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_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_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_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)