Updated tutorial

f2549ac0 · Marco Govoni · 6f1bf1d0 · f2549ac0
Commit f2549ac0 authored Jun 25, 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-public/westpy/raw/master/doc/westpy_100.ipynb).

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 # 1.1 Getting Started: Ground State

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 We are going to generate an input file for the [QuantumEspresso](https://www.quantum-espresso.org/) code or [Qbox](http://qboxcode.org/). 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            :  2018-06-25 06:50:25.196476
+    Today            :  2018-06-25 07:01:41.214544

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 ## Step 2: 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", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf")
 geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf")
 ```

-%%%% Output: error
-
-    ---------------------------------------------------------------------------
-    ImportError                               Traceback (most recent call last)
-    <ipython-input-5-7844f98bee7b> in <module>()
-    ----> 1 geom.addSpecies( "C", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf")
-          2 geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf")
-    ~/Library/Python/3.6/lib/python/site-packages/westpy-3.1.0-py3.6.egg/westpy/geometry.py in addSpecies(self, symbol, url)
-         69       .. note:: You can use this method to add either upf or xml pseudopotentials. However it is forbidded to mix them.
-         70       """
-    ---> 71       from westpy import extractFileNameFromUrl
-         72       fname = extractFileNameFromUrl(url)
-         73       this_pseudo_format = None
-    ImportError: cannot import name 'extractFileNameFromUrl'
-
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 ## Step 3.1: 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
+
 %% Cell type:markdown id: tags:

 We can inspect the file pw.in

 %% Cell type:code id: tags:

 ``` 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 3.2: 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", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml")
 gs.updateSpecies("H", "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
+
 %% Cell type:markdown id: tags:

 We can inspect the file qbox.in

 %% Cell type:code id: tags:

 ``` 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
+    
+
 %% Cell type:markdown id: tags:

 We can optionally also download the pseudopotentials files.

 %% Cell type:code id: tags:

 ``` 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
 ```