Add all.png to git

scripts/module/module_handler.py

@@ -155,7 +155,7 @@ def create_png(l_module):
 
     # Save
     path = '{0}.png'.format("_".join(l_module))
-    print "png saved in {0}".format(path)
+    # print "png saved in {0}".format(path)
     graph.write_png(path)
 
 if __name__ == '__main__':

scripts/module/pydot.py

@@ -31,7 +31,8 @@ import sys
 try:
     import dot_parser
 except Exception as e:
-    print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
+    pass
+    # print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
 
 
 GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',

scripts/run_Makefile_common.sh

@@ -66,3 +66,6 @@ ${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh
 
 # Update EZFIO interface
 ${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
+
+# Create png
+${QPACKAGE_ROOT}/scripts/module/module_handler.py create_png

scripts/update_README.py

@@ -2,7 +2,7 @@
 
 """Updates the README.rst file as the include directive is disabled on GitHub."""
 __date__ = "Thu Apr  3 23:06:18 CEST 2014"
-__author__ = "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
+__author__ = "Anthony Scemama & TApplencourt<scemama@irsamc.ups-tlse.fr>"
 
 
 README = "README.rst"
@@ -21,12 +21,6 @@ header = """
 
 """
 
-try:
-    # subprocess.check_output("git status".split())
-    has_git = True
-except OSError:
-    has_git = False
-
 
 def fetch_splitted_data():
     """Read the README.rst file and split it in strings:

src/AOs/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Nuclei
+Nuclei Utils

src/AOs/README.rst

@@ -40,6 +40,7 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/Ezfio_files/README.rst

@@ -28,6 +28,24 @@ Documentation
   'x' : READ/WRITE, FORMATTED
   .br
 
+`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
+  Initial CPU and wall times when printing in the output files
+
+`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L1>`_
+  Initial CPU and wall times when printing in the output files
+
+`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
+  Write an logical value in output
+
+`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
+  Write a double precision value in output
+
+`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
+  Write an integer value in output
+
+`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
+  Write a time stamp in the output for chronological reconstruction
+
 
 
 

src/FCIdump/README.rst

@@ -10,6 +10,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+
 
 
 Needed Modules

src/MonoInts/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-MOs Pseudo Utils
+MOs Pseudo

src/MonoInts/README.rst

@@ -6,7 +6,6 @@ Needed Modules
 
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============
@@ -115,6 +114,9 @@ Documentation
   mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)>
   where Rk is the geometry of the kth atom
 
+`mo_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_pseudo_ints.irp.f#L1>`_
+  interaction nuclear electron on the MO basis
+
 `save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1>`_
   Undocumented