def get_kpointsdata_ncf(self, name=None, index=None, only_used=False): """ This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the ``inp.xml`` file. This only works if the kpoints are listed in the in inpxml. This is NOT a calcfunction and does not keep the provenance! :param name: str, optional, if given only the kpoint set with the given name is returned :param index: int, optional, if given only the kpoint set with the given index is returned :returns: :class:`~aiida.orm.KpointsData` node """ from aiida.orm import KpointsData from masci_tools.util.xml.xml_getters import get_kpoints_data # HINT, TODO:? in this routine, the 'cell' you might get in an other way # exp: StructureData.cell, but for this you have to make a structureData Node, # which might take more time for structures with lots of atoms. # then just parsing the cell from the inp.xml # as in the routine get_structureData xmltree, schema_dict = self.load_inpxml() if name is None and index is None: kpoints, weights, cell, pbc = get_kpoints_data(xmltree, schema_dict, only_used=only_used) else: kpoints, weights, cell, pbc = get_kpoints_data(xmltree, schema_dict, name=name, index=index, only_used=only_used) if isinstance(kpoints, dict): kpoints_data = {} for (label, kpoints_set), weights_set in zip(kpoints.items(), weights.values()): kps = KpointsData() kps.set_cell(cell) kps.pbc = pbc kps.set_kpoints(kpoints_set, cartesian=False, weights=weights_set) #kpoints_data.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE) kps.label = 'fleurinp.kpts' kpoints_data[label] = kps else: kpoints_data = KpointsData() kpoints_data.set_cell(cell) kpoints_data.pbc = pbc kpoints_data.set_kpoints(kpoints, cartesian=False, weights=weights) #kpoints_data.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE) kpoints_data.label = 'fleurinp.kpts' return kpoints_data
def test_fleurinp_modifier_set_kpointsdata(create_fleurinp): """Test if setting a kpoints list to a fleurinp data node works""" from aiida.orm import KpointsData fleurinp_tmp = create_fleurinp(inpxmlfilefolder) fleurinp_tmp.store() # needed? struc = fleurinp_tmp.get_structuredata_ncf() kps = KpointsData() kps.set_cell(struc.cell) kps.pbc = struc.pbc kpoints_pos = [[0.0, 0.0, 0.0], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0], [0.5, 0.0, 0.5], [0.5, 0.5, 0.5], [1.0, 1.0, 1.0]] kpoints_weight = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0] # Fleur renormalizes kps.set_kpoints(kpoints_pos, cartesian=False, weights=kpoints_weight) kps.store() # needed, because node has to be loaded... #print(fleurinp_tmp) fm = FleurinpModifier(fleurinp_tmp) fm.set_kpointsdata(kps) fm.show(validate=True, display=False) fm.freeze() # check if kpoint node is input into modification # uuid of node show also work fm = FleurinpModifier(fleurinp_tmp) fm.set_kpointsdata(kps.uuid) fm.freeze()
def change_fleurinp(self): """ create a new fleurinp from the old with certain parameters """ # TODO allow change of kpoint mesh?, tria? wf_dict = self.ctx.wf_dict if self.ctx.scf_needed: try: fleurin = self.ctx.scf.outputs.fleurinp except NotExistent: error = 'Fleurinp generated in the SCF calculation is not found.' self.control_end_wc(error) return self.exit_codes.ERROR_SCF_CALCULATION_FAILED else: if 'fleurinp' not in self.inputs: fleurin = get_fleurinp_from_remote_data(self.inputs.remote) else: fleurin = self.inputs.fleurinp # how can the user say he want to use the given kpoint mesh, ZZ nkpts : False/0 fleurmode = FleurinpModifier(fleurin) fchanges = wf_dict.get('inpxml_changes', []) # apply further user dependend changes if fchanges: try: fleurmode.add_task_list(fchanges) except (ValueError, TypeError) as exc: error = ( 'ERROR: Changing the inp.xml file failed. Tried to apply inpxml_changes' f', which failed with {exc}. I abort, good luck next time!' ) self.control_end_wc(error) return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED kpath = wf_dict['kpath'] explicit = wf_dict['kpoints_explicit'] distance = wf_dict['kpoints_distance'] nkpts = wf_dict['kpoints_number'] listname = wf_dict['klistname'] if explicit is not None: try: