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_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_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 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___init__(self):
raise SkipTest
rt = os.path.join(testdir, 'new_template.txt')
wd = os.path.join(testdir, 'workdir')
iopt = InputOptions()
pr = os.path.join(testdir, 'workdir', 'personal_recipe.txt')
myrtp = RecipeTemplateParser(inputOptions=iopt,
working_directory=wd,
templateFile=rt,
personalRecipe=pr)
self.assertTrue(os.path.isfile, myrtp.metafile)
def parse(self):
"""Parses information from the *.inp style input file.
Returns:
options <InputOptions>: a dictionary of sections and values,
where each section is its own
dictionary:
options.options['section'] = dict()
"""
options = InputOptions()
infile = file(self.keywords['inputfile'])
eof = False
while (not eof):
line = infile.readline() #.lower() #Remove the lowercasing
# This works because the blank lines in the file are really
# newline (\n)!
# This is why strip() didn't work, cause it removed that \n,
# creating an empty string.
if (not line):
eof = True
elif (line.startswith('#')) or (line.startswith('!')):
# Lines that start with a # or a ! are treated as a comment and
# are skipped
pass
elif (line.startswith('$')) and (self.section_end not in line):
section_name = line[1:].strip()
if section_name not in self.section_parsers:
error = 'Section %s not recognized' % section_name
MASTError(self.__class__.__name__, error)
return
section_content = list()
self.logger.debug('Found section %s. Reading in options.' %
section_name)
elif (self.section_end in line) and (section_name):
self.section_parsers[section_name](section_name,
section_content, options)
self.logger.debug('Finished parsing the %s section.' %
section_name)
else:
if (section_name != 'recipe') and (section_name !=
'personal_recipe'):
line = line.strip()
if (line):
section_content.append(line)
infile.close()
self.perform_element_mapping(options)
self.set_structure_from_inputs(options)
self.logger.debug(options) # change to debug level
self.validate_execs(options)
return options
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_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_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_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
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
