Commit beae7704 authored by Marco Govoni's avatar Marco Govoni
Browse files

Updated links

parent 4a754ddd
%% Cell type:markdown id: tags:
This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-public/westpy/raw/master/doc/tutorials/westpy_100.ipynb).
%% Cell type:markdown id: tags:
# 1.0 Getting Started: Ground State
%% Cell type:markdown id: tags:
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.
%% Cell type:markdown id: tags:
## Step 1: Load westpy
%% Cell type:code id: tags:
``` python
from westpy import *
```
%%%% Output: stream
_ _ _____ _____ _____
| | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, |
| | __/ |
|_| |___/
WEST version : 3.1.0
Today : 2018-06-25 18:12:53.140481
%% Cell type:markdown id: tags:
## Step 2: Geometry
%% Cell type:code id: tags:
``` python
geom = Geometry()
```
%% Cell type:markdown id: tags:
Let's define a cubic cell of edge 25 Bohr.
%% Cell type:code id: tags:
``` python
geom.setCell((25,0,0),(0,25,0),(0,0,25))
```
%% Cell type:markdown id: tags:
We load the atomic positions from a XYZ file, available online.
%% Cell type:code id: tags:
``` python
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/CH4.xyz" )
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/methane/CH4.xyz" )
```
%% Cell type:markdown id: tags:
We associate pseudopotential files to each species.
%% Cell type:code id: tags:
``` 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")
```
%% Cell type:markdown id: tags:
## Step 3.1: Ground State
%% Cell type:markdown id: tags:
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.
%% Cell type:code id: tags:
``` python
gs = GroundState(geom,xc="PBE",ecut=40.0)
```
%% Cell type:markdown id: tags:
We are now able to generate the input file for QuantumEspresso.
%% Cell type:code id: tags:
``` 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
%% 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.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
%% Cell type:markdown id: tags:
## Step 3.2: Ground State with Qbox
%% Cell type:markdown id: tags:
To generate the input for Qbox we can simply update Species to use the xml formats.
%% Cell type:code id: tags:
``` 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")
```
%% Cell type:markdown id: tags:
We are now able to generate the input file for QuantumEspresso.
%% Cell type:code id: tags:
``` 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
%% Cell type:code id: tags:
``` python
```
......
%% Cell type:markdown id: tags:
This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-public/westpy/raw/master/doc/tutorials/westpy_101.ipynb).
%% Cell type:markdown id: tags:
# 1.1 Ground State Calculation with Qbox
%% Cell type:markdown id: tags:
We are going to generate an input file for the [Qbox](http://qboxcode.org/) code. The code will compute the ground state electronic stucture for the methane molecule using Density Functional Theory.
%% Cell type:markdown id: tags:
## Step 1: Load westpy
%% Cell type:code id: tags:
``` python
from westpy import *
```
%%%% Output: stream
_ _ _____ _____ _____
| | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, |
| | __/ |
|_| |___/
WEST version : 3.1.0
Today : 2018-06-25 18:13:37.507463
%% Cell type:markdown id: tags:
## Step 2: Geometry
%% Cell type:code id: tags:
``` python
geom = Geometry()
```
%% Cell type:markdown id: tags:
Let's define a cubic cell of edge 25 Bohr.
%% Cell type:code id: tags:
``` python
geom.setCell((25,0,0),(0,25,0),(0,0,25))
```
%% Cell type:markdown id: tags:
We load the atomic positions from a XYZ file, available online.
%% Cell type:code id: tags:
``` python
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/CH4.xyz" )
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/methane/CH4.xyz" )
```
%% Cell type:markdown id: tags:
We associate pseudopotential files to each species.
%% Cell type:code id: tags:
``` python
geom.addSpecies( "C", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml")
geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml")
```
%% Cell type:markdown id: tags:
## Step 3.1: Ground State
%% Cell type:markdown id: tags:
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.
%% Cell type:code id: tags:
``` python
gs = GroundState(geom,xc="PBE",ecut=40.0)
```
%% Cell type:markdown id: tags:
We are now able to generate the input file for Qbox.
%% Cell type:code id: tags:
``` 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 C_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: C_ONCV_PBE-1.0.xml , from url: http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml
%% Cell type:code id: tags:
``` python
```
......
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