Updated tutorial 100

cb0be03b · Marco Govoni · 2804e1d1 · cb0be03b
Commit cb0be03b authored Jun 24, 2018 by Marco Govoni
--- a/doc/westpy_100.ipynb
+++ b/doc/westpy_100.ipynb
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-This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-devel/westpy/blob/master/doc/westpy_100.ipynb).
+This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-public/westpy/blob/master/doc/westpy_100.ipynb).

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 # 1 Getting Started: Ground State

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 We are going to generate an input file for the QuantumEspresso code or Qbox. Each code will compute the ground state electronic stucture for the methane molecule using Density Functional Theory.

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 ## Step 1: Load westpy

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 ``` python
 from westpy import *
 ```

 %%%% Output: stream

    
     _    _ _____ _____ _____
    | |  | |  ___/  ___|_   _|
    | |  | | |__ \ `--.  | |_ __  _   _
    | |/\| |  __| `--. \ | | '_ \| | | |
    \  /\  / |___/\__/ / | | |_) | |_| |
     \/  \/\____/\____/  \_/ .__/ \__, |
                           | |     __/ |
                           |_|    |___/
    
    WEST version     :  3.1.0
    Today            :  2018-06-24 20:14:52.640543

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 ## Step 1: Geometry

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 ``` python
 geom = Geometry()
 ```

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 Let's define a cubic cell of edge 25 Bohr.

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 ``` python
 geom.setCell((25,0,0),(0,25,0),(0,0,25))
 ```

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 We load the atomic positions from a XYZ file, available online.

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 ``` python
 geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/database/gw100/xyz/CH4.xyz" )
 ```

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 We associate pseudopotential files to each species.

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 ``` python
 geom.addSpecies( "C", "C_ONCV_PBE-1.0.upf", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf")
 geom.addSpecies( "H", "H_ONCV_PBE-1.0.upf", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf")
 ```

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 ## Step 2: Ground State

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 The ground state calculation is defined by the geometry, a choice of the exchange-correlation functional, and by setting an energy cutoff for the wavefunctions.

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 ``` python
 gs = GroundState(geom,xc="PBE",ecut=40.0)
 ```

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 We are now able to generate the input file for QuantumEspresso.

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 ``` python
 gs.generateInputPW()
 ```

 %%%% Output: stream

    
    Generated file:  pw.in

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 We can inspect the file pw.in

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 ``` python
 with open("pw.in","r") as file :
    data = file.read()
    print(data)
 ```

 %%%% Output: stream

    &CONTROL
    calculation       = 'scf'
    restart_mode      = 'from_scratch'
    pseudo_dir        = './'
    outdir            = './'
    prefix            = 'calc'
    wf_collect        = .TRUE.
    /
    &SYSTEM
    ibrav             = 0
    nat               = 5
    ntyp              = 2
    ecutwfc           = 40.0
    nbnd              = 8
    input_dft         = 'PBE'
    nosym             = .TRUE.
    noinv             = .TRUE.
    /
    &ELECTRONS
    diago_full_acc = .TRUE.
    conv_tol       = 1.d-8
    /
    ATOMIC_SPECIES
    C 12.011 C_ONCV_PBE-1.0.upf
    H 1.008 H_ONCV_PBE-1.0.upf
    ATOMIC_POSITIONS {bohr}
    C 0.0 0.0 0.0
    H 1.185992116575257 -1.185803143962673 1.185992116575257
    H -1.185992116575257 1.185992116575257 1.185992116575257
    H -1.185992116575257 -1.185992116575257 -1.185992116575257
    H 1.185992116575257 1.185992116575257 -1.185992116575257
    K_POINTS {gamma}
    CELL_PARAMETERS {bohr}
    25.0 0.0 0.0
    0.0 25.0 0.0
    0.0 0.0 25.0
    

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 We can optionally also download the pseudopotentials files.

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 ``` python
 gs.downloadPseudopotentials()
 ```

 %%%% Output: stream

    Downloaded file:  C_ONCV_PBE-1.0.upf , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf
    Downloaded file:  H_ONCV_PBE-1.0.upf , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf

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 ## Step 3: Ground State with Qbox

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 To generate the input for Qbox we can simply update Species to use the xml formats.

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 ``` python
 gs.updateSpecies("C", "C_ONCV_PBE-1.0.xml", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml")
 gs.updateSpecies("H", "H_ONCV_PBE-1.0.xml", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml")
 ```

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 We are now able to generate the input file for QuantumEspresso.

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 ``` python
 gs.generateInputQbox()
 ```

 %%%% Output: stream

    
    Generated file:  qbox.in

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 We can inspect the file qbox.in

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 ``` python
 with open("qbox.in","r") as file :
    data = file.read()
    print(data)
 ```

 %%%% Output: stream

    set cell 25.0 0.0 0.0 0.0 25.0 0.0 0.0 0.0 25.0
    species Carbon C_ONCV_PBE-1.0.xml
    species Hydrogen H_ONCV_PBE-1.0.xml
    atom C1 Carbon 0.0 0.0 0.0
    atom H2 Hydrogen 1.185992116575257 -1.185803143962673 1.185992116575257
    atom H3 Hydrogen -1.185992116575257 1.185992116575257 1.185992116575257
    atom H4 Hydrogen -1.185992116575257 -1.185992116575257 -1.185992116575257
    atom H5 Hydrogen 1.185992116575257 1.185992116575257 -1.185992116575257
    set ecut 40.0
    set wf_dyn JD
    set xc PBE
    set scf_tol 1.e-8
    randomize_wf
    run -atomic_density 0 100 5
    save gs.xml
    

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 We can optionally also download the pseudopotentials files.

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 ``` python
 gs.downloadPseudopotentials()
 ```

 %%%% Output: stream

    Downloaded file:  C_ONCV_PBE-1.0.xml , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml
    Downloaded file:  H_ONCV_PBE-1.0.xml , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml

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 ``` python
 ```