From 87f7a9b5bfb192721b290e702a0af9e8de9f500b Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Jan 2016 21:17:39 +0100 Subject: [PATCH] Updated Tutorial (markdown) --- Tutorial.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/Tutorial.md b/Tutorial.md index 628a0ff..f7cebe7 100644 --- a/Tutorial.md +++ b/Tutorial.md @@ -1,4 +1,4 @@ -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 ``$QP_ROOT/quantum_package.rc`` file. +In this tutorial, we will run a CIPSI calculation on the HCN molecule in two basis sets. Before using the quantum package, you need to load the needed environment variables by sourcing the ``$QP_ROOT/quantum_package.rc`` file. For example:: `source $HOME/quantum_package/quantum_package.rc` @@ -16,7 +16,7 @@ This command will compile everything and install the `Hartree-Fock` and `Full-CI ``` #Create the EZFIO input file -The EZFIO is a HDF5 like format. The same EZFIO will serve from both input and output data. +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. First, create an `xyz` file containing the coordinates of the molecule. The file ``hcn.xyz`` contains: @@ -39,12 +39,12 @@ Now, this `xyz` file is used to generate an `EZFIO` input directory using the `` [-p] Using pseudopotentials ``` -To generate ``hcn.ezfio`` in the (enormous) 6-31G basis set, we use:: +To generate ``hcn.ezfio`` in the 6-31G basis set, we use:: `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. +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 @@ -52,21 +52,21 @@ First, create the canonical MOs by running an SCF calculation:: ``` qp_run SCF hcn.ezfio ``` -The expected SCF energy is -92.8278567. +The expected SCF energy is -92.8278567 au. -Now we want to run the full-ci calculation. Type +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. +By default, this will select the most important 10.000 determinants in the wave-function (this number is set by the `determinants/n_det_max` variable). When this point is reached, the second order perturbative correction is computed (handled 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'. +The variational energy should be '-93.043096' and the Full-CI approximation energy should be '-93.051924'. -#Speed up the calculus (Frozen core method) +# Freeze core electrons in the CI -We will enlarge the basis set (up to `cc-pvdz`) and frozen the orbital for speed-up the calculus. +We will enlarge the basis set to `cc-pvdz` and freeze the core orbitals in the CI calculation. First create the new EZFIO with the relevant basis-set `qp_create_ezfio_from_xyz -b "cc-pvdz" hcn.xyz -o hcn_large.ezfio` @@ -77,7 +77,7 @@ Then run the SCF ``` 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 -core range Range of core orbitals @@ -90,7 +90,7 @@ We set 2 first canonical orbitals as `core` and all the remaining MOs are set as qp_set_mo_class hcn_large.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 ``hcn_large.ezfio`` to modify the options of the selected Full-CI calculation:: ``` qp_edit hcn_large.ezfio ``` @@ -107,7 +107,7 @@ And run the Full-CI calculation:: ``` qp_run full_ci hcn_large.ezfio ``` -The expected variationnel energy is -93.16819314. +The expected variational energy is -93.16819314. From the current wave function, we can generate the corresponding natural orbitals:: ```