def test_set_structure_from_inputs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
compare_struct = pymatgen.io.vaspio.Poscar.from_file(
"nebphononsposcar").structure
self.assertEqual(myoptions.options['structure']['structure'],
compare_struct)
def test_parse(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(
myoptions.options.keys(),
['mast', 'structure', 'defects', 'recipe', 'ingredients', 'neb'])
def test_parse_structure_section_noposfile(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/structure_noposfile_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_structure_section('structure', cleanlines, myoptions)
#print myoptions
self.assertEqual(myoptions.options['structure']['atom_list'],
['Al', 'Mg', 'Al', 'Fe'])
self.assertEqual(myoptions.options['structure']['coord_type'],
'fractional')
self.assertTrue(
np.array_equal(myoptions.options['structure']['lattice'],
np.array([[3.5, 1, 2], [3, 3.5, 4], [5, 6, 3.5]])))
self.assertTrue(
np.array_equal(
myoptions.options['structure']['coordinates'],
np.array([[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5]])))
self.assertItemsEqual(myoptions.options['structure']['element_map'],
dict({
'X1': 'Al',
'X2': 'Mg',
'X3': 'Fe'
}))
def set_up_recipe_plan(self, fulldir, verbose=0):
"""Set up a recipe plan from the recipe directory.
Args:
fulldir <str>: full path of recipe directory
verbose <int>: verbosity
"""
self.logger.info("--------------------------------")
self.logger.info("Setting up recipe plan for %s" % fulldir)
self.logger.info("--------------------------------")
os.chdir(fulldir) #need to change directories in order to submit jobs?
myipparser = InputParser(inputfile=os.path.join(fulldir, 'input.inp'))
myinputoptions = myipparser.parse()
input_options_keys = myinputoptions.get_sections()
key = 'personal_recipe'
if key in input_options_keys:
self.logger.debug("Key - personal recipe was found")
personal_recipe_contents = myinputoptions.get_item(
'personal_recipe', 'personal_recipe_list')
rsetup = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=myinputoptions,
structure=myinputoptions.get_item(
'structure', 'structure'),
workingDirectory=fulldir)
recipe_plan_obj = rsetup.start()
recipe_plan_obj.get_statuses_from_file()
self.logger.debug("Returning recipe plan object to calling method.")
return recipe_plan_obj
def test_parse_phonon_section(self):
raise SkipTest
#Phonon section in input file is now obsolete!
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/phonon_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_phonon_section('phonon', cleanlines, myoptions)
print myoptions
mdict = dict()
mdict['perfect'] = dict()
mdict['perfect']['phonon_center_site'] = '0.5 0.5 0'
mdict['perfect']['phonon_center_radius'] = '1'
mdict['vac1'] = dict()
mdict['vac1']['phonon_center_site'] = '0.5 0.5 0'
mdict['vac1']['phonon_center_radius'] = '1'
mdict['vac2'] = dict()
mdict['vac2']['phonon_center_site'] = '0.0 0.0 0'
mdict['vac2']['phonon_center_radius'] = '1'
mdict['vac1-vac2'] = dict()
mdict['vac1-vac2']['phonon_center_site'] = '0.25 0.25 0'
mdict['vac1-vac2']['phonon_center_radius'] = '1'
self.assertEqual(myoptions.options['phonon']['phonon'], mdict)
def test_perform_element_mapping(self):
myip = InputParser(inputfile="element_mapping.inp")
myoptions = myip.parse()
self.assertItemsEqual(myoptions.options.keys(), [
'mast', 'structure', 'defects', 'recipe', 'ingredients', 'neb',
'chemical_potentials'
])
self.assertEqual(
myoptions.options['defects']['defects']['group1']['subdefect_1']
['symbol'], 'Xe')
self.assertEqual(
myoptions.options['defects']['defects']['group1']['subdefect_2']
['symbol'], 'Ar')
self.assertEqual(
myoptions.options['defects']['defects']['group2']['subdefect_1']
['symbol'], 'Ar')
self.assertEqual(
myoptions.options['defects']['defects']['group2']['subdefect_2']
['symbol'], 'Xe')
self.assertEqual(
myoptions.options['neb']['nebs']['group1-group2']['lines'][0][0],
'Ar')
self.assertEqual(
myoptions.options['neb']['nebs']['group1-group2']['lines'][1][0],
'Xe')
def test_parse_defect_formation(self):
myip = InputParser(inputfile="defect_formation_energy.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(myoptions.options.keys(), [
'mast', 'structure', 'defects', 'recipe', 'ingredients',
'chemical_potentials', 'summary'
])
def test___init__(self):
#raise SkipTest #SD
#rfile=os.path.join(testdir,'personalized')
wdir=os.path.join(testdir,'workdir')
struc=None
#iopt=InputOptions()
#iopt=MAST.parsers.inputparser.InputParser(inputfile='input.inp').parse()
iopt=InputParser(inputfile='input.inp').parse()
rfile = iopt.get_item('personal_recipe', 'personal_recipe_list')
myrs=RecipeSetup(recipeFile=rfile, workingDirectory=wdir, inputOptions=iopt, structure=struc)
self.assertEqual(type(myrs.metafile),MAST.utility.metadata.Metadata)
def test_parse_recipe_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
print testdir
minput = MASTFile("%s/recipe_neb.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line)
myoptions = InputOptions()
myip.parse_recipe_section('recipe', cleanlines, myoptions)
#print myoptions
mdict = dict()
#mdict['recipe_file'] = os.path.join(os.getenv("MAST_RECIPE_PATH"),'defects_test.txt')
mdict['recipe_file'] = cleanlines
self.assertEqual(myoptions.options['recipe'], mdict)
def test_parse_mast_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/mast_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_mast_section('mast', cleanlines, myoptions)
mdict = dict()
mdict['mast'] = dict()
mdict['mast']['system_name'] = "SystemName!"
