def test_effmassline_work(self): """Testing EffMassLineWork.""" si_structure = abidata.structure_from_cif("si.cif") scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") flow = flowtk.Flow.temporary_flow() with self.assertRaises(ValueError): work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=2) # Run SCF from scratch. work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=9) t0, t1 = work[0], work[1] assert t1.depends_on(t0) assert t1.input["kptopt"] == 0 assert t1.input["iscf"] == -2 flow.register_work(work) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok # From DEN file flow = flowtk.Flow.temporary_flow() work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=10, red_dirs=(1, 0, 0), cart_dirs=[(1, 0, 0), (1, 1, 0)], den_node=abidata.ref_file("si_DEN.nc")) flow.register_work(work) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok
def test_gruneisen_work(self): """Testing GruneisenWork.""" si_structure = abidata.structure_from_cif("si.cif") gs_inp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") flow = flowtk.Flow.temporary_flow() voldelta = gs_inp.structure.volume * 0.02 work = GruneisenWork.from_gs_input(gs_inp, voldelta, ngqpt=[2, 2, 2], with_becs=False) flow.register_work(work) assert len(work.relax_tasks) == 3 assert all(t.input["optcell"] == 3 for t in work) assert all(t.input["ionmov"] == 3 for t in work) assert all(t.input["ecutsm"] == 0.5 for t in work) assert all(t.input["dilatmx"] == 1.05 for t in work) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok with self.assertRaises(ValueError): GruneisenWork.from_gs_input(gs_inp, voldelta, ngqpt=[3, 3, 3], with_becs=False)
def test_phonopy_work(self): """Testing PhononWork.""" self.skip_if_not_phonopy() si_structure = abidata.structure_from_cif("si.cif") same_structure = abiph.structure_from_atoms(abiph.atoms_from_structure(si_structure)) assert si_structure == same_structure # TODO: Spin gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") #gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized") flow = flowtk.Flow.temporary_flow() scdims = [2, 2, 2] phpy_work = abiph.PhonopyWork.from_gs_input(gsinp, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(phpy_work) self.assert_equal(scdims, phpy_work.scdims) assert hasattr(phpy_work, "phonon") assert len(phpy_work.phonopy_tasks) == len(phpy_work) assert len(phpy_work.phonopy_tasks) == 1 assert len(phpy_work.bec_tasks) == 0 # Gruneisen with phonopy grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(grun_work) self.assert_equal(scdims, grun_work.scdims) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok
def abinp_phonons(options): """Build Abinit input for phonon calculations.""" structure = get_structure(options) pseudos = get_pseudotable(options) gsinp = factories.gs_input(structure, pseudos, kppa=options.kppa, ecut=None, pawecutdg=None, scf_nband=None, accuracy="normal", spin_mode=options.spin_mode, smearing=options.smearing, charge=0.0, scf_algorithm=None) multi = factories.phonons_from_gsinput(gsinp, ph_ngqpt=None, qpoints=None, with_ddk=True, with_dde=True, with_bec=False, ph_tol=None, ddk_tol=None, dde_tol=None, wfq_tol=None, qpoints_to_skip=None) # Add getwfk variables. for inp in multi[1:]: inp["getwfk"] = 1 return finalize(multi, options)
def itest_phonopy_flow(fwp, tvars): """ Testing phonopy flow with the scheduler. """ if not has_phonopy(): raise unittest.SkipTest("This test requires phonopy") #print("tvars:\n %s" % str(tvars)) si_structure = abidata.structure_from_cif("si.cif") gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), kppa=10, ecut=2, spin_mode="unpolarized") gsinp["paral_kgb"] = tvars.paral_kgb flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager) scdims = [2, 2, 2] phpy_work = abiph.PhonopyWork.from_gs_input(gsinp, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(phpy_work) assert hasattr(phpy_work, "phonon") assert len(phpy_work.phonopy_tasks) == len(phpy_work) assert len(phpy_work.phonopy_tasks) == 1 assert len(phpy_work.bec_tasks) == 0 nptu.assert_equal(scdims, phpy_work.scdims) # Will remove output files (WFK) flow.set_garbage_collector() flow.use_smartio() flow.build_and_pickle_dump(abivalidate=True) scheduler = flow.make_scheduler() assert scheduler.start() == 0 assert not scheduler.exceptions flow.show_status() assert flow.all_ok assert all(work.finalized for work in flow) # The WFK files should have been removed because we called set_garbage_collector for task in flow[0]: assert not task.outdir.has_abiext("WFK") out_filenames = set( [os.path.basename(f) for f in phpy_work.outdir.list_filepaths()]) nmiss = 0 for f in [ "POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf", "band-dos.conf", "README.md" ]: if f not in out_filenames: nmiss += 1 print("Cannot find %s in work.outdir" % f) assert nmiss == 0
def abinp_gs(options): """Build Abinit input for ground-state calculation.""" structure = abilab.Structure.from_file(options.filepath) pseudos = get_pseudotable(options) gsinp = factories.gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy="normal", spin_mode="unpolarized", smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None) return finalize(gsinp, options)