fleurmode.set_kpointlist(**explicit) except (ValueError, TypeError) as exc: error = ( 'ERROR: Changing the inp.xml file failed. Tried to apply kpoints_explicit' f', which failed with {exc}. I abort, good luck next time!' ) self.control_end_wc(error) return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED if listname is None: if wf_dict.get('mode') == 'band': listname = 'path-2' if nkpts is None and distance is None: nkpts = 500 if 'kpoints' in self.inputs: fleurmode.set_kpointsdata(self.inputs.kpoints, switch=True) if kpath == 'auto': if fleurin.inp_version >= '0.32' and listname is not None: fleurmode.switch_kpointset(listname) elif isinstance(kpath, dict): if fleurin.inp_version < '0.32': if distance is not None: raise ValueError( 'set_kpath only supports specifying the number of points for the kpoints' ) fleurmode.set_kpath(kpath, nkpts) else: raise ValueError( 'set_kpath is only supported for inputs up to Max4') elif kpath == 'seek': #Use aiida functionality struc = fleurin.get_structuredata() if distance is not None: output = get_explicit_kpoints_path(struc, reference_distance=distance) else: output = get_explicit_kpoints_path(struc) primitive_struc = output['primitive_structure'] #check if primitive_structure and input structure are identical: maxdiff_cell = sum( abs(np.array(primitive_struc.cell) - np.array(struc.cell))).max() if maxdiff_cell > 3e-9: self.report(f'Error in cell : {maxdiff_cell}') self.report( 'WARNING: The structure data from the fleurinp is not the primitive structure type, which is mandatory in some cases' ) output['explicit_kpoints'].store() fleurmode.set_kpointsdata(output['explicit_kpoints'], switch=True) elif kpath == 'skip': return else: #Use ase struc = fleurin.get_structuredata() path = bandpath(kpath, cell=struc.cell, npoints=nkpts, density=distance) special_points = path.special_points labels = [] for label, special_kpoint in special_points.items(): for index, kpoint in enumerate(path.kpts): if sum(abs(np.array(special_kpoint) - np.array(kpoint))).max() < 1e-12: labels.append((index, label)) labels = sorted(labels, key=lambda x: x[0]) kpts = KpointsData() kpts.set_cell(struc.cell) kpts.pbc = struc.pbc weights = np.ones(len(path.kpts)) / len(path.kpts) kpts.set_kpoints(kpoints=path.kpts, cartesian=False, weights=weights, labels=labels) kpts.store() fleurmode.set_kpointsdata(kpts, switch=True) sigma = wf_dict['sigma'] emin = wf_dict['emin'] emax = wf_dict['emax'] if fleurin.inp_version < '0.32': if wf_dict.get('mode') == 'dos': fleurmode.set_inpchanges({'ndir': -1}) if wf_dict.get('mode') == 'dos': change_dict = { 'dos': True, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma } else: change_dict = { 'band': True, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma } fleurmode.set_inpchanges(change_dict) try: fleurmode.show(display=False, validate=True) except etree.DocumentInvalid: error = ( 'ERROR: input, user wanted inp.xml changes did not validate') self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_INPUT_FILE except ValueError as exc: error = ( 'ERROR: input, user wanted inp.xml changes could not be applied.' f'The following error was raised {exc}') self.control_end_wc(error) return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED fleurinp_new = fleurmode.freeze() self.ctx.fleurinp_banddos = fleurinp_new
def get_kpointsdata_ncf(self): """ This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the ``inp.xml`` file. This only works if the kpoints are listed in the in inpxml. This is NOT a calcfunction and does not keep the provenance! :returns: :class:`~aiida.orm.KpointsData` node """ from aiida.orm import KpointsData # HINT, TODO:? in this routine, the 'cell' you might get in an other way # exp: StructureData.cell, but for this you have to make a structureData Node, # which might take more time for structures with lots of atoms. # then just parsing the cell from the inp.xml # as in the routine get_structureData # Disclaimer: this routine needs some xpath expressions. # these are hardcoded here, therefore maintainance might be needed, # if you want to circumvent this, you have # to get all the paths from somewhere. ####### # all hardcoded xpaths used and attributes names: bravaismatrix_bulk_xpath = '/fleurInput/cell/bulkLattice/bravaisMatrix/' bravaismatrix_film_xpath = '/fleurInput/cell/filmLattice/bravaisMatrix/' kpointlist_xpath = '/fleurInput/calculationSetup/bzIntegration/kPointList/' kpoint_tag = 'kPoint' kpointlist_attrib_posscale = 'posScale' kpointlist_attrib_weightscale = 'weightScale' #kpointlist_attrib_count = 'count' kpoint_attrib_weight = 'weight' row1_tag_name = 'row-1' row2_tag_name = 'row-2' row3_tag_name = 'row-3' ######## if 'inp.xml' not in self.files: print( 'cannot get a KpointsData because fleurinpdata has no inp.xml file yet' ) # TODO what to do in this case? return False # else read in inpxml if self._schema_file_path: # Schema there, parse with schema xmlschema_doc = etree.parse(self._schema_file_path) xmlschema = etree.XMLSchema(xmlschema_doc) parser = etree.XMLParser(attribute_defaults=True, encoding='utf-8') with self.open(path='inp.xml', mode='r') as inpxmlfile: tree = etree.parse(inpxmlfile, parser) tree.xinclude() # remove comments from inp.xml comments = tree.xpath('//comment()') for c in comments: p = c.getparent() p.remove(c) if not xmlschema.validate(tree): raise ValueError( 'Input file is not validated against the schema.') else: # schema not there, parse without print('parsing inp.xml without XMLSchema') with self.open(path='inp.xml', mode='r') as inpxmlfile: tree = etree.parse(inpxmlfile) tree.xinclude() # remove comments from inp.xml comments = tree.xpath('//comment()') for c in comments: p = c.getparent() p.remove(c) root = tree.getroot() # get cell matrix from inp.xml cell = None row1 = root.xpath(bravaismatrix_bulk_xpath + row1_tag_name) # [0].text.split() if row1: # bulk calculation row1 = row1[0].text.split() row2 = root.xpath(bravaismatrix_bulk_xpath + row2_tag_name)[0].text.split() row3 = root.xpath(bravaismatrix_bulk_xpath + row3_tag_name)[0].text.split() # TODO? allow math? for i, cor in enumerate(row1): row1[i] = float(cor) * BOHR_A for i, cor in enumerate(row2): row2[i] = float(cor) * BOHR_A for i, cor in enumerate(row3): row3[i] = float(cor) * BOHR_A cell = [row1, row2, row3] # set boundary conditions pbc1 = [True, True, True] elif root.xpath(bravaismatrix_film_xpath + row1_tag_name): # film calculation row1 = root.xpath(bravaismatrix_film_xpath + row1_tag_name)[0].text.split() row2 = root.xpath(bravaismatrix_film_xpath + row2_tag_name)[0].text.split() row3 = root.xpath(bravaismatrix_film_xpath + row3_tag_name)[0].text.split() for i, cor in enumerate(row1): row1[i] = float(cor) * BOHR_A for i, cor in enumerate(row2): row2[i] = float(cor) * BOHR_A for i, cor in enumerate(row3): row3[i] = float(cor) * BOHR_A # row3 = [0, 0, 0]#? TODO:what has it to be in this case? cell = [row1, row2, row3] pbc1 = [True, True, False] if cell is None: print('Could not extract Bravias matrix out of inp.xml. Is the ' 'Bravias matrix explicitly given? i.e Latnam definition ' 'not supported.') return None # get kpoints only works if kpointlist in inp.xml kpoints = root.xpath(kpointlist_xpath + kpoint_tag) if kpoints: posscale = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_posscale) weightscale = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_weightscale) #count = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_count) kpoints_pos = [] kpoints_weight = [] for kpoint in kpoints: kpoint_pos = kpoint.text.split() for i, kval in enumerate(kpoint_pos): kpoint_pos[i] = float(kval) / float(posscale[0]) kpoint_weight = float( kpoint.get(kpoint_attrib_weight)) / float( weightscale[0]) kpoints_pos.append(kpoint_pos) kpoints_weight.append(kpoint_weight) totalw = 0 for weight in kpoints_weight: totalw = totalw + weight kps = KpointsData() kps.set_cell(cell) kps.pbc = pbc1 kps.set_kpoints(kpoints_pos, cartesian=False, weights=kpoints_weight) #kps.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE) kps.label = 'fleurinp.kpts' # return {label: kps} return kps else: # TODO parser other kpoints formats, if they fit in an AiiDA node print('No kpoint list in inp.xml') return None