self.assertItemsEqual(myoptions.options.keys(), ['mast'])
self.assertItemsEqual(myoptions.options['mast'].keys(),
['system_name', 'mast_auto_correct'])
self.assertEqual(myoptions.options['mast']['system_name'],
mdict['mast']['system_name'])
self.assertEqual(myoptions.get_item('mast', 'mast_auto_correct'),
"True")
def test_parse_chemical_potentials_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/chemical_potential_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_chemical_potentials_section('chemical_potentials',
cleanlines, myoptions)
print myoptions
mdict = dict()
mdict['As rich'] = dict()
mdict['As rich']['As'] = 3.5
mdict['As rich']['Ga'] = 4.5
mdict['Ga rich'] = dict()
mdict['Ga rich']['As'] = 4.5
mdict['Ga rich']['Ga'] = 3.5
self.assertEqual(myoptions.options['chemical_potentials'], mdict)
def test_parse_ingredients_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/ingredient_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_ingredients_section('ingredients', cleanlines, myoptions)
print myoptions
mdict = dict()
mdict['global'] = dict()
mdict['global']['mast_complete_method'] = 'complete_singlerun'
mdict['global']['mast_update_children_method'] = 'give_structure'
mdict['global']['mast_queue'] = 'default'
mdict['global']['mast_run_method'] = 'run_singlerun'
mdict['global']['lcharg'] = 'False'
mdict['global']['mast_multiplyencut'] = '1.5'
mdict['global']['mast_ppn'] = '1'
mdict['global']['ismear'] = '1'
mdict['global']['nsw'] = '191'
mdict['global']['mast_exec'] = 'mpiexec //share/apps/vasp5.2_cNEB'
mdict['global']['mast_nodes'] = '1'
mdict['global']['mast_xc'] = 'PW91'
mdict['global']['prec'] = 'Accurate'
mdict['global']['mast_kpoints'] = [2, 2, 2, 'M']
mdict['global']['mast_write_method'] = 'write_singlerun'
mdict['global']['ldauu'] = '1 3 5'
mdict['global']['ibrion'] = '2'
mdict['global']['mast_ready_method'] = 'ready_singlerun'
mdict['global']['isif'] = '2'
mdict['global']['mast_program'] = 'vasp'
mdict['global']['lwave'] = 'False'
mdict['global']['sigma'] = '0.2'
mdict['phononingredient'] = dict()
mdict['phononingredient']['mast_exec'] = 'phon several words WiTh CaPs'
mdict['phononingredient']['ibrion'] = '5'
mdict['phononingredient']['mast_program'] = 'phon'
maxdiff = self.maxDiff
self.maxDiff = None
self.assertEqual(myoptions.options['ingredients'], mdict)
self.maxDiff = maxdiff
def test_parse_neb_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/neb_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_neb_section('neb', cleanlines, myoptions)
print myoptions
mdict = dict()
mdict['nebs'] = dict()
mdict['nebs']['vac1-vac2'] = dict()
mdict['nebs']['vac1-vac2']['images'] = 3
mdict['nebs']['vac1-vac2']['lines'] = list()
mdict['nebs']['vac1-vac2']['phonon'] = dict()
mdict['nebs']['vac1-vac2']['lines'].append(
list(['Cr', ' 0.5 0.5 0.0', ' 0.0 0.0 0.0']))
mdict['nebs']['vac1-vac2']['lines'].append(
list(['Fe', ' 0.2 0.1 0.3', ' 0.2 0.1 0.4']))
mdict['nebs']['vac1-vac3'] = dict()
mdict['nebs']['vac1-vac3']['images'] = 5
mdict['nebs']['vac1-vac3']['lines'] = list()
mdict['nebs']['vac1-vac3']['lines'].append(
list(['Al', ' 0.1 0.1 0.0', ' 0.3 0.4 0.1']))
mdict['nebs']['vac1-vac3']['phonon'] = dict()
mdict['nebs']['vac1-vac3']['phonon']['solvent1'] = dict()
mdict['nebs']['vac1-vac3']['phonon']['solvent1'][
'phonon_center_site'] = '0.3 0.2 0.1'
mdict['nebs']['vac1-vac3']['phonon']['solvent1'][
'phonon_center_radius'] = 3.0
mdict['nebs']['vac1-vac3']['phonon']['solvent1']['threshold'] = 0.1
mdict['nebs']['vac1-vac3']['phonon']['solute1'] = dict()
