def main(api="", queryid=""): """Get VASP inputs for Materials Project structure Args: api <str>: Materials Project API key queryid <str>: Materials Project ID of the structure Returns: creates a folder named with that mpid, and including some VASP input files. """ if api == "": print "Must have an API key from materialsproject.org" return None if queryid == "": print "No MP structure ID given. Exiting." return None rest_adapter = MPRester(api) entries=list() proplist=list() proplist.append('pretty_formula') proplist.append('structure') proplist.append('potcar') proplist.append('material_id') myentry = rest_adapter.mpquery(criteria={'material_id':queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s as material_id. Trying entry_id." % queryid myentry = rest_adapter.mpquery(criteria={'entry_id':queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s" % queryid return None entries.extend(myentry) workdir = os.getcwd() from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet for entry in entries: mpvis = MPVaspInputSet() myname = str(entry['pretty_formula']) #print entry['structure'].composition #print entry['structure'].formula #myname = entry['pretty_formula'] myname = myname.replace("(","_").replace(")","_") myname = myname + "_" + entry['material_id'] os.mkdir(myname) os.chdir(myname) mystructure = entry['structure'] if mystructure.num_sites <= 10: mystructure.make_supercell([2,2,2]) #mystructure.perturb(0.01) incar = mpvis.get_incar(mystructure) incar.write_file("INCAR") potcar = mpvis.get_potcar(mystructure) potcar.write_file("POTCAR") #potcar_symbols = mpvis.get_potcar_symbols(mystructure) myposcar=Poscar(mystructure) mykpoints=mpvis.get_kpoints(mystructure) mykpoints.write_file("KPOINTS") myposcar.write_file("POSCAR") os.chdir(workdir)
def run_task(self, fw_spec): chgcar_start = False # read the VaspInput from the previous run poscar = Poscar.from_file(zpath('POSCAR')) incar = Incar.from_file(zpath('INCAR')) # figure out what GGA+U values to use and override them # LDAU values to use mpvis = MPVaspInputSet() ggau_incar = mpvis.get_incar(poscar.structure).to_dict incar_updates = {k: ggau_incar[k] for k in ggau_incar.keys() if 'LDAU' in k} for k in ggau_incar: # update any parameters not set explicitly in previous INCAR if k not in incar and k in ggau_incar: incar_updates[k] = ggau_incar[k] incar.update(incar_updates) # override the +U keys # start from the CHGCAR of previous run if os.path.exists('CHGCAR'): incar['ICHARG'] = 1 chgcar_start = True # write back the new INCAR to the current directory incar.write_file('INCAR') return FWAction(stored_data={'chgcar_start': chgcar_start})
def run_task(self, fw_spec): chgcar_start = False # read the VaspInput from the previous run poscar = Poscar.from_file(zpath('POSCAR')) incar = Incar.from_file(zpath('INCAR')) # figure out what GGA+U values to use and override them # LDAU values to use mpvis = MPVaspInputSet() ggau_incar = mpvis.get_incar(poscar.structure).to_dict incar_updates = { k: ggau_incar[k] for k in ggau_incar.keys() if 'LDAU' in k } for k in ggau_incar: # update any parameters not set explicitly in previous INCAR if k not in incar and k in ggau_incar: incar_updates[k] = ggau_incar[k] incar.update(incar_updates) # override the +U keys # start from the CHGCAR of previous run if os.path.exists('CHGCAR'): incar['ICHARG'] = 1 chgcar_start = True # write back the new INCAR to the current directory incar.write_file('INCAR') return FWAction(stored_data={'chgcar_start': chgcar_start})
def __init__(self,save_old_file=False): # read in what is there json_filename = 'run_data.json' try: with open(json_filename,'r') as f: data =json.load(f) except: print("CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS") return last_step = data['relaxation'][-1] structure = pymatgen.Structure.from_dict(last_step['structure']) composition = structure.composition energy = last_step['electronic']['e_0_energy'] set = MPVaspInputSet() incar = set.get_incar(structure) poscar = set.get_poscar(structure) potcar = set.get_potcar(structure) parameters = self.parse_pseudo_inputs(poscar,incar,potcar) entry = pymatgen.entries.computed_entries.ComputedEntry(composition, energy, parameters=parameters ) data['ComputedEntry'] = entry if save_old_file: shutil.move('run_data.json','run_data_OLD.json') pmg_dump(data, 'run_data.json') return
