xespresso 1.0.0

Quantum ESPRESSO Calculator for Atomic Simulation Environment (ASE).

xespresso

Quantum ESPRESSO Calculator for Atomic Simulation Environment (ASE).

For the introduction of ASE , please visit https://wiki.fysik.dtu.dk/ase/index.html

Functions:

• Support all QE packages, including: pw, band, neb, dos, projwfc, pp ...
• Spin-polarized calculation
• LD(S)A+U
• Automatic submit job
• Automatic set up "nscf" calculation
• Read and plot dos, pdos and layer resolved pdos
• Plot NEB

Author

• Xing Wang [e-mail]

Dependencies

• Python
• ASE

Installation

Clone this repo. Add it to your PYTHONPATH and PATH. On windows, you can edit the system environment variables.

export PYTHONPATH="Your-Location":$PYTHONPATH
export ASE_ESPRESSO_COMMAND="/path/to/PACKAGE.x  PARALLEL  -in  PREFIX.PACKAGEi  >  PREFIX.PACKAGEo"
export ESPRESSO_PSEUDO="/path/to/pseudo"

Examples

Automatic submit job

A example of setting parameters for the queue. See example/queue.py

queue = {'nodes': 1, 
         'ntasks-per-node': 4, 
		 'account': 'dcb', 
		 'partition': 'all', 
		 'time': '0:10:00'}
calc = Espresso(queue = queue)

Add new species

Some atoms are special:

• atoms with different starting_magnetization
• atoms with different U values
• atoms with special basis set

For example, Fe with spin state AFM. See example/spin.py

atoms.arrays['species'] = atoms.get_chemical_symbols()
atoms.arrays['species'][1] = 'Fe1'

Setting parameters with "(i), i=1,ntyp"

Hubbard, starting_magnetization, starting_charge and so on. See example/dft+u.py

input_ntyp = {
'starting_magnetization': {'Fe1': 1.0, 'Fe2': -1.0},
'Hubbard_U': {'Fe1': 3.0, 'Fe2': 3.0},
}
input_data['input_ntyp'] = input_ntyp,

Control parallelization levels

To control the number of processors in each group: -ni, -nk, -nb, -nt, -nd) are used.

calc = Espresso(pseudopotentials = pseudopotentials, 
                 package = 'pw',
                 parallel = '-nk 2 -nt 4 -nd 144',  # parallel parameters
				 }

nscf calculation

A example of nscf calculation following the above one.

calc.read_results()
calc.nscf(queue = queue, kpts = (12, 12, 12))
calc.nscf_calculate()

calculate dos and pdos

A example of calculating and plotting the pdos from the nscf calculation.

calc.read_results()
calc.post(queue = queue, package = 'dos', Emin = fe - 30, Emax = fe + 30, DeltaE = 0.1)
calc.post(queue = queue, package = 'projwfc', Emin = fe - 30, Emax = fe + 30, DeltaE = 0.1)

calculate work function

calc.post(queue = queue, package = 'pp', plot_num = 11, fileout = 'potential.cube', iflag = 3, output_format=6)
calc.get_work_function()

restar from previous calculation

calc.read_results()
atoms = calc.results['atoms']       
calc.run(atoms = atoms, restart = 1)

NEB calculation

See example/neb.py

from xespresso.neb import NEBEspresso
calc = NEBEspresso(
                 package = 'neb',
                 images = images,
                 climbing_images = [5],
                 path_data = path_data
				 )
calc.calculate()
calc.read_results()
calc.plot()