def abinp_gs(options): """Build Abinit input for ground-state calculation.""" structure = abilab.Structure.from_file(options.filepath) pseudos = get_pseudotable(options) gsinp = factories.gs_input(structure, pseudos, kppa=options.kppa, ecut=None, pawecutdg=None, scf_nband=None, accuracy="normal", spin_mode=options.spin_mode, smearing=options.smearing, charge=0.0, scf_algorithm=None) return finalize(gsinp, options)
def itest_phonopy_flow(fwp, tvars): """ Testing phonopy Gruneisen flow with the scheduler. """ if not has_phonopy(): raise unittest.SkipTest("This test requires phonopy") #print("tvars:\n %s" % str(tvars)) si_structure = abidata.structure_from_cif("si.cif") gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), kppa=10, ecut=2, spin_mode="unpolarized") gsinp["paral_kgb"] = tvars.paral_kgb flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager) scdims = [2, 2, 2] # Grunesein with phonopy grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(grun_work) assert len(grun_work) == 3 nptu.assert_equal(scdims, grun_work.scdims) # Will remove output files (WFK) flow.set_garbage_collector() flow.use_smartio() flow.build_and_pickle_dump(abivalidate=True) scheduler = flow.make_scheduler() assert scheduler.start() == 0 assert not scheduler.exceptions flow.show_status() assert flow.all_ok # Initialial work + 3 phonopy works. assert len(flow) == 4 assert all(work.finalized for work in flow) # The WFK files should have been removed because we called set_garbage_collector # FIXME: This does not work because new works that have been created. #for task in flow.iflat_tasks(): # assert not task.outdir.has_abiext("WFK") for work in flow[1:]: out_filenames = set([os.path.basename(f) for f in work.outdir.list_filepaths()]) nmiss = 0 for f in ["POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf", "band-dos.conf", "README.md"]: if f not in out_filenames: nmiss += 1 print("Cannot find %s in work.outdir" % f) assert nmiss == 0
def on_gs_input_btn(self): if self.gs_input_btn.clicks == 0: return from abipy.abio.factories import gs_input from abipy.data.hgh_pseudos import HGH_TABLE gs_inp = gs_input( self.structure, HGH_TABLE, kppa=self.kppra.value, ecut=8, spin_mode=self.label2mode[self.spin_mode.value], smearing=None) gs_inp.pop_vars(("charge", "chksymbreak")) gs_inp.set_vars(ecut="?? # depends on pseudos", nband="?? # depends on pseudos") if self.gs_type.value == "relax": gs_inp.set_vars(optcell=2, ionmov=2, ecutsm=0.5, dilatmx=1.05) gs_inp.set_mnemonics(False) return html_with_copy_to_clipboard(gs_inp._repr_html_())
def abinp_phonons(options): """Build Abinit input for phonon calculations.""" structure = get_structure(options) pseudos = get_pseudotable(options) gsinp = factories.gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy="normal", spin_mode="unpolarized", smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None) multi = factories.phonons_from_gsinput(gsinp, ph_ngqpt=None, qpoints=None, with_ddk=True, with_dde=True, with_bec=False, ph_tol=None, ddk_tol=None, dde_tol=None, wfq_tol=None, qpoints_to_skip=None) # Add getwfk variables. for inp in multi[1:]: inp["getwfk"] = 1 return finalize(multi, options)
def test_infinite_flow(self): si_structure = abidata.structure_from_cif("si.cif") gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4) flow = flowtk.Flow.temporary_flow() work = flowtk.Work() gstask = work.register_scf_task(gsinp) flow.register_work(work) flow.allocate() mocks.infinite_flow(flow) flow.check_status() assert (t.status == flow.S_INIT for t in flow) mocks.change_task_start(gstask, mocked_status="Error") assert gstask.start() == 1 and gstask.status == gstask.S_ERROR
def test_effmass_autodfpt_work(self): """Testing EffMassAutoDFPTWork.""" si_structure = abidata.structure_from_cif("si.cif") scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") flow = flowtk.Flow.temporary_flow() # Run SCF from scratch. work = EffMassAutoDFPTWork.from_scf_input(scf_input) assert len(work) == 2 assert work[1].depends_on(work[0]) flow.register_work(work) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok
def test_phonopy_work(self): """Testing PhononWork.""" self.skip_if_not_phonopy() si_structure = abidata.structure_from_cif("si.cif") same_structure = abiph.structure_from_atoms( abiph.atoms_from_structure(si_structure)) assert si_structure == same_structure # TODO: Spin gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") #gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized") flow = flowtk.Flow.temporary_flow() scdims = [2, 2, 2] phpy_work = abiph.PhonopyWork.from_gs_input(gsinp, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(phpy_work) self.assert_equal(scdims, phpy_work.scdims) assert hasattr(phpy_work, "phonon") assert len(phpy_work.phonopy_tasks) == len(phpy_work) assert len(phpy_work.phonopy_tasks) == 1 assert len(phpy_work.bec_tasks) == 0 # Gruneisen with phonopy grun_work = abiph.PhonopyGruneisenWork.from_gs_input( gsinp, voldelta=0.1, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(grun_work) self.assert_equal(scdims, grun_work.scdims) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok
def test_effmass_dfpt_work(self): """Testing EffMassDFPTWork.""" si_structure = abidata.structure_from_cif("si.cif") scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized") flow = flowtk.Flow.temporary_flow() # Run SCF from scratch. work = EffMassDFPTWork.from_scf_input(scf_input, k0_list=(0, 0, 0), effmass_bands_f90=[2, 4]) assert len(work) == 3 t0, t1, t2 = work assert t1.input["iscf"] == -2 assert t2.input["kptopt"] == 0 assert t2.input["efmas"] == 1 and t2.input["rfelfd"] == 2 assert t2.depends_on(t1) flow.register_work(work) flow.allocate() flow.check_status() isok, checks = flow.abivalidate_inputs() assert isok
