmd)),
+                "   description = Generate Dot Dependancies Tree of $module"
+                ""]
+
+    return l_string
+
+
+def ninja_dot_tree_build(path_module):
+
+    l_string = ["build {0}: build_dot_tree".format(join(path_module.abs, "tree_dependency.png")),
+                "   module = {0}".format(path_module.abs),
+                ""]
+
+    return l_string
+
+
+#
+# |\/|  _. o ._
+# |  | (_| | | |
+#
 if __name__ == "__main__":
 
     arguments = docopt(__doc__)
@@ -527,7 +557,6 @@ if __name__ == "__main__":
     # |_ | | \/   \/ (_| |  | (_| |_) | (/_ _>
     #
 
-    pwd_config_file = sys.argv[1]
     l_string = ninja_create_env_variable(pwd_config_file)
 
     #  _
@@ -541,11 +570,13 @@ if __name__ == "__main__":
     l_string += ninja_irpf90_make_rule()
     l_string += ninja_readme_rule()
 
-    l_string += ninja_binary_rule()
+    l_string += ninja_binaries_rule()
 
     l_string += ninja_ezfio_config_rule()
     l_string += ninja_ezfio_rule()
 
+    l_string += ninja_dot_tree_rule()
+
     #  _
     # |_)     o |  _|    _   _  ._   _  ._ _. |
     # |_) |_| | | (_|   (_| (/_ | | (/_ | (_| |
@@ -570,20 +601,20 @@ if __name__ == "__main__":
 
     d_genealogy = get_dict_genealogy_desc()
     d_genealogy_path = dict_module_genelogy_path(d_genealogy)
-    d_irp = get_irp_dependancy(d_genealogy_path)
+    d_irp = get_irp_dependency(d_genealogy_path)
 
-    d_binary_production = get_dict_binary("production")
-    d_binary_development = get_dict_binary("development")
+    d_binaries_production = get_dict_binaries("production")
+    d_binaries_development = get_dict_binaries("development")
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # M o d u l e _ t o _ i r p #
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
 
     if arguments["--production"]:
-        l_module_to_irp = d_binary_production.keys()
+        l_module_to_irp = d_binaries_production.keys()
 
     elif arguments["--development"]:
-        l_module_to_irp = d_binary_development.keys()
+        l_module_to_irp = d_binaries_development.keys()
 
     for module_to_compile in l_module_to_irp:
 
@@ -600,13 +631,18 @@ if __name__ == "__main__":
         # ~#~#~#~#~#~#~#~ #
         l_string += ninja_irpf90_make_build(module_to_compile, l_children, d_irp)
 
+        # ~#~#~#~#~#~#~#~ #
+        # d o t _ t r e e #
+        # ~#~#~#~#~#~#~#~ #
+        l_string += ninja_dot_tree_build(module_to_compile)
+
     # ~#~#~#~#~#~#~ #
     #  b i n a r y  #
     # ~#~#~#~#~#~#~ #
+    for module_to_compile in d_binaries_production.keys():
 
-    for module_to_compile in d_binary_production.keys():
-
-        l_string += ninja_binary_build(module_to_compile, l_children, d_binary_production)
+        l_string += ninja_binaries_build(module_to_compile, l_children, d_binaries_production)
         l_string += ninja_readme_build(module_to_compile)
 
-    print "\n".join(l_string)
+    with open(join(QPACKAGE_ROOT, "build.ninja"), "w+") as f:
+        f.write("\n".join(l_string))

scripts/module/build_modules.sh

@@ -2,7 +2,7 @@
 #
 # This script should run from the directory $QPACKAGE_ROOT/src
 
-# Check is we are in `QPROOT_SRC` and all the dependancy are corect
+# Check is we are in `QPACKAGE_ROOT_SRC` and all the dependency are correct
 ${QPACKAGE_ROOT}/scripts/module/check_src.sh
 
 NPROC=$(cat /proc/cpuinfo | grep MHz | wc -l)

scripts/module/create_gitignore.sh

@@ -13,9 +13,10 @@ then
 fi
 source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 
-check_current_dir_is_module
 
