Updated Tutorial (markdown)

Tutorial.md

@@ -1,4 +1,4 @@
-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 ``$QP_ROOT/quantum_package.rc`` file.
+In this tutorial, we will run a CIPSI calculation on the HCN molecule in two basis set. Before using the quantum package, you need to load the needed environment variables by sourcing the ``$QP_ROOT/quantum_package.rc`` file.
 For example::
 
 `source $HOME/quantum_package/quantum_package.rc`
@@ -39,19 +39,42 @@ Now, this `xyz` file is used to generate an `EZFIO` input directory using the ``
   [-p]           Using pseudopotentials
 ```
 
-To generate ``hcn.ezfio`` in the cc-pVDZ basis set, we use::
+To generate ``hcn.ezfio`` in the (enormous) 6-31G basis set, we use::
 
-`qp_create_ezfio_from_xyz -b "cc-pvdz" hcn.xyz`
+`qp_create_ezfio_from_xyz -b "6-31G" hcn.xyz`
 
 
 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::
 ```
   qp_run SCF hcn.ezfio
 ```
+The expected SCF energy is -92.8278567.
 
+Now we want to run the full-ci calculation. Type
+
+```
+  qp_run full_ci hcn.ezfio
+```
+
+By default, this will create the lowers 10.000 determinant wave-function (this number is set by the `n_det_max` variable). When this point is reach, we will compute the second order perturbative energies (the PT2, handle by the `do_pt2_end` variable) to generate a really good approximation of the full-ci.
+
+The variational energie should be '-93.043096' and the full-ci approximation energie should be '-93.051924'.
+
+#Speed up the calculus
+
+We will enlarge the basis set (up to `cc-pvdz`), and see who to do a CAS for speed-up the calculus.
+
+First create the new EZFIO with the relevant basis-set
+`qp_create_ezfio_from_xyz -b "cc-pvdz" hcn.xyz -o hcn_large.ezfio`
+
+Then run the SCF
+```
+  qp_run SCF hcn_large.ezfio
+```
 The expected SCF energy is -92.8832967.
 
 We want to run the selected full-ci calculation in the valence only. For this, we will use the ``qp_set_mo_class`` utility. The options are
@@ -63,34 +86,36 @@ We want to run the selected full-ci calculation in the valence only. For this, w
 -virt range    Range of virtual orbitals
 
 We set 2 first canonical orbitals as `core` and all the remaining MOs are set as active ::
+```
+  qp_set_mo_class hcn_large.ezfio -core "[1,2]" -act "[3-35]"
+```
 
-  qp_set_mo_class hcn.ezfio -core "[1,2]" -act "[3-35]"
+Then, edit the ``hcn_large.ezfio`` directory to modify the options of the selected Full-CI calculation::
-
+```
-Then, edit the ``hcn.ezfio`` directory to modify the options of the selected Full-CI calculation::
+  qp_edit hcn_large.ezfio
-
+```
-  qp_edit hcn.ezfio
 
 This will open a temporary file enabling the modification of the EZFIO directory. Search for the `Selected Full-CI` section, and set the ``n_det_max_fci`` option to 10000::
-
+```
   n_det_max = 10000
-
+```
 De-activate the calculation of the PT2-energy::
-
+```
   do_pt2_end = false
-
+```
 And run the Full-CI calculation::
-
+```
   qp_run full_ci hcn.ezfio
-
+```
-The expected variational energy is -93.16819314.
+The expected variationnel energy is -93.16819314.
 
 From the current wave function, we can generate the corresponding natural orbitals::
-
+```
   qp_run save_natorb hcn.ezfio
-
+```
 Re-activate the calculation of the PT2-energy using qp_edit::
-
+```
   do_pt2_end = true
-
+```
 And run the calculation again. The expected variational energy is -93.176409148 and the energy + the PT2 contribution is -93.194541427.