def itest_phonopy_gruneisen_flow(fwp, tvars): """ Testing phonopy Gruneisen flow with the scheduler. """ if not has_phonopy(): raise unittest.SkipTest("This test requires phonopy") #print("tvars:\n %s" % str(tvars)) si_structure = abidata.structure_from_cif("si.cif") gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), kppa=10, ecut=2, spin_mode="unpolarized") gsinp["paral_kgb"] = tvars.paral_kgb flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager) scdims = [2, 2, 2] # Grunesein with phonopy grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None) flow.register_work(grun_work) assert len(grun_work) == 3 nptu.assert_equal(scdims, grun_work.scdims) # Will remove output files (WFK) flow.set_garbage_collector() flow.use_smartio() flow.build_and_pickle_dump(abivalidate=True) scheduler = flow.make_scheduler() assert scheduler.start() == 0 assert not scheduler.exceptions flow.show_status() if not flow.all_ok: flow.debug() raise RuntimeError() # Initialial work + 3 phonopy works. assert len(flow) == 4 assert all(work.finalized for work in flow) # The WFK files should have been removed because we called set_garbage_collector # FIXME: This does not work because new works that have been created. #for task in flow.iflat_tasks(): # assert not task.outdir.has_abiext("WFK") for work in flow[1:]: out_filenames = set( [os.path.basename(f) for f in work.outdir.list_filepaths()]) nmiss = 0 for f in [ "POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf", "band-dos.conf", "README.md" ]: if f not in out_filenames: nmiss += 1 print("Cannot find %s in work.outdir" % f) assert nmiss == 0
def main(): def show_examples_and_exit(err_msg=None, error_code=1): """Display the usage of the script.""" sys.stderr.write(get_epilog()) if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n") sys.exit(error_code) parser = get_parser(with_epilog=True) # Parse command line. try: options = parser.parse_args() except Exception as exc: show_examples_and_exit(error_code=1) if not options.command: show_examples_and_exit(error_code=1) # loglevel is bound to the string value obtained from the command line argument. # Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug import logging numeric_level = getattr(logging, options.loglevel.upper(), None) if not isinstance(numeric_level, int): raise ValueError('Invalid log level: %s' % options.loglevel) logging.basicConfig(level=numeric_level) if options.verbose > 2: print(options) if options.command == "spglib": structure = abilab.Structure.from_file(options.filepath) print( structure.spget_summary(symprec=options.symprec, angle_tolerance=options.angle_tolerance, verbose=options.verbose)) #remove_equivalent_atoms(structure) elif options.command == "abispg": structure = abilab.Structure.from_file(options.filepath) spgrp = structure.abi_spacegroup if spgrp is not None: print(structure.spget_summary(verbose=options.verbose)) else: # Here we compare Abinit wrt spglib. If spgrp is None, we create a temporary # task to run the code in dry-run mode. print("FILE does not contain Abinit symmetry operations.") print( "Calling Abinit in --dry-run mode with chkprim = 0 to get space group." ) from abipy.data.hgh_pseudos import HGH_TABLE gsinp = factories.gs_input(structure, HGH_TABLE, spin_mode="unpolarized") gsinp["chkprim"] = 0 abistructure = gsinp.abiget_spacegroup(tolsym=options.tolsym) print(abistructure.spget_summary(verbose=options.verbose)) diff_structures( [structure, abistructure], mode=options.diff_mode, headers=["Input structure", "After Abinit symmetrization"], fmt="abivars") # Save file. save_structure(abistructure, options) elif options.command == "convert": fmt = options.format if fmt == "cif" and options.filepath.endswith(".cif"): fmt = "abivars" print(abilab.Structure.from_file(options.filepath).convert(fmt=fmt)) elif options.command == "supercell": structure = abilab.Structure.from_file(options.filepath) options.scaling_matrix = np.array(options.scaling_matrix) if len(options.scaling_matrix) == 9: options.scaling_matrix.shape = (3, 3) if options.verbose: print("scaling matrix: ", options.scaling_matrix) supcell = structure * options.scaling_matrix #supcell = structure.make_supercell(scaling_matrix, to_unit_cell=True) print(supcell.convert(fmt=options.format)) elif options.command == "abisanitize": print("\nCalling abi_sanitize to get a new structure in which:") print(" * Structure is refined.") print(" * Reduced to primitive settings.") print( " * Lattice vectors are exchanged if the triple product is negative\n" ) structure = abilab.Structure.from_file(options.filepath) sanitized = structure.abi_sanitize( symprec=options.symprec, angle_tolerance=options.angle_tolerance, primitive=not options.no_primitive, primitive_standard=options.primitive_standard) index = [options.filepath, "abisanitized"] dfs = abilab.dataframes_from_structures([structure, sanitized], index=index, with_spglib=True) abilab.print_dataframe(dfs.lattice, title="Lattice parameters:") abilab.print_dataframe( dfs.coords, title="Atomic positions (columns give the site index):") if not options.verbose: print("\nUse -v for more info") #print(sanitized.convert(fmt="cif")) else: #print("\nDifference between structures:") if len(structure) == len(sanitized): table = [] for line1, line2 in zip( str(structure).splitlines(), str(sanitized).splitlines()): table.append([line1, line2]) print( str( tabulate(table, headers=["Initial structure", "Abisanitized"]))) else: print("\nInitial structure:") print(structure) print("\nabisanitized structure:") print(sanitized) # Save file. save_structure(sanitized, options) elif options.command == "irefine": structure = abilab.Structure.from_file(options.filepath) sanitized = structure.copy() symprec, angle_tolerance = options.symprec, options.angle_tolerance print( "Calling abi_sanitize with increasing tolerances to reach target space group:", options.target_spgnum) print("Using symprec_step: ", options.symprec_step, ", angle_tolerance_step:", options.angle_tolerance_step, "ntrial", options.ntrial) itrial = 0 while itrial < options.ntrial: print(">>> Trying with symprec: %s, angle_tolerance: %s" % (symprec, angle_tolerance)) sanitized = sanitized.abi_sanitize( symprec=symprec, angle_tolerance=angle_tolerance, primitive=not options.no_primitive, primitive_standard=options.primitive_standard) spg_symb, spg_num = sanitized.get_space_group_info( symprec=symprec, angle_tolerance=angle_tolerance) print(">>> Space-group number:", spg_symb, ", symbol:", spg_num, "for trial:", itrial) if spg_num == options.target_spgnum: print(2 * "\n", "# Final structure with space group number:", spg_symb, ", symbol:", spg_num, 2 * "\n") print(sanitized.convert(fmt="cif")) break # Increment counter and tols. itrial += 1 symprec += options.symprec_step angle_tolerance += options.angle_tolerance_step else: print("Cannot find space group number:", options.target_spgnum, "after", options.ntrial, "iterations") return 1 # Save file. #save_structure(sanitized, options) elif options.command == "conventional": print( "\nCalling get_conventional_standard_structure to get conventional structure:" ) print( "The standards are defined in Setyawan, W., & Curtarolo, S. (2010). " ) print( "High-throughput electronic band structure calculations: Challenges and tools. " ) print( "Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010\n" ) structure = abilab.Structure.from_file(options.filepath) conv = structure.get_conventional_standard_structure( international_monoclinic=True, symprec=options.symprec, angle_tolerance=options.angle_tolerance) index = [options.filepath, "conventional"] dfs = abilab.dataframes_from_structures([structure, conv], index=index, with_spglib=True) abilab.print_dataframe(dfs.lattice, title="Lattice parameters:") if options.verbose: abilab.print_dataframe( dfs.coords, title="Atomic positions (columns give the site index):") if not options.verbose: print("\nUse -v for more info") else: #print("\nDifference between structures:") if len(structure) == len(conv): table = [] for line1, line2 in zip( str(structure).splitlines(), str(conv).splitlines()): table.append([line1, line2]) print( str( tabulate(table, headers=["Initial structure", "Conventional"]))) else: print("\nInitial structure:\n", structure) print("\nConventional structure:\n", conv) # Save file. save_structure(conv, options) elif options.command == "neighbors": abilab.Structure.from_file( options.filepath).print_neighbors(radius=options.radius) elif options.command == "interpolate": initial_structure = abilab.Structure.from_file(options.filepaths[0]) end_structure = abilab.Structure.from_file(options.filepaths[1]) structures = initial_structure.interpolate( end_structure, nimages=options.nimages, interpolate_lattices=False, pbc=True, autosort_tol=options.autosort_tol) structures = list(map(abilab.Structure.as_structure, structures)) for i, s in enumerate(structures): print(marquee("Structure #%d" % i, mark="=")) print(s.convert(fmt=options.format)) print(" ") elif options.command == "xrd": structure = abilab.Structure.from_file(options.filepath) two_theta_range = tuple(float(t) for t in options.two_theta_range) structure.plot_xrd(wavelength=options.wavelength, two_theta_range=two_theta_range, symprec=options.symprec, annotate_peaks=not options.no_annotate_peaks) elif options.command == "oxistate": print( abilab.Structure.from_file( options.filepath).get_oxi_state_decorated()) elif options.command == "ipython": structure = abilab.Structure.from_file(options.filepath) print( "Invoking Ipython, `structure` object will be available in the Ipython terminal" ) import IPython IPython.start_ipython(argv=[], user_ns={"structure": structure}) elif options.command == "notebook": structure = abilab.Structure.from_file(options.filepath) structure.make_and_open_notebook(nbpath=None, foreground=options.foreground) elif options.command == "visualize": structure = abilab.Structure.from_file(options.filepath) print(structure) print("Visualizing structure with:", options.appname) structure.visualize(appname=options.appname) elif options.command == "kpath": structure = abilab.Structure.from_file(options.filepath) print("# Abinit Structure") print(structure.abi_string) print("\n# K-path in reduced coordinates:") print("# tolwfr 1e-20 iscf -2 getden ??") print(" ndivsm 10") print(" kptopt", -(len(structure.hsym_kpoints) - 1)) print(" kptbounds") for k in structure.hsym_kpoints: print(" %+.5f %+.5f %+.5f" % tuple(k.frac_coords), "#", k.name) elif options.command == "bz": abilab.Structure.from_file(options.filepath).plot_bz() elif