本文整理汇总了Python中MAST.ingredients.chopingredient.ChopIngredient.run_defect方法的典型用法代码示例。如果您正苦于以下问题：Python ChopIngredient.run_defect方法的具体用法？Python ChopIngredient.run_defect怎么用？Python ChopIngredient.run_defect使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类MAST.ingredients.chopingredient.ChopIngredient的用法示例。
在下文中一共展示了ChopIngredient.run_defect方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_run_scale_defect
# 需要导入模块: from MAST.ingredients.chopingredient import ChopIngredient [as 别名]
# 或者: from MAST.ingredients.chopingredient.ChopIngredient import run_defect [as 别名]
def test_run_scale_defect(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = label1\n")
metad.data.append("scaling_size = [2,2,2]\n")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['label1']=dict()
kdict['label1']['subdefect1']=dict()
kdict['label1']['subdefect1']['symbol']='Cr'
kdict['label1']['subdefect1']['type']='interstitial'
kdict['label1']['subdefect1']['coordinates']=np.array([0.8, 0.7, 0.6])
kdict['label1']['subdefect2']=dict()
kdict['label1']['subdefect2']['symbol']='Sr'
kdict['label1']['subdefect2']['type']='antisite'
kdict['label1']['subdefect2']['coordinates']=np.array([0.5,0.5,0.0])
kdict['label1']['subdefect3']=dict()
kdict['label1']['subdefect3']['symbol']='Cr'
kdict['label1']['subdefect3']['type']='interstitial'
kdict['label1']['subdefect3']['coordinates']=np.array([0.3,0.3,0.2])
kdict['label1']['subdefect4']=dict()
kdict['label1']['subdefect4']['symbol']='Fe'
kdict['label1']['subdefect4']['type']='substitution'
kdict['label1']['subdefect4']['coordinates']=np.array([0.25,0.75,0.75])
kdict['label1']['subdefect5']=dict()
kdict['label1']['subdefect5']['symbol']='O'
kdict['label1']['subdefect5']['type']='vacancy'
kdict['label1']['subdefect5']['coordinates']=np.array([0.5,0.25,0.75])
kdict['label1']['subdefect6']=dict()
kdict['label1']['subdefect6']['symbol']='Fe'
kdict['label1']['subdefect6']['type']='substitution'
kdict['label1']['subdefect6']['coordinates']=np.array([0.25,0.25,0.25])
kdict['label1']['subdefect7']=dict()
kdict['label1']['subdefect7']['symbol']='La'
kdict['label1']['subdefect7']['type']='vacancy'
kdict['label1']['subdefect7']['coordinates']=np.array([0,0,0.5])
kdict['label1']['subdefect8']=dict()
kdict['label1']['subdefect8']['symbol']='Ni'
kdict['label1']['subdefect8']['type']='interstitial'
kdict['label1']['subdefect8']['coordinates']=np.array([0.4,0.1,0.3])
kdict['label1']['coord_type'] = 'fractional'
kdict['label1']['threshold'] = 0.01
kdict['label1']['charge'] = '2'
mdict=dict()
mdict['mast_program'] = 'vasp'
mdict['mast_defect_settings']=dict()
mdict['mast_defect_settings'].update(kdict['label1'])
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myperf = MASTFile("files/POSCAR_perfect")
myperf.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,program_keys=mdict, structure=my_structure)
myri.run_scale()
#copy contcar to poscar
os.rename("%s/CONTCAR" % ingdir, "%s/POSCAR" % ingdir)
myri.run_defect()
my_defected = Poscar.from_file("%s/CONTCAR" % ingdir).structure.get_sorted_structure()
defected_compare = Poscar.from_file("files/POSCAR_scaled_defected").structure.get_sorted_structure()
self.assertEquals(my_defected, defected_compare)示例2: test_run_defect
# 需要导入模块: from MAST.ingredients.chopingredient import ChopIngredient [as 别名]
# 或者: from MAST.ingredients.chopingredient.ChopIngredient import run_defect [as 别名]
def test_run_defect(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = label1\n")
metad.data.append("scaling_size = [1,1,1]\n")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['label1']=dict()
kdict['label1']['subdefect1']=dict()
kdict['label1']['subdefect1']['symbol']='Cr'
kdict['label1']['subdefect1']['type']='interstitial'
kdict['label1']['subdefect1']['coordinates']=np.array([0.8, 0.7, 0.6])
kdict['label1']['subdefect2']=dict()
kdict['label1']['subdefect2']['symbol']='Sr'
kdict['label1']['subdefect2']['type']='antisite'
kdict['label1']['subdefect2']['coordinates']=np.array([0.5,0.5,0.0])
kdict['label1']['subdefect3']=dict()
kdict['label1']['subdefect3']['symbol']='Cr'
kdict['label1']['subdefect3']['type']='interstitial'
kdict['label1']['subdefect3']['coordinates']=np.array([0.3,0.3,0.2])
kdict['label1']['subdefect4']=dict()
kdict['label1']['subdefect4']['symbol']='Fe'
kdict['label1']['subdefect4']['type']='substitution'
kdict['label1']['subdefect4']['coordinates']=np.array([0.25,0.75,0.75])
kdict['label1']['subdefect5']=dict()
kdict['label1']['subdefect5']['symbol']='O'
kdict['label1']['subdefect5']['type']='vacancy'
kdict['label1']['subdefect5']['coordinates']=np.array([0.5,0.25,0.75])
kdict['label1']['subdefect6']=dict()
kdict['label1']['subdefect6']['symbol']='Fe'
kdict['label1']['subdefect6']['type']='substitution'
kdict['label1']['subdefect6']['coordinates']=np.array([0.25,0.25,0.25])
kdict['label1']['subdefect7']=dict()
kdict['label1']['subdefect7']['symbol']='La'
kdict['label1']['subdefect7']['type']='vacancy'
kdict['label1']['subdefect7']['coordinates']=np.array([0,0,0.5])
kdict['label1']['subdefect8']=dict()
kdict['label1']['subdefect8']['symbol']='Ni'
kdict['label1']['subdefect8']['type']='interstitial'
kdict['label1']['subdefect8']['coordinates']=np.array([0.4,0.1,0.3])
kdict['label1']['coord_type'] = 'fractional'
kdict['label1']['threshold'] = 0.01
kdict['label1']['charge'] = '2'
ddict=dict()
ddict['mast_defect_settings']=dict()
ddict['mast_defect_settings'].update(kdict['label1']) #single defect grouping
ddict['mast_program'] = 'vasp'
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myperf = MASTFile("files/POSCAR_perfect")
myperf.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,program_keys=ddict, structure=my_structure)
myri.run_defect()
#
#defect = kdict['label1']
#base_structure = my_structure.copy()
#from MAST.ingredients.pmgextend.structure_extensions import StructureExtensions
#for key in defect:
# if 'subdefect' in key:
# subdefect = defect[key]
# sxtend = StructureExtensions(struc_work1=base_structure)
# base_structure = sxtend.induce_defect(subdefect, defect['coord_type'], defect['threshold'])
# print base_structure
# else:
# pass
#return
#
#
my_defected = Poscar.from_file("%s/CONTCAR" % ingdir).structure.get_sorted_structure()
defected_compare = Poscar.from_file("files/POSCAR_multi").structure.get_sorted_structure()
self.assertEquals(my_defected, defected_compare)
self.assertFalse(os.path.isfile("%s/submitlist" % self.test_control))