Quickstart

Were we will show some small snippets of code as examples of how to tuse the code. The general idea is that yambopy provides a class for each step of the calculation.

qepy

qepy is the module to handle the Quantum espresso <http://www.quantum-espresso.org/> part of the calculation Here we will start with qepy to generate the input files for the scf and nscf calculations.

PwIn

Here we show how to create the input file for a scf calculation

from qepy import *

#create input file from scratch
qe = PwIn()

#input structure
qe.atoms = [['Si',[0.125,0.125,0.125]],
            ['Si',[-.125,-.125,-.125]]]
qe.atypes = {'Si': [28.086,"Si.pbe-mt_fhi.UPF"]}

#control variables
qe.control['prefix'] = "'si'" #strings need double "''"
qe.control['wf_collect'] = '.true.' #logicals

#system
qe.system['celldm(1)'] = 10.3
qe.system['ecutwfc'] = 30
qe.system['occupations'] = "'fixed'"
qe.system['nat'] = 2
qe.system['ntyp'] = 1
qe.system['ibrav'] = 2

#electrons
qe.electrons['conv_thr'] = 1e-8

#write file
qe.write('si.scf')

schedulerpy

schedulerpy is a module to abstract the job execution of the environment. Here is the example to run the scf and nscf calculation using the input files we just created.

from schedulerpy import *

# scheduler 1 node and 4 cores
shell = Scheduler.factory(nodes=1,cores=4)

# scheduler of pbs type
shell = Scheduler.factory(scheduler='pbs')

#add commands to the shell
shell.add_command("echo 'hello world'")

#view commands on the screen
print( shell )

#write to a file
shell.write("commands.sh")

#submit or run the job
shell.run()

yambopy

yambopy is the module to read/write input files, and read output files from yambo. More recently we started to read some netcdf databases created by yambo. Here we will show how to create input files for a GW and BSE calculations.

YamboIn

from yambopy import *

#creathe input file in 'bse' folder with SAVE
y = YamboIn('yambo -b -o b -k sex -y d -V all',folder='bse')

# define variables
y['FFTGvecs'] = [30,'Ry'] # scalar + units
y['BndsRnXs'] = [1,30] # array with integers
y['BSEBands'] = [3,6] # array with integers
y['BEnRange'] = [[0,8],'eV'] # array + units
y['BEnSteps'] = 500 # numbers
y['KfnQPdb'] = 'E < yambo/ndb.QP' #strings

#write the file
 y.write('bse/yambo_run.in')

#create ypp input file
y = YamboIn('ypp -e -a -V all',filename='ypp.in')

#read local file
y = YamboIn(filename='bse/yambo_run.in')

#analyse the data
ya = YamboAnalyser(folder)
print(ya)

# plot eel and eps from BSE
ya.plot_bse('eel')
ya.plot_bse('eps')

YamboAnalyser

Here we read the GW band-structure that we just calculated. And the BSE absorption spectra.

yambopy (bash)

We also include a python script that can be added to the PATH and executed from the unix command line and provides many features of yambopy in a direct way.

$ yambopy #lists all possible commands
$ yambopy plotem1s #help about this command