def test_place_parent_energy_files(self):
ingdir="writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp_neb'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
os.mkdir(ingdir + '/00')
os.mkdir(ingdir + '/04')
mywi.place_parent_energy_files()
self.assertTrue(os.path.isfile(ingdir + '/00/OSZICAR'))
self.assertTrue(os.path.isfile(ingdir + '/04/OSZICAR'))
oszinit = MASTFile(ingdir + "/00/OSZICAR")
oszfinal = MASTFile(ingdir + "/04/OSZICAR")
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfinal.data, pefin.data)
def test_get_parent_structures(self):
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_init = MASTFile("unsorted/parent_structure_labelinit")
#unsorted_init = MASTFile("unsorted/parent_structure_labelinit_scrambled")
unsorted_init.to_file("%s/parent_structure_labelinit" % ingdir)
unsorted_fin = MASTFile("unsorted/parent_structure_labelfin")
unsorted_fin.to_file("%s/parent_structure_labelfin" % ingdir)
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
[sinit, sfin] = mywi.get_parent_structures()
init_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit").structure
fin_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelfin").structure
#print sinit
#print init_compare
#print sfin
#print fin_compare
self.assertEqual(sinit.sites, init_compare.sites)
self.assertEqual(sinit.lattice, init_compare.lattice)
self.assertEqual(sfin.sites, fin_compare.sites)
self.assertEqual(sfin.lattice, fin_compare.lattice)
def test_run_scale(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['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=kdict,
structure=my_structure)
myri.run_scale()
my_scaled = Poscar.from_file("%s/CONTCAR" %
ingdir).structure.get_sorted_structure()
scaled_compare = Poscar.from_file(
"files/POSCAR_scaled").structure.get_sorted_structure()
self.assertEquals(my_scaled, scaled_compare)
def test_give_phonon_single_forces_and_displacements(self):
ingdir="%s/writedir/single_phonon_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_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
mypos = MASTFile("files/phonon_initial_POSCAR")
mypos.to_file("%s/POSCAR" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myxdat = MASTFile("files/XDATCAR_compare")
myxdat.to_file("%s/XDATCAR" % ingdir)
mydynmat = MASTFile("files/DYNMAT_compare")
mydynmat.to_file("%s/DYNMAT" % ingdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_phonon_single_forces_and_displacements("next_ingred")
newpos = MASTFile("%s/writedir/next_ingred/POSCAR_prePHON" % testdir)
newdyn = MASTFile("%s/writedir/next_ingred/DYNMAT" % testdir)
newxdat = MASTFile("%s/writedir/next_ingred/XDATCAR" % testdir)
comparepos = MASTFile("files/phonon_initial_POSCAR")
comparedyn = MASTFile("files/DYNMAT_compare")
comparexdat = MASTFile("%s/XDATCAR" % ingdir)
self.assertEqual(newpos.data, comparepos.data)
self.assertEqual(newdyn.data, comparedyn.data)
self.assertEqual(newxdat.data, comparexdat.data)
def test_give_phonon_single_forces_and_displacements(self):
ingdir = "%s/writedir/single_phonon_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_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
mypos = MASTFile("files/phonon_initial_POSCAR")
mypos.to_file("%s/POSCAR" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myxdat = MASTFile("files/XDATCAR_compare")
myxdat.to_file("%s/XDATCAR" % ingdir)
mydynmat = MASTFile("files/DYNMAT_compare")
mydynmat.to_file("%s/DYNMAT" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_phonon_single_forces_and_displacements("next_ingred")
newpos = MASTFile("%s/writedir/next_ingred/POSCAR_prePHON" % testdir)
newdyn = MASTFile("%s/writedir/next_ingred/DYNMAT" % testdir)
newxdat = MASTFile("%s/writedir/next_ingred/XDATCAR" % testdir)
comparepos = MASTFile("files/phonon_initial_POSCAR")
comparedyn = MASTFile("files/DYNMAT_compare")
comparexdat = MASTFile("%s/XDATCAR" % ingdir)
self.assertEqual(newpos.data, comparepos.data)
self.assertEqual(newdyn.data, comparedyn.data)
self.assertEqual(newxdat.data, comparexdat.data)
def test_place_parent_energy_files(self):
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
os.mkdir(ingdir + '/00')
os.mkdir(ingdir + '/04')
mywi.place_parent_energy_files()
self.assertTrue(os.path.isfile(ingdir + '/00/OSZICAR'))
self.assertTrue(os.path.isfile(ingdir + '/04/OSZICAR'))
oszinit = MASTFile(ingdir + "/00/OSZICAR")
oszfinal = MASTFile(ingdir + "/04/OSZICAR")
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfinal.data, pefin.data)
def test_give_neb_structures_to_neb(self):
ingdir = "%s/writedir/neb_labelinit-labelfin" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = dict()
for subdir in ['00', '01', '02', '03', '04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_neb_structures_to_neb("next_ingred")