mdict['nebs']['vac1-vac3']['phonon']['solute1'][
'phonon_center_site'] = '0.2 0.1 0.5'
mdict['nebs']['vac1-vac3']['phonon']['solute1'][
'phonon_center_radius'] = 0.1
mdict['nebs']['vac1-vac3']['phonon']['solute1']['threshold'] = 0.05
self.assertEqual(myoptions.options['neb'], mdict)
def test___init__(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
s_dict = dict({\
'mast' : myip.parse_mast_section,
'structure' : myip.parse_structure_section,
'ingredients' : myip.parse_ingredients_section,
'defects' : myip.parse_defects_section,
'recipe' : myip.parse_recipe_section,
'neb' : myip.parse_neb_section,
'chemical_potentials' : myip.parse_chemical_potentials_section,
'summary' : myip.parse_summary_section,
'personal_recipe' : myip.parse_personal_recipe_section,
'scaling' : myip.parse_scaling_section,
})
self.assertItemsEqual(myip.section_parsers, s_dict)
def test_parse_structure_section_posfile(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/structure_posfile_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_structure_section('structure', cleanlines, myoptions)
#print myoptions
mdict = dict()
mdict['structure'] = dict()
mdict['structure']['posfile'] = "POSCAR_startpos"
#mdict['structure']['posfile'] = os.path.join(testdir, "POSCAR_startpos")
self.assertItemsEqual(myoptions.options.keys(), ['structure'])
self.assertEqual(myoptions.options['structure']['posfile'],
mdict['structure']['posfile'])
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/structure_posfile_lines_nosuch.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
self.assertRaises(MASTError, myip.parse_structure_section, 'structure',
cleanlines, myoptions)
def test_validate_execs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
myoptions.options['ingredients']['global'].pop('mast_exec')
myoptions.options['ingredients']['diffcoeff'].pop('mast_exec')
self.assertRaises(MASTError, myip.validate_execs, myoptions)
def test_parse_defects_section(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/defects_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_defects_section('defects', cleanlines, myoptions)
print myoptions.options['defects']
#Test coordinates first, to avoid dictionary-equal error on comparing arryas
self.assertTrue(
np.array_equal(
myoptions.options['defects']['defects']
['defect_3']['subdefect_1']['coordinates'],
np.array([0., 0., 0.], 'float')))
self.assertTrue(
np.array_equal(
myoptions.options['defects']['defects']
['Vac@Al-Sub@Fe']['subdefect_1']['coordinates'],
np.array([0., 0., 0.], 'float')))
self.assertTrue(
np.array_equal(
myoptions.options['defects']['defects']['Vac@Al-Sub@Fe']
['subdefect_2']['coordinates'],
np.array([0.5, 0.5, 0.], 'float')))
self.assertTrue(
np.array_equal(
myoptions.options['defects']['defects']['AntiGe@Fe']
['subdefect_1']['coordinates'],
np.array([0.1, 0.3, 0.4], 'float')))
self.assertTrue(
np.array_equal(
myoptions.options['defects']['defects']['MgInt']['subdefect_1']
['coordinates'], np.array([0., 0.2, 0.3], 'float')))
self.assertItemsEqual(
myoptions.options['defects']['defects']['Vac@Al-Sub@Fe']
['phonon'].keys(), ['host1', 'sub2'])
#Have to blank out the numpy arrays so that the rest of the diff'ing will work
myoptions.options['defects']['defects']['defect_3']['subdefect_1'][
'coordinates'] = 'blank'
myoptions.options['defects']['defects']['Vac@Al-Sub@Fe'][
'subdefect_1']['coordinates'] = 'blank'
myoptions.options['defects']['defects']['Vac@Al-Sub@Fe'][
'subdefect_2']['coordinates'] = 'blank'
myoptions.options['defects']['defects']['AntiGe@Fe']['subdefect_1'][
