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Updated Tutorial (markdown)

Thomas Applencourt 2017-05-08 17:11:27 -05:00
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Tutorial.md

@ -4,7 +4,7 @@ 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 and install the `Hartree-Fock` and `Full-CI` module This command will compile everything and install the `Hartree-Fock` and `Full-CI` module
@ -13,7 +13,7 @@ This command will compile everything and install the `Hartree-Fock` and `Full-CI
qp_module.py install Full_CI_ZMQ qp_module.py install Full_CI_ZMQ
ninja ninja
``` ```
#Create the EZFIO input file # Create the EZFIO input file
The EZFIO is a hierarchical data format which uses the hierarchy of the file system to organize the data. The EZFIO file is a database which will contain the input and output data. To access the data in the EZFIO file, you can use the provided API, or tools such as `qp_edit`, or even look at the files present in the directories. The EZFIO is a hierarchical data format which uses the hierarchy of the file system to organize the data. The EZFIO file is a database which will contain the input and output data. To access the data in the EZFIO file, you can use the provided API, or tools such as `qp_edit`, or even look at the files present in the directories.
@ -45,7 +45,7 @@ To generate ``hcn.ezfio`` in the 6-31G basis set, we use::
You can edit interactively the EZFIO file with all the options available for all the binaries installed using the `qp_edit` command. You can edit interactively the EZFIO file with all the options available for all the binaries installed using the `qp_edit` command.
#Run the SCF and Full-CI calculations # 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::
``` ```
@ -77,12 +77,13 @@ Then run the SCF
The expected SCF energy is -92.8832967. 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 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
```
-act range Range of active orbitals -act range Range of active orbitals
-core range Range of core orbitals -core range Range of core orbitals
-del range Range of deleted orbitals -del range Range of deleted orbitals
-inact range Range of inactive orbitals -inact range Range of inactive orbitals
-virt range Range of virtual orbitals -virt range Range of virtual orbitals
```
We set 2 first canonical orbitals as `core` and all the remaining MOs are set as active :: We set 2 first canonical orbitals as `core` and all the remaining MOs are set as active ::
``` ```