for subdir in ['01', '02', '03']:
givenstr = MASTFile(
"%s/writedir/next_ingred/parent_structure_labelinit-labelfin_%s"
% (testdir, subdir))
self.assertEqual(myrelaxed[subdir].data, givenstr.data)
def test_write_phonon_single(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_phonon_single()
self.assertTrue(mywi.checker.is_ready_to_run())
compare_phon_single = MASTFile("files/phon_single_POSCAR")
phon_singlepos = MASTFile("%s/POSCAR" % ingdir)
self.assertEqual(phon_singlepos.data, compare_phon_single.data)
def test_get_my_phonon_params(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
[mysite, myrad, mythresh] = mywi.get_my_phonon_params()
self.assertEqual(mysite, "0.33 0.25 0.0")
self.assertEqual(myrad, "1")
self.assertEqual(mythresh, "0.075")
def test_give_structure_and_charge_density_full_copy(self):
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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
mychg = MASTFile("files/CHGCAR")
mychg.to_file("%s/CHGCAR" % ingdir)
mywave = MASTFile("files/WAVECAR")
mywave.to_file("%s/WAVECAR" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_structure_and_charge_density_full_copy("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
self.assertTrue(
os.path.exists("%s/writedir/next_ingred/CHGCAR" % testdir))
def test_give_structure_and_energy_to_neb(self):
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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
myenergy = MASTFile("files/OSZICAR_relaxed")
myenergy.to_file("%s/OSZICAR" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_structure_and_energy_to_neb("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/parent_structure_label1" %
testdir)
givenenergy = MASTFile("%s/writedir/next_ingred/parent_energy_label1" %
testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
self.assertEqual(myenergy.data, givenenergy.data)
def test_get_parent_image_structures(self):
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_01 = MASTFile("unsorted/parent_structure_labelinit-labelfin_01")
unsorted_01.to_file("%s/parent_structure_labelinit-labelfin_01" % ingdir)
unsorted_02 = MASTFile("unsorted/parent_structure_labelinit-labelfin_02")
unsorted_02.to_file("%s/parent_structure_labelinit-labelfin_02" % ingdir)
unsorted_03 = MASTFile("unsorted/parent_structure_labelinit-labelfin_03")
unsorted_03.to_file("%s/parent_structure_labelinit-labelfin_03" % ingdir)
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
imstrs = mywi.get_parent_image_structures()
compare_01 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_01").structure
compare_02 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_02").structure
compare_03 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_03").structure
self.assertEqual(imstrs[0].sites, compare_01.sites)
self.assertEqual(imstrs[0].lattice, compare_01.lattice)
self.assertEqual(imstrs[1].sites, compare_02.sites)
self.assertEqual(imstrs[1].lattice, compare_02.lattice)
self.assertEqual(imstrs[2].sites, compare_03.sites)
self.assertEqual(imstrs[2].lattice, compare_03.lattice)
def test_give_saddle_structure(self):
ingdir="%s/writedir/neb_labelinit-labelfin" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
kdict['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed=dict()
myosz=dict()
mywav=dict()
mychg=dict()
for subdir in ['00','01','02','03','04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myosz[subdir] = MASTFile("files/OSZICAR_%s" % subdir)
myosz[subdir].to_file("writedir/neb_labelinit-labelfin/%s/OSZICAR" % subdir)
mychg[subdir] = MASTFile("files/CHGCAR")
mychg[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CHGCAR" % subdir)
mywav[subdir] = MASTFile("files/WAVECAR")
mywav[subdir].to_file("writedir/neb_labelinit-labelfin/%s/WAVECAR" % subdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_saddle_structure("next_ingred") #should be OSZ3
saddle = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed['03'].data, saddle.data)
saddledir = myuci.get_saddle_dir()
self.assertEqual(saddledir, "03")
def test_write_neb_subfolders(self):
ingdir="writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
parent_01 = MASTFile("statfiles/parent_structure_labelinit-labelfin_01")
parent_01.to_file(ingdir + "/parent_structure_labelinit-labelfin_01")
parent_02 = MASTFile("statfiles/parent_structure_labelinit-labelfin_02")
parent_02.to_file(ingdir + "/parent_structure_labelinit-labelfin_02")
parent_03 = MASTFile("statfiles/parent_structure_labelinit-labelfin_03")
parent_03.to_file(ingdir + "/parent_structure_labelinit-labelfin_03")
parent_init = MASTFile("statfiles/parent_structure_labelinit")
parent_init.to_file(ingdir + "/parent_structure_labelinit")
