def sub_create_bands_data(cls, user=None): from aiida.orm.data.array.kpoints import KpointsData from aiida.orm import JobCalculation from aiida.orm.data.structure import StructureData from aiida.common.links import LinkType from aiida.orm.data.array.bands import BandsData import numpy s = StructureData(cell=((2., 0., 0.), (0., 2., 0.), (0., 0., 2.))) s.append_atom(position=(0., 0., 0.), symbols=['Ba', 'Ti'], weights=(1., 0.), name='mytype') if user is not None: s.dbnode.user = user._dbuser s.store() c = JobCalculation(computer=cls.computer, resources={ 'num_machines': 1, 'num_mpiprocs_per_machine': 1 }) if user is not None: c.dbnode.user = user._dbuser c.store() c.add_link_from(s, "S1", LinkType.INPUT) c._set_state(calc_states.RETRIEVING) # define a cell alat = 4. cell = numpy.array([ [alat, 0., 0.], [0., alat, 0.], [0., 0., alat], ]) k = KpointsData() k.set_cell(cell) k.set_kpoints_path() if user is not None: k.dbnode.user = user._dbuser k.store() b = BandsData() b.set_kpointsdata(k) input_bands = numpy.array( [numpy.ones(4) * i for i in range(k.get_kpoints().shape[0])]) b.set_bands(input_bands, units='eV') if user is not None: b.dbnode.user = user._dbuser b.store() b.add_link_from(c, link_type=LinkType.CREATE) return b
def connect_structure_bands(structure): alat = 4. cell = np.array([ [alat, 0., 0.], [0., alat, 0.], [0., 0., alat], ]) k = KpointsData() k.set_cell(cell) k.set_kpoints_path([('G', 'M', 2)]) b = BandsData() b.set_kpointsdata(k) b.set_bands([[1.0, 2.0], [3.0, 4.0]]) k.store() b.store() return b
def run_bands(self): """ Run the SiestaBaseWorkChain in scf+bands mode on the primitive cell of the relaxed input structure """ self.report('Running bands calculation') try: structure = self.ctx.workchain_relax.out.output_structure except: self.abort_nowait('failed to get the output structure from the relaxation run') return self.ctx.structure_relaxed_primitive = structure inputs = dict(self.ctx.inputs) kpoints_mesh = KpointsData() kpoints_mesh.set_cell_from_structure(self.ctx.structure_relaxed_primitive) kpoints_mesh.set_kpoints_mesh_from_density( distance=self.ctx.protocol['kpoints_mesh_density'], offset=self.ctx.protocol['kpoints_mesh_offset']) bandskpoints = KpointsData() bandskpoints.set_cell(structure.cell, structure.pbc) bandskpoints.set_kpoints_path(kpoint_distance = 0.05) self.ctx.kpoints_path = bandskpoints # Final input preparation, wrapping dictionaries in ParameterData nodes inputs['bandskpoints'] = self.ctx.kpoints_path inputs['kpoints'] = kpoints_mesh inputs['structure'] = self.ctx.structure_relaxed_primitive inputs['parameters'] = ParameterData(dict=inputs['parameters']) inputs['basis'] = ParameterData(dict=inputs['basis']) inputs['settings'] = ParameterData(dict=inputs['settings']) running = submit(SiestaBaseWorkChain, **inputs) self.report('launching SiestaBaseWorkChain<{}> in scf+bands mode'.format(running.pid)) return ToContext(workchain_bands=running)
def execute(args): """ The main execution of the script, which will run some preliminary checks on the command line arguments before passing them to the workchain and running it """ try: code = Code.get_from_string(args.codename) except NotExistent as exception: print "Execution failed: could not retrieve the code '{}'".format(args.codename) print "Exception report: {}".format(exception) return try: structure = load_node(args.structure) except: # # Slightly distorted structure # alat = 5.430 # angstrom cell = [[0.5*alat, 0.5*alat, 0.,], [0., 0.5*alat, 0.5*alat,], [0.5*alat, 0., 0.5*alat,], ] # Si # This was originally given in the "ScaledCartesian" format # structure = StructureData(cell=cell) structure.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) structure.append_atom(position=(0.250*alat,0.245*alat,0.250*alat),symbols=['Si']) #print "Execution failed: failed to load the node for the given structure pk '{}'".format(args.structure) #print "Exception report: {}".format(exception) #return if not isinstance(structure, StructureData): print "The provided pk {} for the structure does not correspond to StructureData, aborting...".format(args.parent_calc) return kpoints = KpointsData() kpoints.set_kpoints_mesh(args.kpoints) bandskpoints = KpointsData() bandskpoints.set_cell(structure.cell, structure.pbc) bandskpoints.set_kpoints_path(kpoint_distance = 0.05) parameters = { 'xc-functional': 'LDA', 'xc-authors': 'CA', 'spinpolarized': False, 'meshcutoff': '150.0 Ry', 'max-scfiterations': 50, 'dm-numberpulay': 4, 'dm-mixingweight': 0.3, 'dm-tolerance': 1.e-4, 'Solution-method': 'diagon', 'electronic-temperature': '25 meV', 'md-typeofrun': 'cg', 'md-numcgsteps': 10, 'md-maxcgdispl': '0.1 Ang', 'md-maxforcetol': '0.04 eV/Ang' } # default basis basis = { 'pao-energy-shift': '100 meV', '%block pao-basis-sizes': """ Si DZP """, } settings = {} options = { 'resources': { 'num_machines': 1 }, 'max_wallclock_seconds': args.max_wallclock_seconds, } run( SiestaBaseWorkChain, code=code, structure=structure, pseudo_family=Str(args.pseudo_family), kpoints=kpoints, bandskpoints=bandskpoints, parameters=ParameterData(dict=parameters), settings=ParameterData(dict=settings), options=ParameterData(dict=options), basis=ParameterData(dict=basis), max_iterations=Int(args.max_iterations), )