def run_task(self, fw_spec): chgcar_start = False vi = VaspInput.from_directory(".") # read the VaspInput from the previous run # figure out what GGA+U values to use and override them mpvis = MPVaspInputSet() incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k} # LDAU values to use vi['INCAR'].update(incar_updates) # override the +U keys # start from the CHGCAR of previous run if os.path.exists('CHGCAR'): vi['INCAR']['ICHARG'] = 1 chgcar_start = True vi['INCAR'].write_file('INCAR') # write back the new INCAR to the current directory return FWAction(stored_data={'chgcar_start': chgcar_start})
def run_task(self, fw_spec): chgcar_start = False # read the VaspInput from the previous run vi = VaspInput.from_directory(".") # figure out what GGA+U values to use and override them # LDAU values to use mpvis = MPVaspInputSet() incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k} vi['INCAR'].update(incar_updates) # override the +U keys # start from the CHGCAR of previous run if os.path.exists('CHGCAR'): vi['INCAR']['ICHARG'] = 1 chgcar_start = True # write back the new INCAR to the current directory vi['INCAR'].write_file('INCAR') return FWAction(stored_data={'chgcar_start': chgcar_start})
def get_LDAU(self): """ Produce LDAU related variables, to be passed to VASP as strings """ # let's simply use the Materials Project results as default. self.check_structure_is_read() dummy_input_set = MPVaspInputSet() dummy_incar = dummy_input_set.get_incar(self.structure) LDAU_dict = {} for key in self._LDAU_KEYS: if key in dummy_incar: LDAU_dict[key] = dummy_incar[key] # no need to hack the poscar or potcar poscar_need_hack = False potcar_need_hack = False return LDAU_dict, poscar_need_hack, potcar_need_hack
def __init__(self, save_old_file=False): # read in what is there json_filename = 'run_data.json' try: with open(json_filename, 'r') as f: data = json.load(f) except: print( "CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS" ) return last_step = data['relaxation'][-1] structure = pymatgen.Structure.from_dict(last_step['structure']) composition = structure.composition energy = last_step['electronic']['e_0_energy'] set = MPVaspInputSet() incar = set.get_incar(structure) poscar = set.get_poscar(structure) potcar = set.get_potcar(structure) parameters = self.parse_pseudo_inputs(poscar, incar, potcar) entry = pymatgen.entries.computed_entries.ComputedEntry( composition, energy, parameters=parameters) data['ComputedEntry'] = entry if save_old_file: shutil.move('run_data.json', 'run_data_OLD.json') pmg_dump(data, 'run_data.json') return
def get_MaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16, supplementary_incar_dict=None): if os.path.exists(workdir): print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB' return -1 os.mkdir(workdir) input_set = MPVaspInputSet() incar = input_set.get_incar(structure) # set the number of parallel processors to sqrt(nproc), # as recommended in manual. incar.update({'NPAR':int(np.sqrt(nproc))}) if supplementary_incar_dict != None: incar.update(supplementary_incar_dict) poscar = input_set.get_poscar(structure) kpoints = input_set.get_kpoints(structure) potcar = input_set.get_potcar(structure) incar.write_file(workdir+'INCAR') poscar.write_file(workdir+'POSCAR', vasp4_compatible = True) kpoints.write_file(workdir+'KPOINTS') potcar.write_file(workdir+'POTCAR') with open(workdir+'job.sh','w') as f: f.write(submit_template.format(job_name,nproc)) with open(workdir+'clean.sh','w') as f: f.write(clean_template) return 0
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet( {"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet( {"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet(mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet() def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEquals(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEquals(syms, ['P', 'Fe_pv', 'O']) def test_lda_potcar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe"], coords) p = MITVaspInputSet(potcar_functional="LDA").get_potcar(struct) self.assertEqual(p.functional, 'LDA') def test_get_nelect(self): coords = [[0]*3, [0.5]*3, [0.75]*3] lattice = Lattice.cubic(4) s = Structure(lattice, ['Si', 'Si', 