'coordinates'] = 'blank'
myoptions.options['defects']['defects']['MgInt']['subdefect_1'][
'coordinates'] = 'blank'
mdict = dict()
mdict['coord_type'] = 'fractional'
mdict['num_defects'] = 4
mdict['defects'] = dict()
mdict['defects']['defect_3'] = dict()
mdict['defects']['defect_3']['threshold'] = 0.0001
mdict['defects']['defect_3']['charge'] = [0] #charge of 0
mdict['defects']['defect_3']['coord_type'] = 'fractional'
mdict['defects']['defect_3']['subdefect_1'] = dict()
mdict['defects']['defect_3']['subdefect_1']['symbol'] = 'Al'
mdict['defects']['defect_3']['subdefect_1']['type'] = 'vacancy'
mdict['defects']['defect_3']['subdefect_1'][
'coordinates'] = 'blank' #np.array([0.,0.,0.],'float')
mdict['defects']['defect_3']['phonon'] = {}
mdict['defects']['Vac@Al-Sub@Fe'] = dict()
mdict['defects']['Vac@Al-Sub@Fe']['threshold'] = 0.0001
mdict['defects']['Vac@Al-Sub@Fe']['charge'] = [
-2, -1, 0, 1, 2, 3, 4, 5
]
mdict['defects']['Vac@Al-Sub@Fe']['coord_type'] = 'fractional'
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_1'] = dict()
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_1']['symbol'] = 'Al'
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_1']['type'] = 'vacancy'
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_1'][
'coordinates'] = 'blank' #np.array([0.,0.,0.],'float')
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_2'] = dict()
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_2']['symbol'] = 'Fe'
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_2'][
'type'] = 'substitution'
mdict['defects']['Vac@Al-Sub@Fe']['subdefect_2'][
'coordinates'] = 'blank' #np.array([0.5,0.5,0.],'float')
mdict['defects']['Vac@Al-Sub@Fe']['phonon'] = {}
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['host1'] = dict()
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['host1'][
'phonon_center_site'] = '0.1 0.2 0.3'
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['host1'][
'phonon_center_radius'] = 3.0
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['host1'][
'threshold'] = 0.07
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['sub2'] = dict()
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['sub2'][
'phonon_center_site'] = '0.2 0.4 0.0'
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['sub2'][
'phonon_center_radius'] = 1.0
mdict['defects']['Vac@Al-Sub@Fe']['phonon']['sub2']['threshold'] = 0.1
mdict['defects']['AntiGe@Fe'] = dict()
mdict['defects']['AntiGe@Fe']['threshold'] = 0.0001
mdict['defects']['AntiGe@Fe']['charge'] = [3]
mdict['defects']['AntiGe@Fe']['coord_type'] = 'fractional'
mdict['defects']['AntiGe@Fe']['subdefect_1'] = dict()
mdict['defects']['AntiGe@Fe']['subdefect_1']['symbol'] = 'Ge'
mdict['defects']['AntiGe@Fe']['subdefect_1']['type'] = 'antisite'
mdict['defects']['AntiGe@Fe']['subdefect_1'][
'coordinates'] = 'blank' #np.array([0.1,0.3,0.4],'float')
mdict['defects']['AntiGe@Fe']['phonon'] = {}
mdict['defects']['MgInt'] = dict()
mdict['defects']['MgInt']['threshold'] = 0.0001
mdict['defects']['MgInt']['charge'] = [0, 1, 2, 3]
mdict['defects']['MgInt']['coord_type'] = 'fractional'
mdict['defects']['MgInt']['subdefect_1'] = dict()
mdict['defects']['MgInt']['subdefect_1']['symbol'] = 'Mg'
mdict['defects']['MgInt']['subdefect_1']['type'] = 'interstitial'
mdict['defects']['MgInt']['subdefect_1'][
'coordinates'] = 'blank' #np.array([0.,0.2,0.3],'float')
mdict['defects']['MgInt']['phonon'] = {}
maxdiff = self.maxDiff
self.maxDiff = None
self.assertEqual(myoptions.options['defects'], mdict)
self.maxDiff = maxdiff
