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Updated Tutorial (markdown)

Thomas Applencourt 2016-01-08 17:55:41 +01:00
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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.ezfio`` directory to modify the options of the selected Full-CI calculation::
qp_edit hcn.ezfio
Then, edit the ``hcn_large.ezfio`` directory to modify the options of the selected Full-CI calculation::
```
qp_edit hcn_large.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.