parent_fin = MASTFile("statfiles/parent_structure_labelfin")
parent_fin.to_file(ingdir + "/parent_structure_labelfin")
peinit = MASTFile("statfiles/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("statfiles/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_neb_subfolders()
self.assertFalse(os.path.isfile("%s/00/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/01/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/02/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/03/submit.sh" % ingdir))
self.assertFalse(os.path.isfile("%s/04/submit.sh" % ingdir))
oszinit = MASTFile("%s/00/OSZICAR" % ingdir)
oszfin = MASTFile("%s/04/OSZICAR" % ingdir)
pos00 = MASTFile("%s/00/POSCAR" % ingdir)
pos01 = MASTFile("%s/01/POSCAR" % ingdir)
pos02 = MASTFile("%s/02/POSCAR" % ingdir)
pos03 = MASTFile("%s/03/POSCAR" % ingdir)
pos04 = MASTFile("%s/04/POSCAR" % ingdir)
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfin.data, pefin.data)
self.assertEqual(pos01.data, parent_01.data)
self.assertEqual(pos02.data, parent_02.data)
self.assertEqual(pos03.data, parent_03.data)
self.assertEqual(pos00.data, parent_init.data)
self.assertEqual(pos04.data, parent_fin.data)
def test_complete_neb_subfolders(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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
myoutcar = MASTFile("files/OUTCAR_completed")
myoszicar = MASTFile("files/OSZICAR_completed")
for subdir in ['00','01','02','03','04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00','04']:
mywr.write_singlerun()
mywr.write_submit_script()
myoutcar.to_file("%s/OUTCAR" % subname)
myoszicar.to_file("%s/OSZICAR" % subname)
myci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
self.assertTrue(myci.complete_neb_subfolders())
os.remove("%s/03/OUTCAR" % ingdir)
self.assertFalse(myci.complete_neb_subfolders())
def test_write_neb_with_parent_image_structures(self):
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
psinit = MASTFile("files/parent_structure_labelinit")
psinit.to_file("%s/parent_structure_labelinit" % ingdir)
psfin = MASTFile("files/parent_structure_labelfin")
psfin.to_file("%s/parent_structure_labelfin" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp_neb'
kdict['mast_coordinates'] = list()
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_01' % testdir)
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_02' % testdir)
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_03' % testdir)
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
kdict['mast_neb_settings']['lines'] = neblines
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_neb()
self.assertTrue(mywi.checker.is_ready_to_run())
pos_compare_00 = MASTFile("files/POSCAR_grafted_00")
pos_compare_01 = MASTFile("files/POSCAR_grafted_01")
pos_compare_02 = MASTFile("files/POSCAR_grafted_02")
pos_compare_03 = MASTFile("files/POSCAR_grafted_03")
pos_compare_04 = MASTFile("files/POSCAR_grafted_04")
mypos00 = MASTFile("writedir/neb_labelinit-labelfin/00/POSCAR")
mypos01 = MASTFile("writedir/neb_labelinit-labelfin/01/POSCAR")
mypos02 = MASTFile("writedir/neb_labelinit-labelfin/02/POSCAR")
mypos03 = MASTFile("writedir/neb_labelinit-labelfin/03/POSCAR")
mypos04 = MASTFile("writedir/neb_labelinit-labelfin/04/POSCAR")
self.assertEqual(pos_compare_00.data, mypos00.data)
self.assertEqual(pos_compare_01.data, mypos01.data)
self.assertEqual(pos_compare_02.data, mypos02.data)
self.assertEqual(pos_compare_03.data, mypos03.data)
self.assertEqual(pos_compare_04.data, mypos04.data)
def test__fullpath_childname(self):
ingdir="%s/writedir/single_label1" % 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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myuci = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
fullpath = myuci._fullpath_childname("next_ingred")
self.assertEqual(fullpath, "%s/writedir/next_ingred" % testdir)
def test_complete_singlerun(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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myoutcar = MASTFile("files/OUTCAR_completed")
myoutcar.to_file("%s/OUTCAR" % ingdir)
myoszicar = MASTFile("files/OSZICAR_completed")
myoszicar.to_file("%s/OSZICAR" % ingdir)
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myrdi.complete_singlerun())
os.remove("%s/OUTCAR" % ingdir)
self.assertFalse(myrdi.complete_singlerun())
def test_run_singlerun(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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)
def test_write_neb_with_parent_image_structures(self):
ingdir="writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
psinit = MASTFile("files/parent_structure_labelinit")
psinit.to_file("%s/parent_structure_labelinit" % ingdir)
psfin = MASTFile("files/parent_structure_labelfin")
