diff --git a/Tutorial.rest b/Tutorial.md similarity index 66% rename from Tutorial.rest rename to Tutorial.md index 1af67db..1206197 100644 --- a/Tutorial.rest +++ b/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::