Added README.rst in all directories

data/.gitignore

@@ -0,0 +1,3 @@
+cache/*
+*.ezfio
+

data/Makefile

@@ -0,0 +1,27 @@
+WWW_SERVER = http://qmcchem.ups-tlse.fr/files/scemama
+IRPF90_TGZ = irpf90-latest-noarch-src.tar.gz
+EZFIO_TGZ  = EZFIO.latest.tar.gz
+
+.PHONY: doc src
+
+default: src
+
+EZFIO: 
+	$(info ===== Fetching EZFIO from the web =====)
+	@wget "$(WWW_SERVER)/$(EZFIO_TGZ)" || \
+	  (echo Unable to download EZFIO : $(WWW_SERVER)/$(EZFIO_TGZ) ; exit 1)
+	@tar -zxf $(EZFIO_TGZ) && rm $(EZFIO_TGZ)
+
+irpf90:
+	$(info ===== Fetching IRPF90 from the web =====)
+	@wget "$(WWW_SERVER)/$(IRPF90_TGZ)" || \
+	  (echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1)
+	@tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ)
+	$(MAKE) -C irpf90
+
+doc:
+	$(MAKE) -C doc
+
+src: irpf90 EZFIO
+	export QPACKAGE_ROOT=$$PWD ; \
+	$(MAKE) -C src

data/README.rst

@@ -0,0 +1,28 @@
+====
+Data
+====
+
+
+This directory contains all the data files needed for the Quantum Package.
+These include:
+
+* Input data for the test suites 
+* Atomic basis sets
+
+*Important*: EZFIO files are large and should not be tracked by git.
+
+To avoid tracking large binary files with git, only the MD5 digests of the files
+present in the directory are tracked. Input EZFIO files should be archived using the
+``archive_ezfio.sh`` script. The name of the archive will be the md5 digest.
+
+The corresponding files are loaded by running::
+
+  $ make pull
+
+And the new files are uploaded with::
+
+  $ make push
+
+All previously downloaded files are stored in the ``cache`` directory.
+
+

scripts/create_rst_templates.sh

@@ -13,19 +13,19 @@ fi
 
 function asksure() {
   echo -n $@ "(Y/N) "
-  while read -r -n 1 -s answer; do
+  answer=w
-    if [[ $answer = [YyNn] ]]; then
+  while [[ $answer != [YyNn] ]]
-    [[ $answer = [Yy] ]] && retval=0
+  do
-    [[ $answer = [Nn] ]] && retval=1
+     read answer
-      break
+     [[ $answer = [Yy] ]] && retval=0 || retval=1
-    fi
   done
   return $retval
 }
 
+README="True"
 if [[ -f README.rst ]]
 then
-  asksure "Overwrite existing README.rst file?" || exit 1
+  asksure "Overwrite existing README.rst file?" || README="False"
 fi
 
 UNDERLINE="======="
@@ -36,7 +36,9 @@ do
   i+=1
 done
 
-cat << EOF > README.rst
+if [[ ${README} == "True" ]]
+then
+cat << EOF > ./README.rst
 $UNDERLINE
 $MODULE Module
 $UNDERLINE
@@ -55,4 +57,7 @@ Needed Modules
 .. include:: ./NEEDED_MODULES
 
 EOF
+fi
+
+touch ./ASSUMPTIONS.rst
 

src/AOs/README.rst

@@ -0,0 +1,17 @@
+==========
+AOs Module
+==========
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/Bitmask/README.rst

@@ -0,0 +1,17 @@
+==============
+Bitmask Module
+==============
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/Electrons/ASSUMPTIONS.rst

@@ -0,0 +1,4 @@
+* ``elec_num`` >= 0
+* ``elec_alpha_num`` >= 0
+* ``elec_beta_num`` >= 0
+* ``elec_alpha_num`` >= ``elec_beta_num``

src/Electrons/README.rst

@@ -1,3 +1,19 @@
-This module contains the data relative to electrons: the number of alpha and beta electrons.
+================
+Electrons Module
+================
+
+Describes the electrons. For the moment, only the number of alpha and beta electrons
+are provided by this module.
 
 
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/Electrons/electrons.irp.f

@@ -5,7 +5,7 @@
 
  implicit none
  BEGIN_DOC
-!  Numbers of alpha ("up") , beta ("down) and total electrons
+!  Numbers of alpha ("up") , beta ("down") and total electrons
  END_DOC
  PROVIDE ezfio_filename
  call ezfio_get_electrons_elec_alpha_num(elec_alpha_num)

src/Ezfio_files/README.rst

@@ -0,0 +1,17 @@
+==================
+Ezfio_files Module
+==================
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/MOs/README.rst

@@ -1,12 +1,17 @@
-Modifying MOs
+==========
-=============
+MOs Module
-
+==========
-When modifying MOs, the label of the current MOs should change accordingly by changing the mo_label. For example:
-
-.. code-block::  fortran
-
-  mo_coef = new_mo_coef
-  mo_label = "MyNewLabel"
-  TOUCH mo_coef mo_label
 
 
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/NEEDED_MODULES

@@ -1 +1 @@
-AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils Mimi
+AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils 

src/Nuclei/README.rst

@@ -0,0 +1,17 @@
+=============
+Nuclei Module
+=============
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/Output/README.rst

@@ -0,0 +1,17 @@
+=============
+Output Module
+=============
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+

src/Utils/README.rst

@@ -0,0 +1,17 @@
+============
+Utils Module
+============
+
+
+
+Assumptions
+-----------
+
+.. include:: ./ASSUMPTIONS.rst
+
+
+Needed Modules
+--------------
+
+.. include:: ./NEEDED_MODULES
+