Updated Tutorial (rest => markdown)

Tutorial.md

@@ -1,44 +1,51 @@
-In this tutorial, we will run a CIPSI calculation on the HCN molecule. Before using the quantum package, you need to load the needed environment variables by sourcing the ``quantum_package.rc`` file.
+In this tutorial, we will run a CIPSI calculation on the HCN molecule. Before using the quantum package, you need to load the needed environment variables by sourcing the ``$QP_ROOT/quantum_package.rc`` file.
 For example::
 
-  source $HOME/quantum_package/quantum_package.rc
+`source $HOME/quantum_package/quantum_package.rc`
 
 
-Ensure all required binaries are compiled
------------------------------------------
+##Ensure all required binaries are compiled
 
-This command will compile everything::
+This command will compile everything and install the `Hartree-Fock` and `Full-CI` module
 
-  make build
+```
+  cd $QP_ROOT
+  qp_module.py install Full_CI
+  ninja
+  make -C ocaml/
+```
+#Create the EZFIO input file
 
-
-Create the EZFIO input file
----------------------------
+The EZFIO is a HDF5 like format. The same EZFIO will serve from both input and output data.
 
 First, create an `xyz` file containing the coordinates of the molecule. The file ``hcn.xyz`` contains:
 
-.. code-block:: text
-
+```
  3
  HCN molecule
  C    0.0    0.0    0.0
  H    0.0    0.0    1.064
  N    0.0    0.0    -1.156
+```
 
 Now, this `xyz` file is used to generate an `EZFIO` input directory using the ``qp_create_ezfio_from_xyz`` command. The main options of that command are
 
--b string      Name of the basis set.
--c int         Total charge of the molecule. Default is 0.
--m int         Spin multiplicity (2S+1) of the molecule. Default is 1.
--o file        Name of the created EZFIO file.
+```
+  -b string      Name of basis set.
+  [-c int]       Total charge of the molecule. Default is 0.
+  [-d float]     Add dummy atoms. x * (covalent radii of the atoms)
+  [-m int]       Spin multiplicity (2S+1) of the molecule. Default is 1.
+  [-o file]      Name of the created EZFIO file.
+  [-p]           Using pseudopotentials
+```
 
 To generate ``hcn.ezfio`` in the cc-pVDZ basis set, we use::
 
-  qp_create_ezfio_from_xyz -b "cc-pvdz" hcn.xyz
+`qp_create_ezfio_from_xyz -b "cc-pvdz" hcn.xyz`
 
 
-Run the SCF and Full-CI calculations
-------------------------------------
+You can see a review of the EZFIO file & all the option available for all the binary installed using the `qp_edit` command.
+#Run the SCF and Full-CI calculations
 
 First, create the canonical MOs by running an SCF calculation::