-cat << EOF > .gitignore
+function do_gitingore()
+{ 
+  cat << EOF > .gitignore
 #
 # Do not modify this file. Add your ignored files to the gitignore
 # (without the dot at the beginning) file.
@@ -26,13 +27,35 @@ irpf90.make
 tags
 Makefile.depend
 irpf90_entities
-.gitignore
+build.ninja
+.ninja_log
+.ninja_deps
 EOF
+  
+  if [[ -f gitignore ]]
+  then
+    cat gitignore >> .gitignore
+  fi
+  
+  find . -type l | sed "s@./@@" >> .gitignore
+  find . -type f -executable -print | sed "s@./@@" >> .gitignore
+}
 
-if [[ -f gitignore ]]
+
+if [[ -z $1 ]]
 then
-  cat gitignore >> .gitignore
+  check_current_dir_is_module
+  do_gitingore
+else
+  check_current_dir_is_src
+  for i in $@
+  do
+    if [[ -d $i ]]
+    then
+       cd $i
+       do_gitingore
+       cd $OLDPWD
+    fi
+  done
 fi
 
-find . -type l | sed "s@./@@" >> .gitignore
-find . -type f -executable -print | sed "s@./@@" >> .gitignore

scripts/module/module_handler.py

@@ -27,8 +27,8 @@ import os.path
 from cache import cache
 
 from collections import namedtuple
-Dependancy = namedtuple('Dependancy', ['src', 'obj'])
-Module_info = namedtuple('Module_info', ['l_children', 'l_dependancy'])
+Dependency = namedtuple('Dependency', ['src', 'obj'])
+Module_info = namedtuple('Module_info', ['l_children', 'l_dependency'])
 
 
 def get_list_from_makefile(data, sep):
@@ -64,7 +64,7 @@ def get_dict_genealogy():
         try:
             with open(os.path.join(dir_, o, "Makefile"), "r") as f:
                 data = f.readlines()
-                l_depend = Dependancy(get_list_from_makefile(data, "SRC="),
+                l_depend = Dependency(get_list_from_makefile(data, "SRC="),
                                       get_list_from_makefile(data, "OBJ="))
         except IOError:
             l_depend = []
@@ -150,35 +150,22 @@ def module_genealogy(module_name):
     return him_and_all_children(d_ref, d_ref[module_name].l_children)
 
 
-def file_dependancy(module_name):
+def file_dependency(module_name):
 
     d_ref = get_dict_genealogy()
-    l_src, l_obj = d_ref[module_name].l_dependancy
+    l_src, l_obj = d_ref[module_name].l_dependency
 
     l_children_module = him_and_all_children(d_ref, d_ref[module_name].l_children)
     for module in l_children_module:
-        l_src_dump, l_obj_dump = d_ref[module].l_dependancy
+        l_src_dump, l_obj_dump = d_ref[module].l_dependency
         l_src.extend("{0}/{1}".format(module, i) for i in l_src_dump)
         l_obj.extend("IRPF90_temp/{0}/{1}".format(module, os.path.basename(i)) for i in l_obj_dump)
 
-    return Dependancy(l_src, l_obj)
-
-
-def create_png_from_path(path):
-    " Change a path like this into a module list"
-    "path = /home/razoa/quantum_package/src/Molden/NEEDED_CHILDREN_MODULES"
-
-    l_module = os.path.split(path)[0].split("/")[-1]
-
-    import pydot
-    try:
-        create_png([l_module])
-    except pydot.InvocationException:
-        pass
+    return Dependency(l_src, l_obj)
 
 
 def create_png(l_module):
-    """Create the png of the dependancy tree for a l_module"""
+    """Create the png of the dependency tree for a l_module"""
 
     # Init
     import pydot
@@ -207,10 +194,7 @@ def create_png(l_module):
         draw_module_edge(module, d_ref[module].l_children)
 
     # Save
-    path = '{0}.png'.format("tree_dependancy")
-    # path = '{0}.png'.format("_".join(l_module))
-    # print "png saved in {0}".format(path)
-
+    path = '{0}.png'.format("tree_dependency")
     graph.write_png(path)
 
 if __name__ == '__main__':
@@ -232,7 +216,7 @@ if __name__ == '__main__':
         print " ".join(sorted(l_all_needed_molule))
 
     if arguments["create_png"]:
-        create_png_from_path(path_file)
+        create_png([path_file])
 
     if arguments["head_module"]:
         for module, boss in get_dict_module_boss().iteritems():

scripts/module/update_README.py

@@ -81,7 +81,7 @@ def update_needed(data):
     modules = file.read()
     file.close()
 
