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Updated Tutorial (rest => markdown)

Thomas Applencourt 2016-01-08 17:34:18 +01:00
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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:: 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
The EZFIO is a HDF5 like format. The same EZFIO will serve from both input and output data.
Create the EZFIO input file
---------------------------
First, create an `xyz` file containing the coordinates of the molecule. The file ``hcn.xyz`` contains: First, create an `xyz` file containing the coordinates of the molecule. The file ``hcn.xyz`` contains:
.. code-block:: text ```
3 3
HCN molecule HCN molecule
C 0.0 0.0 0.0 C 0.0 0.0 0.0
H 0.0 0.0 1.064 H 0.0 0.0 1.064
N 0.0 0.0 -1.156 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 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. -b string Name of basis set.
-m int Spin multiplicity (2S+1) of the molecule. Default is 1. [-c int] Total charge of the molecule. Default is 0.
-o file Name of the created EZFIO file. [-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:: 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:: First, create the canonical MOs by running an SCF calculation::