Added scripts

scripts/check_dependencies.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+# 
+# usage:
+#  check_dependencies.sh MOs AOs Electrons
+#
+# Checks that the list of dependencies given in
+# argument is consistent. If the dependencies
+# are OK the exit code is 0, otherwise it is 1. 
+# If no argument is given, the dependencies are
+# read in the Makefile.
+# Thu Apr  3 01:44:23 CEST 2014
+
+function unique_list()
+{
+  for d in $@
+  do
+    echo $d
+  done | sort | uniq
+}
+
+if [[ -z $1 ]]
+then
+  exit 0
+fi
+
+if [[ $1 == "-" ]]
+then
+  COMMAND_LINE=$(grep -e "^INCLUDE_DIRS" Makefile 2>/dev/null | cut -d '=' -f 2)
+else
+  COMMAND_LINE=$(unique_list $@)
+fi
+
+for d in $COMMAND_LINE
+do
+  if [[ ! -d ${SCI_ROOT}/src/$d ]]
+  then
+    echo Error: Directory $d does not exist 
+    exit 2
+  fi
+
+done
+
+DEPS_LONG=""
+for i in $COMMAND_LINE
+do
+  DEPS_LONG+=" $i "
+  DEPS_LONG+=$(grep -e '^INCLUDE_DIRS' ${SCI_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
+done
+
+DEPS=$(unique_list $DEPS_LONG)
+
+if [[ ! "$COMMAND_LINE" == "$DEPS" ]]
+then
+  DEPS=$(check_dependencies.sh $DEPS)
+fi
+echo $DEPS
+
+if [[ "$COMMAND_LINE" == "$DEPS" ]]
+then
+  exit 0
+else
+  exit 1
+fi

scripts/create_Makefile.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+# 
+# usage:
+#  create_Makefile.sh MOs AOs Electrons
+# Creates the Makefile with the dependencies on other modules given
+# in the command line. This command is supposed to be run in a module
+# directory and searches the dependencies in ../
+# Thu Apr  3 01:44:41 CEST 2014
+
+DEPS_LONG=""
+for i in $@
+do
+  DEPS_LONG+=" $i "
+  DEPS_LONG+=$(grep 'INCLUDE_DIRS' ${SCI_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
+done
+
+DEPS=($(
+for d in $DEPS_LONG
+do
+  echo $d
+done | sort | uniq
+))
+
+# Create the Makefile
+cat << EOF > Makefile
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = ${DEPS[@]}
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include \$(SCI_ROOT)/src/Makefile.config
+include \$(SCI_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: \$(filter-out IRPF90_temp/%, \$(wildcard */*.irp.f)) \$(wildcard *.irp.f) \$(wildcard *.inc.f) Makefile \$(EZFIO)
+	\$(IRPF90)
+
+Makefile.depend: Makefile
+	\$(SCI_ROOT)/scripts/create_Makefile_depend.sh
+EOF
+
+

scripts/create_Makefile_depend.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+# 
+# This script is automatically invoked by Makefiles and should not be invoked
+# by users.
+# Creates the Makefile.depend file. This file contains all the external source
+# files included by including other modules.
+# Thu Apr  3 01:44:09 CEST 2014
+
+SRC=""
+OBJ=""
+DEPS=$(grep "INCLUDE_DIRS" Makefile 2>/dev/null | cut -d '=' -f 2) 
+
+for M in ${DEPS}
+do
+  # X is the list of external source files
+  X=$(grep 'SRC=' ${SCI_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
+  for f in ${X}
+  do
+    SRC+=" ${M}/${f}"
+  done
+  X=$(grep 'OBJ=' ${SCI_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
+  for f in ${X}
+  do
+    OBJ+=" IRPF90_temp/${M}/${f/IRPF90_temp//}"
+  done
+done
+
+# Create the Makefile.depend
+cat << EOF > Makefile.depend
+# This file was created by the $0 script. Do not modify it by hand.
+
+SRC+=${SRC}
+OBJ+=${OBJ}
+EOF
+
+

scripts/create_module.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# 
+# usage:
+#  create_module.sh MOs AOs Electrons
+# Prepares all the files for the creation of a new module.
+# The first argument is the name of the module
+# All remaining aruments are dependencies.
+# Thu Apr  3 01:44:58 CEST 2014
+
+MODULE=$1
+shift
+DEPS=$@
+
+# Check if module already exists
+if [ -d ${MODULE} ]
+then
+  echo "Error: Module $MODULE already exists"
+  exit 1
+fi
+
+# Create module directory and go into it
+mkdir ${MODULE}
+cd ${MODULE}
+
+# Create the Makefile
+${SCI_ROOT}/create_Makefile.sh
+
+

scripts/prepare_module.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
-
+# This script is used by module Makefiles, and should not be used by users.
 # Checks if all the other module directories are properly linked in the
 # current directory. If not, the links are created.
+# Wed Apr  2 14:35:42 CEST 2014
 
 for dir in $@
 do

scripts/save_current_mos.sh

@@ -1,4 +1,8 @@
 #!/bin/bash
+# This script is used by the MOs module, and should not be used by users.
+# It copies the EZFIO/mo_basis directory in the save/EZFIO/mo_basis/xxx
+# directory, where xxx is the corresponding mo_label.
+# Wed Apr  2 14:35:15 CEST 2014
 
 EZFIO=$1
 

src/coding_rules.rst

@@ -0,0 +1,77 @@
+======================
+Programming guidelines
+======================
+
+Each module (directory) contains the following:
+
+* A :file:`readme.rst` file to document the current module.
+* An :file:`assumptions.rst` file. This file should document all the implicit
+  assumptions used in the module. For example, if the atomic orbitals are
+  assumed to be normalized, this should be mentioned in the
+  :file:`AOs/assumptions.rst` file.
+* A set of :file:`.irp.f` files containing provider, subroutines and functions
+* A :file:`tests` directory that should contain the test programs of the module
+  (see testing section)
+* A :file:`Makefile` that should compile
+* Optionally some :file:`*.ezfio_config` configuration files for the EZFIO
+  library
+
+A new module may be created by invoking the :file:`create_module.sh` script.
+
+Every subroutine, function or provider should be documented using the
+BEGIN_DOC ... END_DOC block. The documentation should be written in
+ReStructured Text format to enable the automatic generation of the Sphinx
+documentation.
+
+
+Testing
+=======
+
+Each module contains a :file:`tests` directory which contains the test script.
+Each module should be tested by running::
+
+  make test
+
+Before merging into the master branch, the module should pass **all** the tests.
+This enables the possibility tu use :command:`git bisect` to quickly find bugs.
+
+
+Input data
+==========
+
+Every program is supposed to use an EZFIO database containing all the
+persistent data. This database can be modified in using the generated Fortran
+functions or the generated Python module.
+
+The definition of the data needed by the module should be put in the
+:file:`*.ezfio_config` file.
+
+Input data can also be read from the standard input to enable the use of
+a program with a pipe, but the read statements should be present **only** in
+the main program.
+
+
+Output data
+===========
+
+ Print to stdout statements should only appear in programs, not in providers,
+subroutines or functions. This enables the possibility easily use the programs
+with pipes.
+
+To print, you should write in an output file provided by the :file:`Output`
+module.
+
+
+
+Modifying MOs
+=============
+
+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
+
+