xespresso 1.1.5

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
• numpy
• scipy
• matplotlib

Installation using pip

pip install --upgrade --user xespresso

Installation from source

You can get the source using git:

git clone https://github.com/superstar54/xespresso.git

Add xespresso to your PYTHONPATH. On windows, you can edit the system environment variables.

export PYTHONPATH="/path/to/xespresso":$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': 4, 
         'ntasks-per-node': 20, 
         'partition': 'all', 
         'time': '23:10:00'}
calc = Espresso(queue = queue)

Automatic check a new calculation required or not

Before the calculation, first check the working directory. If the same geometry and parameters are used, try to check the results are available or not.

calc = Espresso(label = 'scf/fe')

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.info['species'] = atoms.get_chemical_symbols()
atoms.info['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
                 }

Non self-consistent 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()

Restart 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()