options.command == "ngkpt": d = abilab.Structure.from_file(options.filepath).calc_ksampling( options.nksmall) print("ngkpt %d %d %d" % (d.ngkpt[0], d.ngkpt[1], d.ngkpt[2])) print("nshiftk ", len(d.shiftk), "\nshiftk") for s in d.shiftk: print(" %s %s %s" % (s[0], s[1], s[2])) elif options.command == "ktables": structure = abilab.Structure.from_file(options.filepath) k = Ktables(structure, options.mesh, options.is_shift, not options.no_time_reversal) print(k) print("") print( "NB: These results are obtained by calling spglib with the structure read from file." ) print( "The k-points might differ from the ones expected by Abinit, especially if the space groups differ." ) if not options.verbose: print("\nUse -v to obtain the BZ --> IBZ mapping.") else: print() k.print_bz2ibz() elif options.command == "abikmesh": structure = abilab.Structure.from_file(options.filepath) from abipy.data.hgh_pseudos import HGH_TABLE gsinp = factories.gs_input(structure, HGH_TABLE, spin_mode="unpolarized", kppa=options.kppa) if options.kppa is not None: print("Calling Abinit to compute the IBZ with kppa:", options.kppa, "and shiftk:", options.shiftk) options.ngkpt = None else: print("Calling Abinit to compute the IBZ with ngkpt:", options.ngkpt, "and shiftk", options.shiftk) ibz = gsinp.abiget_ibz(ngkpt=options.ngkpt, shiftk=options.shiftk, kptopt=options.kptopt) if options.verbose: print(gsinp) print("Found %d points in the IBZ:" % len(ibz.points)) for i, (k, w) in enumerate(zip(ibz.points, ibz.weights)): print("%6d) [%+.3f, %+.3f, %+.3f] weight=%.3f" % (i, k[0], k[1], k[2], w)) #elif options.command == "kmesh_jhu": # structure = abilab.Structure.from_file(options.filepath) # ksampling = structure.ksampling_from_jhudb(kppra=1000) # #print(ksampling) elif options.command == "lgk": structure = abilab.Structure.from_file(options.filepath) spgrp = structure.abi_spacegroup if spgrp is None: cprint("Your file does not contain Abinit symmetry operations.", "yellow") cprint( "Will call spglib to obtain the space group (assuming time-reversal: %s)" % (not options.no_time_reversal), "yellow") spgrp = AbinitSpaceGroup.from_structure( structure, has_timerev=not options.no_time_reversal, symprec=options.symprec, angle_tolerance=options.angle_tolerance) print() print(marquee("Structure", mark="=")) print(structure.spget_summary(verbose=options.verbose)) print("\n") print(marquee("Little Group", mark="=")) ltk = spgrp.find_little_group(kpoint=options.kpoint) print(ltk.to_string(verbose=options.verbose)) elif options.command == "kstar": structure = abilab.Structure.from_file(options.filepath) # TODO #kstar = structure.get_star_kpoint(options.kpoint, has_timerev=not options.no_time_reversal) # Call spglib to get spacegroup if Abinit spacegroup is not available. if structure.abi_spacegroup is None: structure.spgset_abi_spacegroup( has_timerev=not options.no_time_reversal) kpoint = Kpoint(options.kpoint, structure.reciprocal_lattice) kstar = kpoint.compute_star(structure.abi_spacegroup, wrap_tows=True) print("Found %s points in the star of %s\n" % (len(kstar), repr(kpoint))) for k in kstar: print(4 * " ", repr(k)) elif options.command == "mp_id": # Get the Structure corresponding to material_id. structure = abilab.Structure.from_mpid(options.mpid, final=True, api_key=options.mapi_key, endpoint=options.endpoint) # Convert to format and print it. print(structure.convert(fmt=options.format)) elif options.command == "mp_match": mp = abilab.mp_match_structure(options.filepath) if not mp.structures: cprint("No structure found in database", "yellow") return 1 if options.notebook: return mp.make_and_open_notebook(foreground=options.foreground) else: mp.print_results(fmt=options.format, verbose=options.verbose) if options.browser: mp.open_browser(limit=None if options.verbose == 2 else 10) elif options.command == "mp_search": mp = abilab.mp_search(options.chemsys_formula_id) if not mp.structures: cprint("No structure found in Materials Project database", "yellow") return 1 if options.select_spgnum: mp = mp.filter_by_spgnum(options.select_spgnum) if options.notebook: return mp.make_and_open_notebook(foreground=options.foreground) else: mp.print_results(fmt=options.format, verbose=options.verbose) if options.browser: mp.open_browser(limit=None if options.verbose == 2 else 10) elif options.command == "mp_pd": if os.path.exists(options.file_or_elements): structure = abilab.Structure.from_file(options.file_or_elements) elements = structure.symbol_set else: elements = options.file_or_elements.split("-") if options.verbose > 1: print("Building phase-diagram for elements:", elements) with abilab.restapi.get_mprester(api_key=options.mapi_key, endpoint=options.endpoint) as rest: pdr = rest.get_phasediagram_results(elements) pdr.print_dataframes(verbose=options.verbose) pdr.plot(show_unstable=options.show_unstable) elif options.command == "cod_search": cod = abilab.cod_search(options.formula, primitive=options.primitive) if not cod.structures: cprint("No structure found in COD database", "yellow") return 1 if options.select_spgnum: cod = cod.filter_by_spgnum(options.select_spgnum) if options.notebook: return cod.make_and_open_notebook(foreground=options.foreground) else: cod.print_results(fmt=options.format, verbose=options.verbose) elif options.command == "cod_id": # Get the Structure from COD structure = abilab.Structure.from_cod_id(options.cod_identifier, primitive=options.primitive) # Convert to format and print it. print(structure.convert(fmt=options.format)) elif options.command == "animate": filepath = options.filepath if any(filepath.endswith(ext) for ext in ("HIST", "HIST.nc")): with abilab.abiopen(filepath) as hist: structures = hist.structures elif "XDATCAR" in filepath: structures = Xdatcar(filepath).structures if not structures: raise RuntimeError( "Your Xdatcar contains only one structure. Due to a bug " "in the pymatgen routine, your structures won't be parsed correctly" "Solution: Add another structure at the end of the file.") else: raise ValueError("Don't know how to handle file %s" % filepath) xsf_write_structure(sys.stdout, structures) else: raise ValueError("Unsupported command: %s" % options.command) return 0
def main(): def show_examples_and_exit(err_msg=None, error_code=1): """Display the usage of the script.""" sys.stderr.write(get_epilog()) if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n") sys.exit(error_code) parser = get_parser(with_epilog=True) # Parse command line. try: options = parser.parse_args() except Exception as exc: show_examples_and_exit(error_code=1) if not options.command: show_examples_and_exit(error_code=1) # loglevel is bound to the string value obtained from the command line argument. # Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug import logging numeric_level = getattr(logging, options.loglevel.upper(), None) if not isinstance(numeric_level, int): raise ValueError('Invalid log level: %s' % options.loglevel) logging.basicConfig(level=numeric_level) if options.verbose > 2: print(options) if options.command == "spglib": structure = abilab.Structure.from_file(options.filepath) print(structure.spget_summary(symprec=options.symprec, angle_tolerance=options.angle_tolerance, verbose=options.verbose)) #remove_equivalent_atoms(structure) elif options.command == "abispg": structure = abilab.Structure.from_file(options.filepath) check_ordered_structure(structure) spgrp = structure.abi_spacegroup if spgrp is not None: print(structure.spget_summary(verbose=options.verbose)) else: # Here we compare Abinit wrt spglib. If spgrp is None, we create a temporary # task to run the code in dry-run mode. print("FILE does not contain Abinit symmetry operations.") print("Calling Abinit in --dry-run mode with chkprim = 0 to get space group.") from abipy.data.hgh_pseudos import HGH_TABLE gsinp = factories.gs_input(structure, HGH_TABLE, spin_mode="unpolarized") gsinp["chkprim"] = 0 abistructure = gsinp.abiget_spacegroup(tolsym=options.tolsym) print(abistructure.spget_summary(verbose=options.verbose)) diff_structures([structure, abistructure], mode=options.diff_mode, headers=["Input structure", "After Abinit symmetrization"], fmt="abivars") # Save file. save_structure(abistructure, options) elif options.command == "convert": fmt = options.format if fmt == "cif" and options.filepath.endswith(".cif"): fmt = "abivars" print(abilab.Structure.from_file(options.filepath).convert(fmt=fmt)) elif options.command == "supercell": structure = abilab.Structure.from_file(options.filepath) options.scaling_matrix = np.array(options.scaling_matrix) if len(options.scaling_matrix) == 9: options.scaling_matrix.shape = (3, 3) if options.verbose: print("scaling matrix: ", options.scaling_matrix) supcell = structure * options.scaling_matrix #supcell = structure.make_supercell(scaling_matrix, to_unit_cell=True) print(supcell.convert(fmt=options.format)) elif options.command == "abisanitize": print("\nCalling abi_sanitize to get a new structure in which:") print(" * Structure is refined.") print(" * Reduced to primitive settings.") print(" * Lattice vectors are exchanged if the triple product is negative\n") structure = abilab.Structure.from_file(options.filepath) sanitized = structure.abi_sanitize(symprec=options.symprec, angle_tolerance=options.angle_tolerance, primitive=not options.no_primitive, primitive_standard=options.primitive_standard) index = [options.filepath, "abisanitized"] dfs = abilab.dataframes_from_structures([structure, sanitized], index=index, with_spglib=True) abilab.print_dataframe(dfs.lattice, title="Lattice parameters:") abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):") if not options.verbose: print("\nUse -v for more info") #print(sanitized.convert(fmt="cif")) else: #print("\nDifference between structures:") if len(structure) == len(sanitized): table = [] for line1, line2 in zip(str(structure).splitlines(), str(sanitized).splitlines()): table.append([line1, line2]) print(str(tabulate(table, headers=["Initial structure", "Abisanitized"]))) else: print("\nInitial structure:") print(structure) print("\nabisanitized structure:") print(sanitized) # Save file. save_structure(sanitized, options) elif options.command == "irefine": structure = abilab.Structure.from_file(options.filepath) sanitized = structure.copy() symprec, angle_tolerance = options.symprec, options.angle_tolerance print("Calling abi_sanitize with increasing tolerances to reach target space group:", options.target_spgnum) print("Using symprec_step: ", options.symprec_step, ", angle_tolerance_step:", options.angle_tolerance_step, "ntrial", options.ntrial) itrial = 0 while itrial < options.ntrial: print(">>> Trying with symprec: %s, angle_tolerance: %s" % (symprec, angle_tolerance)) sanitized = sanitized.abi_sanitize(symprec=symprec, angle_tolerance=angle_tolerance, primitive=not options.no_primitive, primitive_standard=options.primitive_standard) spg_symb, spg_num = sanitized.get_space_group_info(symprec=symprec, angle_tolerance=angle_tolerance) print(">>> Space-group number:", spg_symb, ", symbol:", spg_num, "for trial:", itrial) if spg_num == options.target_spgnum: print(2 * "\n", "# Final structure with space group number:", spg_symb, ", symbol:", spg_num, 2 *"\n") print(sanitized.convert(fmt="cif")) break # Increment counter and tols. itrial += 1 symprec += options.symprec_step angle_tolerance += options.angle_tolerance_step else: print("Cannot find space group number:", options.target_spgnum, "after", options.ntrial, "iterations") return 1 # Save file. #save_structure(sanitized, options) elif options.command == "conventional": print("\nCalling get_conventional_standard_structure to get conventional structure:") print("The standards are defined in Setyawan, W., & Curtarolo, S. (2010). ") print("High-throughput electronic band structure calculations: Challenges and tools. ") print("Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010\n") structure = abilab.Structure.from_file(options.filepath) conv = structure.get_conventional_standard_structure(international_monoclinic=True, symprec=options.symprec, angle_tolerance=options.angle_tolerance) index = [options.filepath, "conventional"] dfs = abilab.dataframes_from_structures([structure, conv], index=index, with_spglib=True) abilab.print_dataframe(dfs.lattice, title="Lattice parameters:") if options.verbose: abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):") if not options.verbose: print("\nUse -v for more info") else: #print("\nDifference between structures:") if len(structure) == len(conv): table = [] for line1, line2 in zip(str(structure).splitlines(), str(conv).splitlines()): table.append([line1, line2]) print(str(tabulate(table, headers=["Initial structure", "Conventional"]))) else: print("\nInitial structure:\n", structure) print("\nConventional structure:\n", conv) # Save file. save_structure(conv, options) elif options.command == "neighbors": abilab.Structure.from_file(options.filepath).print_neighbors(radius=options.radius) elif options.command == "interpolate": initial_structure = abilab.Structure.from_file(options.filepaths[0]) end_structure = abilab.Structure.from_file(options.filepaths[1]) structures = initial_structure.interpolate(end_structure, nimages=options.nimages, interpolate_lattices=False, pbc=True, autosort_tol=options.autosort_tol) structures = list(map(abilab.Structure.as_structure, structures)) for i, s in enumerate(structures): print(marquee("Structure #%d" % i, mark="=")) print(s.convert(fmt=options.format)) print(" ") elif options.command == "xrd": structure = abilab.Structure.from_file(options.filepath) two_theta_range = tuple(float(t) for t in options.two_theta_range) structure.plot_xrd(wavelength=options.wavelength, two_theta_range=two_theta_range, symprec=options.symprec, annotate_peaks=not options.no_annotate_peaks) elif options.command == "oxistate": print(abilab.Structure.from_file(options.filepath).get_oxi_state_decorated()) elif options.command == "ipython": structure = abilab.Structure.from_file(options.filepath) print("Invoking Ipython, `structure` object will be available in the Ipython terminal") import IPython IPython.start_ipython(argv=[], user_ns={"structure": structure}) elif options.command == "notebook": structure = abilab.Structure.from_file(options.filepath) structure.make_and_open_notebook(nbpath=None, foreground=options.foreground) elif options.command == "visualize": structure = abilab.Structure.from_file(options.filepath) print(structure) print("Visualizing structure with:", options.appname) structure.visualize(appname=options.appname) elif options.command == "kpath": structure = abilab.Structure.from_file(options.filepath) print(structure.get_kpath_input_string(fmt=options.format, line_density=10)) elif options.command == "bz": abilab.Structure.from_file(options.filepath).plot_bz() elif options.command == "ngkpt": d = abilab.Structure.from_file(options.filepath).calc_ksampling(options.nksmall) print("ngkpt %d %d %d" % (d.ngkpt[0], d.ngkpt[1], d.ngkpt[2])) print("nshiftk ", len(d.shiftk), "\nshiftk") for s in d.shiftk: print(" %s %s %s" % (s[0], s[1], s[2])) elif options.command == "ktables": structure = abilab.Structure.from_file(options.filepath) k = Ktables(structure, options.mesh, options.is_shift, not options.no_time_reversal) print(k) print("") print("NB: These results are obtained by calling spglib with the structure read from file.") print("The k-points might differ from the ones expected by Abinit, especially if the space groups differ.") if not options.verbose: print("\nUse -v to obtain the BZ --> IBZ mapping.") else: print() k.print_bz2ibz() elif options.command == "abikmesh": structure = abilab.Structure.from_file(options.filepath) if options.kppa is None and options.ngkpt is None: raise ValueError("Either ngkpt or kppa must be provided") if options.kppa is not None: print("Calling Abinit to compute the IBZ with kppa:", options.kppa, "and shiftk:", options.shiftk) ibz = IrredZone.from_kppa(structure, options.kppa, options.shiftk, kptopt=options.kptopt, verbose=options.verbose) else: print("Calling Abinit