Aiida: template of single run. not workflows.

pw_run.py

#!/usr/bin/env runaiida
# -*- conding: utf-8 -*-

__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved."
__license__ = "MIT license, see LICENSE.txt file"
__version__ = "0.5.0"
__contributors__ = "Andrea Cepellotti, Giovanni Pizzi, Martin Uhrin, Nicolas Mounet, Riccardo Sabatini, Valentin Bersier"

# example: 
# user$ ./pw_energy.py pw53s@rocks PbO.cif lda_hgh

import sys
import os

from aiida.common.example_helpers import test_and_get_code
from aiida.common.exceptions import NotExistent

import pymatgen as mg
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

UpfData = DataFactory('upf')
ParameterData = DataFactory('parameter')
KpointsData = DataFactory('array.kpoints')
StructureData = DataFactory('structure')

try:
    codename = sys.argv[1]
except IndexError:
    codename = None

code = test_and_get_code(codename, expected_code_type='quantumespresso.pw')

try:
    struname = sys.argv[2]   # structure are file can pass to pymatgen and parse to structure class
except IndexError:
    struname = None

# pymatgen is used for get and standarlize the primitive structure
mgstru = mg.Structure.from_file(struname)
a = SpacegroupAnalyzer(mgstru)
primstru = a.get_primitive_standard_structure()

s = StructureData(pymatgen_structure=primstru)

elements = list(s.get_symbols_set())

# auto import pseudopotentials
valid_pseudo_groups = UpfData.get_upf_groups(filter_elements=elements)
try:
        pseudo_family = sys.argv[3]
except IndexError:
    print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter"
    print >> sys.stderr, "the pseudo family name."
    print >> sys.stderr, "Valid UPF families are:"
    print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups)
    sys.exit(1)

try:
    UpfData.get_upf_group(pseudo_family)
except NotExistent:
    print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family)
    print >> sys.stderr, "but no group with such a name found in the DB."
    print >> sys.stderr, "Valid UPF groups are:"
    print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups)
    sys.exit(1) 

# the parameters of pw.x input
parameters = ParameterData(dict={
    'CONTROL': {
        'calculation': 'scf',
        'restart_mode': 'from_scratch',
        'wf_collect': True,
        'tstress': True,
        'tprnfor': True,
    },
    'SYSTEM': {
        'ecutwfc': 40.,
        'ecutrho': 320.,
    },
    'ELECTRONS': {
        'conv_thr': 1.e-10,
    }})

kpoints = KpointsData()

# method gamma only
#settings = ParameterData(dict={'gamma_only':True})
#kpoints.set_kpoints_mesh([1,1,1])

# method list
#import numpy
#kpoints.set_kpoints([[i,i,0] for i in numpy.linspace(0,1,10)],
#                    weights = [1. for i in range(10)])

# method mesh
kpoints_mesh = 2
kpoints.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh])

# to retrieve the bands
# (the object settings is optional)
settings_dict = {'also_bands': True}
settings = ParameterData(dict=settings_dict)

## For remote codes, it is not necessary to manually set the computer,
## since it is set automatically by new_calc
#computer = code.get_remote_computer()
#calc = code.new_calc(computer=computer)

calc = code.new_calc()
calc.label = "energy calc pw.x"
calc.description = "calculate the energy from a input file"
calc.set_max_wallclock_seconds(120*60) # 2hours

calc.set_resources({"parallel_env": 'orte', "tot_num_mpiprocs": 8})

# if queue is not None:
#     calc.set_queue_name(queue)

calc.use_structure(s)
calc.use_parameters(parameters)
try:
    calc.use_pseudos_from_family(pseudo_family)
    print "Pseudos successfully loaded from family {}".format(pseudo_family)
except NotExistent:
    print ("Pseudo or pseudo family not found. You may want to load the ")
    raise

calc.use_kpoints(kpoints)

if settings is not None:
    calc.use_settings(settings)


calc.store_all()
print "created calculation; calc=Calculation(uuid='{}') # ID={}".format(
    calc.uuid, calc.dbnode.pk)
calc.submit()
print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format(
    calc.uuid, calc.dbnode.pk)

init files. one example for cluster in office.