-    header_image = ".. image:: tree_dependancy.png\n\n"
+    header_image = ".. image:: tree_dependency.png\n\n"
 
     if modules.strip() != "":
         modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]

setup_environment.sh

@@ -23,6 +23,7 @@ export PYTHONPATH=\${PYTHONPATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -pri
 export PATH=\${PATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
 export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
 export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
+export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ninja
 source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
 EOF
 

src/AOs/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Bitmask/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/CAS_SD/.gitignore

@@ -0,0 +1,32 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Generators_CAS
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+Ezfio_files
+cas_sd_selected
+cas_sd

src/CAS_SD/README.rst

@@ -24,7 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

src/CID/.gitignore

@@ -0,0 +1,30 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Determinants
+Electrons
+Utils
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cid
+cid_lapack

src/CID_SC2_selected/.gitignore

@@ -0,0 +1,35 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+CID_selected
+Pseudo
+Integrals_Monoelec
+Bitmask
+CID
+Integrals_Bielec
+CISD_selected
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+CISD
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cid_sc2_selection

src/CID_SC2_selected/README.rst

@@ -19,7 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_
 

src/CID_selected/.gitignore

@@ -0,0 +1,33 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+CID
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+CISD
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cid_selection

src/CIS/.gitignore

@@ -0,0 +1,30 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Determinants
+Electrons
+Utils
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+super_ci
+cis

src/CIS/README.rst

@@ -31,7 +31,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_

src/CISD/.gitignore

@@ -0,0 +1,30 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Determinants
+Electrons
+Utils
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cisd_lapack
+cisd

src/CISD_SC2_selected/.gitignore

@@ -0,0 +1,33 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+CISD_selected
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+CISD
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cisd_sc2_selection

src/CISD_SC2_selected/README.rst

@@ -19,7 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 

src/CISD_selected/.gitignore

@@ -0,0 +1,32 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+CISD
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+cisd_selection

src/DDCI_selected/.gitignore

@@ -0,0 +1,31 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Generators_CAS
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+Ezfio_files
+ddci

src/DDCI_selected/README.rst

@@ -19,7 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

src/DensityMatrix/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Determinants/.gitignore

@@ -0,0 +1,32 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+MOs
+Electrons
+Utils
+Nuclei
+Ezfio_files
+guess_triplet
+guess_singlet
+truncate_wf
+save_natorb
+save_for_qmcchem
+program_beginer_determinants
+save_for_casino
+det_svd
+guess_doublet

src/Electrons/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Ezfio_files/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/FCIdump/.gitignore

@@ -0,0 +1,25 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+MOs
+Determinants
+Electrons
+Utils
+Nuclei
+Ezfio_files
+fcidump

src/FCIdump/README.rst

@@ -21,7 +21,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

src/Full_CI/.gitignore

@@ -0,0 +1,34 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Generators_full
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+Ezfio_files
+target_pt2
+full_ci
+var_pt2_ratio
+full_ci_no_skip

src/Full_CI/README.rst

@@ -24,7 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

src/Generators_CAS/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Generators_full/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Generators_restart/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Hartree_Fock/.gitignore

@@ -0,0 +1,26 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+MOs
+Electrons
+Utils
+Nuclei
+MOGuess
+Ezfio_files
+Huckel_guess
+SCF

src/Integrals_Bielec/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Integrals_Monoelec/.gitignore

@@ -0,0 +1,22 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+AOs
+MOs
+Electrons
+Utils
+Nuclei
+Ezfio_files
+check_orthonormality
+save_ortho_mos

src/MOGuess/.gitignore

@@ -0,0 +1,22 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+AOs
+MOs
+Electrons
+Utils
+Nuclei
+Ezfio_files
+H_CORE_guess

src/MOs/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/MP2/.gitignore

@@ -0,0 +1,31 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+SingleRefMethod
+Ezfio_files
+mp2

src/MP2/README.rst

@@ -19,7 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

src/MRCC/.gitignore

@@ -0,0 +1,31 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+Generators_full
+Pseudo
+Integrals_Monoelec
+Bitmask
+Integrals_Bielec
+AOs
+Selectors_full
+MOs
+Hartree_Fock
+Perturbation
+Determinants
+Electrons
+Utils
+Properties
+Nuclei
+MOGuess
+Ezfio_files
+mrcc