to compute the IBZ with ngkpt:", options.ngkpt, "and shiftk:", options.shiftk) ibz = IrredZone.from_ngkpt(structure, options.ngkpt, options.shiftk, kptopt=options.kptopt, verbose=options.verbose) print(ibz.to_string(verbose=options.verbose)) #elif options.command == "kmesh_jhu": # structure = abilab.Structure.from_file(options.filepath) # ksampling = structure.ksampling_from_jhudb(kppra=1000) # #print(ksampling) elif options.command == "lgk": structure = abilab.Structure.from_file(options.filepath) spgrp = structure.abi_spacegroup if spgrp is None: cprint("Your file does not contain Abinit symmetry operations.", "yellow") cprint("Will call spglib to obtain the space group (assuming time-reversal: %s)" % (not options.no_time_reversal), "yellow") spgrp = AbinitSpaceGroup.from_structure(structure, has_timerev=not options.no_time_reversal, symprec=options.symprec, angle_tolerance=options.angle_tolerance) print() print(marquee("Structure", mark="=")) print(structure.spget_summary(verbose=options.verbose)) print("\n") print(marquee("Little Group", mark="=")) ltk = spgrp.find_little_group(kpoint=options.kpoint) print(ltk.to_string(verbose=options.verbose)) elif options.command == "kstar": structure = abilab.Structure.from_file(options.filepath) # Call spglib to get spacegroup if Abinit spacegroup is not available. if structure.abi_spacegroup is None: structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal) kpoint = Kpoint(options.kpoint, structure.reciprocal_lattice) kstar = kpoint.compute_star(structure.abi_spacegroup, wrap_tows=True) print("Found %s points in the star of %s\n" % (len(kstar), repr(kpoint))) for k in kstar: print(4 * " ", repr(k)) elif options.command == "keq": structure = abilab.Structure.from_file(options.filepath) # Call spglib to get spacegroup if Abinit spacegroup is not available. if structure.abi_spacegroup is None: structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal) k1, k2 = options.kpoints[:3], options.kpoints[3:6] k1tab = structure.abi_spacegroup.symeq(k1, k2) if k1tab.isym != -1: print("\nk1:", k1, "and k2:", k2, "are symmetry equivalent k-points\n") print("Related by the symmetry operation (reduced coords):\n", k1tab.op) print("With umklapp vector Go = TO(k1) - k2 =", k1tab.g0) else: print(k1, "and", k2, "are NOT symmetry equivalent") elif options.command == "mp_id": # Get the Structure corresponding to material_id. structure = abilab.Structure.from_mpid(options.mpid, final=True, api_key=options.mapi_key, endpoint=options.endpoint) # Convert to format and print it. print(structure.convert(fmt=options.format)) elif options.command == "mp_match": mp = abilab.mp_match_structure(options.filepath) if not mp.structures: cprint("No structure found in database", "yellow") return 1 if options.notebook: return mp.make_and_open_notebook(foreground=options.foreground) else: mp.print_results(fmt=options.format, verbose=options.verbose) if options.browser: mp.open_browser(limit=None if options.verbose == 2 else 10) elif options.command == "mp_search": mp = abilab.mp_search(options.chemsys_formula_id) if not mp.structures: cprint("No structure found in Materials Project database", "yellow") return 1 if options.select_spgnum: mp = mp.filter_by_spgnum(options.select_spgnum) if options.notebook: return mp.make_and_open_notebook(foreground=options.foreground) else: mp.print_results(fmt=options.format, verbose=options.verbose) if options.browser: mp.open_browser(limit=None if options.verbose == 2 else 10) elif options.command == "mp_pd": if os.path.exists(options.file_or_elements): structure = abilab.Structure.from_file(options.file_or_elements) elements = structure.symbol_set else: elements = options.file_or_elements.split("-") if options.verbose > 1: print("Building phase-diagram for elements:", elements) with abilab.restapi.get_mprester(api_key=options.mapi_key, endpoint=options.endpoint) as rest: pdr = rest.get_phasediagram_results(elements) pdr.print_dataframes(verbose=options.verbose) pdr.plot(show_unstable=options.show_unstable) elif options.command == "cod_search": cod = abilab.cod_search(options.formula, primitive=options.primitive) if not cod.structures: cprint("No structure found in COD database", "yellow") return 1 if options.select_spgnum: cod = cod.filter_by_spgnum(options.select_spgnum) if options.notebook: return cod.make_and_open_notebook(foreground=options.foreground) else: cod.print_results(fmt=options.format, verbose=options.verbose) elif options.command == "cod_id": # Get the Structure from COD structure = abilab.Structure.from_cod_id(options.cod_identifier, primitive=options.primitive) # Convert to format and print it. print(structure.convert(fmt=options.format)) elif options.command == "animate": filepath = options.filepath if any(filepath.endswith(ext) for ext in ("HIST", "HIST.nc")): with abilab.abiopen(filepath) as hist: structures = hist.structures elif "XDATCAR" in filepath: structures = Xdatcar(filepath).structures if not structures: raise RuntimeError("Your Xdatcar contains only one structure. Due to a bug " "in the pymatgen routine, your structures won't be parsed correctly" "Solution: Add another structure at the end of the file.") else: raise ValueError("Don't know how to handle file %s" % filepath) xsf_write_structure(sys.stdout, structures) else: raise ValueError("Unsupported command: %s" % options.command) return 0