'Fe'], coords) self.assertAlmostEqual(MITVaspInputSet().get_nelect(s), 16) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) incar_hse = self.mphseparamset.get_incar(self.struct) self.assertEqual(incar_hse['LHFCALC'], True) self.assertEqual(incar_hse['HFSCREEN'], 0.2) incar_hse_bsl = self.mpbshseparamsetl.get_incar(self.struct) self.assertEqual(incar_hse_bsl['LHFCALC'], True) self.assertEqual(incar_hse_bsl['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsl['NSW'], 0) incar_hse_bsu = self.mpbshseparamsetu.get_incar(self.struct) self.assertEqual(incar_hse_bsu['LHFCALC'], True) self.assertEqual(incar_hse_bsu['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsu['NSW'], 0) incar_diel = self.mpdielparamset.get_incar(self.struct) self.assertEqual(incar_diel['IBRION'], 8) self.assertEqual(incar_diel['LEPSILON'], True) si = 14 coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice(np.array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_optics(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir self.mpopticsparamset = MPOpticsNonSCFVaspInputSet.from_previous_vasp_run( '{}/static_silicon'.format(test_dir), output_dir='optics_test_dir', nedos=1145) self.assertTrue(os.path.exists('optics_test_dir/CHGCAR')) incar = Incar.from_file('optics_test_dir/INCAR') self.assertTrue(incar['LOPTICS']) self.assertEqual(incar['NEDOS'], 1145) #Remove the directory in which the inputs have been created shutil.rmtree('optics_test_dir') def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[4, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[4, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[6, 6, 4]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 140) self.assertEquals(kpoints.style, 'Reciprocal') kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 240) kpoints = self.mpbshseparamsetl.get_kpoints(self.struct) self.assertAlmostEquals(kpoints.num_kpts, 176) self.assertAlmostEqual(kpoints.kpts[10][0], 0.25) self.assertAlmostEqual(kpoints.kpts[10][1], 0.0) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.66006924) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.51780182) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.30173482) kpoints = self.mpbshseparamsetu.get_kpoints(self.struct) self.assertAlmostEquals(kpoints.num_kpts, 37) self.assertAlmostEqual(kpoints.kpts[10][0], 0.25) self.assertAlmostEqual(kpoints.kpts[10][1], 0.0) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.0) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) d = self.mitparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.to_dict v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.mphseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.to_dict v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], {"Fe": 10, "S": -5, "Mn3+": 100})
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60}, mode="Line") def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEquals(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEquals(syms, ['P', 'Fe_pv', 'O']) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) si = 14 coords = list() coords.append(array([0, 0, 0])) coords.append(array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice( array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[4, 6, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 140) self.assertEquals(kpoints.style, 'Reciprocal') kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 168) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) d = self.mitparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.to_dict v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.to_dict v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], { "Fe": 10, "S": -5, "Mn3+": 100 })
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet( {"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet( {"NBANDS": 60}, mode="Line") def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEquals(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEquals(syms, ['P', 'Fe_pv', 'O']) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) si = 14 coords = list() coords.append(array([0, 0, 0])) coords.append(array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice(array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[4, 6, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 140) self.assertEquals(kpoints.style, 'Reciprocal') kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 168) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) d = self.mitparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.to_dict v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.to_dict v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], {"Fe": 10, "S": -5, "Mn3+": 100})