src/MRCC/README.rst

@@ -8,7 +8,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

src/Makefile

@@ -1,36 +0,0 @@
-ifndef QPACKAGE_ROOT
-  $(error "QPACKAGE_ROOT is not defined. Please source quantum_package.rc")
-endif
-
-include Makefile.config
-
-ALL_MODULES=$(shell cat NEEDED_MODULES)
-EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
-EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
-
-.PHONY: $(ALL_MODULES) ezfio
-
-
-default: ezfio
-	$(QPACKAGE_ROOT)/scripts/module/build_modules.sh $(ALL_MODULES)
-
-veryclean:
-	$(QPACKAGE_ROOT)/scripts/module/clean_modules.sh $(ALL_MODULES)
-
-$(ALL_MODULES): ezfio
-	$(QPACKAGE_ROOT)/scripts/module/build_modules.sh $@ 
-
-# Define the EZFIO rules
-$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
-	$(QPACKAGE_ROOT)/scripts/ezfio_interface/prepare_ezfio.sh
-	cd $(EZFIO_DIR);\
-	export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ;\
-	$(MAKE) ;\
-	$(MAKE) Python
-
-ezfio: $(EZFIO)
-
-# Frequent typos
-clena: clean
-veryclena: veryclean
-

src/Makefile.common

@@ -1 +0,0 @@
-include irpf90.make

src/Makefile.config.example

@@ -1,32 +0,0 @@
-OPENMP  =1
-PROFILE =0
-DEBUG  = 0
-
-IRPF90_FLAGS+= --align=32
-FC     = ifort -g 
-FCFLAGS= 
-FCFLAGS+= -xHost
-#FCFLAGS+= -xAVX
-FCFLAGS+= -O2 
-FCFLAGS+= -ip 
-FCFLAGS+= -opt-prefetch
-FCFLAGS+= -ftz
-MKL=-mkl=parallel 
-
-ifeq ($(PROFILE),1)
-FC    += -p -g
-CXX   += -pg
-endif
-
-ifeq ($(OPENMP),1)
-FC           += -openmp
-IRPF90_FLAGS += --openmp
-CXX          += -fopenmp
-endif
-
-ifeq ($(DEBUG),1)
-FC    += -C -traceback -fpe0 
-FCFLAGS+= -axSSE2
-IRPF90_FLAGS += -a
-#FCFLAGS =-O0
-endif

src/Makefile.config.gfortran

@@ -1,26 +0,0 @@
-OPENMP  =1
-PROFILE =0
-DEBUG  = 0
-
-IRPF90_FLAGS= 
-FC     = gfortran -ffree-line-length-none -march=native
-FCFLAGS= -ffast-math 
-FCFLAGS+= -Ofast
-MKL=-lblas -llapack
-# Uncomment to use gfortan with MKL
-#MKL=-L /opt/intel/composerxe/mkl/lib/intel64/ -lmkl_gf_lp64 -lmkl_core -lmkl_gnu_thread -fopenmp
-
-ifeq ($(PROFILE),1)
-FC    += -p -g
-CXX   += -pg
-endif
-
-ifeq ($(OPENMP),1)
-FC           += -fopenmp
-IRPF90_FLAGS += --openmp
-endif
-
-ifeq ($(DEBUG),1)
-FCFLAGS = -fcheck=all
-#FCFLAGS =-O0
-endif

src/Molden/.gitignore

@@ -0,0 +1,20 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps
+AOs
+MOs
+Electrons
+Utils
+Nuclei
+Ezfio_files
+print_mo

src/Molden/README.rst

@@ -31,7 +31,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

src/Nuclei/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Perturbation/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Properties/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Pseudo/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Selectors_full/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Selectors_no_sorted/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/SingleRefMethod/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps

src/Utils/.gitignore

@@ -0,0 +1,13 @@
+#
+# Do not modify this file. Add your ignored files to the gitignore
+# (without the dot at the beginning) file.
+#
+IRPF90_temp
+IRPF90_man
+irpf90.make
+tags
+Makefile.depend
+irpf90_entities
+build.ninja
+.ninja_log
+.ninja_deps