def get_ModifiedMaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16, U_strategy_instance = None, supplementary_incar_dict = None): """ Inputs will be inspired by MaterialsProject, but this function is appropriate when we are seriously modifying the inputs such that they no longer conform to Materials Project. """ if os.path.exists(workdir): print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB' return -1 os.mkdir(workdir) # let's start with MP input_set = MPVaspInputSet() incar = input_set.get_incar(structure) if U_strategy_instance != None: # reading the structure here insures consistency, rather # than having the strategy read the structure outside this driver. U_strategy_instance.read_structure(structure) # Generate all LDAU-related variables according to specified strategy. LDAU_dict, poscar_need_hack, potcar_need_hack = U_strategy_instance.get_LDAU() incar.update(LDAU_dict) # set the number of parallel processors to sqrt(nproc), # as recommended in manual. incar.update({'NPAR':int(np.sqrt(nproc))}) if supplementary_incar_dict != None: incar.update(supplementary_incar_dict) poscar = input_set.get_poscar(structure) kpoints = input_set.get_kpoints(structure) potcar = input_set.get_potcar(structure) incar.write_file(workdir+'INCAR') poscar.write_file(workdir+'POSCAR', vasp4_compatible = True) kpoints.write_file(workdir+'KPOINTS') potcar.write_file(workdir+'POTCAR') if poscar_need_hack: # do we need specialized hacking of the poscar because of the U strategy? new_poscar_lines = U_strategy_instance.get_new_poscar_lines() with open(workdir+'POSCAR','w') as f: for line in new_poscar_lines: print >>f, line.strip() if potcar_need_hack: # do we need specialized hacking of the potcar because of the U strategy? new_potcar_symbols = U_strategy_instance.get_new_potcar_symbols(potcar) new_potcar = Potcar(new_potcar_symbols) # overwrite the previous potcar new_potcar.write_file(workdir+'POTCAR') with open(workdir+'job.sh','w') as f: f.write(submit_template.format(job_name,nproc)) with open(workdir+'clean.sh','w') as f: f.write(clean_template) return 0
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet( mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet() def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEquals(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEquals(syms, ['P', 'Fe_pv', 'O']) def test_lda_potcar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe"], coords) p = MITVaspInputSet(potcar_functional="LDA").get_potcar(struct) self.assertEqual(p.functional, 'LDA') def test_get_nelect(self): coords = [[0] * 3, [0.5] * 3, [0.75] * 3] lattice = Lattice.cubic(4) s = Structure(lattice, ['Si', 'Si', 'Fe'], coords) self.assertAlmostEqual(MITVaspInputSet().get_nelect(s), 16) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) incar_hse = self.mphseparamset.get_incar(self.struct) self.assertEqual(incar_hse['LHFCALC'], True) self.assertEqual(incar_hse['HFSCREEN'], 0.2) incar_hse_bsl = self.mpbshseparamsetl.get_incar(self.struct) self.assertEqual(incar_hse_bsl['LHFCALC'], True) self.assertEqual(incar_hse_bsl['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsl['NSW'], 0) incar_hse_bsu = self.mpbshseparamsetu.get_incar(self.struct) self.assertEqual(incar_hse_bsu['LHFCALC'], True) self.assertEqual(incar_hse_bsu['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsu['NSW'], 0) incar_diel = self.mpdielparamset.get_incar(self.struct) self.assertEqual(incar_diel['IBRION'], 8) self.assertEqual(incar_diel['LEPSILON'], True) si = 14 coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice( np.array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_optics(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir self.mpopticsparamset = MPOpticsNonSCFVaspInputSet.from_previous_vasp_run( '{}/static_silicon'.format(test_dir), output_dir='optics_test_dir', nedos=1145) self.assertTrue(os.path.exists('optics_test_dir/CHGCAR')) incar = Incar.from_file('optics_test_dir/INCAR') self.assertTrue(incar['LOPTICS']) self.assertEqual(incar['NEDOS'], 1145) #Remove the directory in which the inputs have been created shutil.rmtree('optics_test_dir') def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[2, 4, 6]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEquals(kpoints.kpts, [[6, 6, 4]]) self.assertEquals(kpoints.style, 'Monkhorst') kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 140) self.assertEquals(kpoints.style, 'Reciprocal') kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEquals(kpoints.num_kpts, 168) kpoints = self.mpbshseparamsetl.get_kpoints(self.struct) self.assertAlmostEquals(kpoints.num_kpts, 164) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.66006924) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.51780182) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.30173482) kpoints = self.mpbshseparamsetu.get_kpoints(self.struct) self.assertAlmostEquals(kpoints.num_kpts, 25) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.0) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) d = self.mitparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.to_dict v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.mphseparamset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.to_dict v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.to_dict v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], { "Fe": 10, "S": -5, "Mn3+": 100 })
id_expgap = open("ids.txt", "r") for line in id_expgap: words=line.split() print words id_line=words[0] os.mkdir(id_line) os.chdir(id_line) s = mpr.get_structure_by_material_id(id_line) # obtain structural information from Materials Project database #print json.dumps(s.to_dict) # convert structural infomation into a dictionary and then dump to a json file user_incar_settings={"ALGO":'Normal',"EDIFF":1E-8,"ENCUT":500,"NSW":0,"LWAVE":True} mpvis = MPVaspInputSet(user_incar_settings=user_incar_settings) mpvis.get_incar(s).write_file('INCAR') # from the GW input set, get the incar parameters, generate INCAR print mpvis.get_incar(s) # kp_density = mpvis.get_kpoints(s).kpts[0] # from the GW input set, get the k-point density kpoints = Kpoints.gamma_automatic(kp_density) # generate Gamma centered k-point mesh kpoints.write_file('KPOINTS') # generate KPOINTS file mpvis.get_poscar(s).write_file('POSCAR') # generate POSCAR file mpvis.get_potcar(s).write_file('POTCAR') # generate POTCAR file os.chdir('..') id_expgap.close()
def main(api="", queryid=""): """Get VASP inputs for Materials Project structure Args: api <str>: Materials Project API key queryid <str>: Materials Project ID of the structure Returns: creates a folder named with that mpid, and including some VASP input files. """ if api == "": print "Must have an API key from materialsproject.org" return None if queryid == "": print "No MP structure ID given. Exiting." return None rest_adapter = MPRester(api) entries = list() proplist = list() proplist.append('pretty_formula') proplist.append('structure') proplist.append('potcar') proplist.append('material_id') myentry = rest_adapter.mpquery(criteria={'material_id': queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s as material_id. Trying entry_id." % queryid myentry = rest_adapter.mpquery(criteria={'entry_id': queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s" % queryid return None entries.extend(myentry) workdir = os.getcwd() from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet for entry in entries: mpvis = MPVaspInputSet() myname = str(entry['pretty_formula']) #print entry['structure'].composition #print entry['structure'].formula #myname = entry['pretty_formula'] myname = myname.replace("(", "_").replace(")", "_") myname = myname + "_" + entry['material_id'] os.mkdir(myname) os.chdir(myname) mystructure = entry['structure'] if mystructure.num_sites <= 10: mystructure.make_supercell([2, 2, 2]) #mystructure.perturb(0.01) incar = mpvis.get_incar(mystructure) incar.write_file("INCAR") potcar = mpvis.get_potcar(mystructure) potcar.write_file("POTCAR") #potcar_symbols = mpvis.get_potcar_symbols(mystructure) myposcar = Poscar(mystructure) mykpoints = mpvis.get_kpoints(mystructure) mykpoints.write_file("KPOINTS") myposcar.write_file("POSCAR") os.chdir(workdir)