psfin.to_file("%s/parent_structure_labelfin" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp_neb'
kdict['mast_coordinates']=list()
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_01' % testdir)
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_02' % testdir)
kdict['mast_coordinates'].append('%s/files/POSCAR_coords_03' % testdir)
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_neb()
self.assertTrue(mywi.checker.is_ready_to_run())
pos_compare_00 = MASTFile("files/POSCAR_grafted_00")
pos_compare_01 = MASTFile("files/POSCAR_grafted_01")
pos_compare_02 = MASTFile("files/POSCAR_grafted_02")
pos_compare_03 = MASTFile("files/POSCAR_grafted_03")
pos_compare_04 = MASTFile("files/POSCAR_grafted_04")
mypos00 = MASTFile("writedir/neb_labelinit-labelfin/00/POSCAR")
mypos01 = MASTFile("writedir/neb_labelinit-labelfin/01/POSCAR")
mypos02 = MASTFile("writedir/neb_labelinit-labelfin/02/POSCAR")
mypos03 = MASTFile("writedir/neb_labelinit-labelfin/03/POSCAR")
mypos04 = MASTFile("writedir/neb_labelinit-labelfin/04/POSCAR")
self.assertEqual(pos_compare_00.data, mypos00.data)
self.assertEqual(pos_compare_01.data, mypos01.data)
self.assertEqual(pos_compare_02.data, mypos02.data)
self.assertEqual(pos_compare_03.data, mypos03.data)
self.assertEqual(pos_compare_04.data, mypos04.data)
def test_write_singlerun(self):
ingdir="writedir/single_label1"
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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_singlerun()
self.assertTrue(mywi.checker.is_ready_to_run())
def test_give_structure(self):
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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_structure("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
def test_get_parent_image_structures(self):
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
kdict['mast_neb_settings']['lines'] = neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_01 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_01")
unsorted_01.to_file("%s/parent_structure_labelinit-labelfin_01" %
ingdir)
unsorted_02 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_02")
unsorted_02.to_file("%s/parent_structure_labelinit-labelfin_02" %
ingdir)
unsorted_03 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_03")
unsorted_03.to_file("%s/parent_structure_labelinit-labelfin_03" %
ingdir)
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
imstrs = mywi.get_parent_image_structures()
compare_01 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_01").structure
compare_02 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_02").structure
compare_03 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_03").structure
self.assertEqual(imstrs[0].sites, compare_01.sites)
self.assertEqual(imstrs[0].lattice, compare_01.lattice)
self.assertEqual(imstrs[1].sites, compare_02.sites)
self.assertEqual(imstrs[1].lattice, compare_02.lattice)
self.assertEqual(imstrs[2].sites, compare_03.sites)
self.assertEqual(imstrs[2].lattice, compare_03.lattice)
def test__fullpath_childname(self):
ingdir = "%s/writedir/single_label1" % 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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
fullpath = myuci._fullpath_childname("next_ingred")
self.assertEqual(fullpath, "%s/writedir/next_ingred" % testdir)
def test_ready_structure(self):
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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_pos = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
my_pos.write_file("writedir/single_label1/POSCAR")
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_pos.structure)
self.assertTrue(myrdi.ready_structure())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_structure())
def test_write_singlerun(self):
ingdir = "writedir/single_label1"
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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_singlerun()
self.assertTrue(mywi.checker.is_ready_to_run())
def test_write_singlerun_automesh(self):
ingdir="writedir/single_label1"
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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_kpoint_density']='1000'
mypos=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
mypos.write_file("writedir/single_label1/POSCAR")
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=mypos.structure)
mywi.write_singlerun_automesh()
mykpts = pymatgen.io.vaspio.Kpoints.from_file("writedir/single_label1/KPOINTS")
self.assertEqual(mykpts.to_dict['kpoints'][0],[8,8,8])
#print mykpts
self.assertTrue(mywi.checker.is_ready_to_run())
def test_run_strain(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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_strain']=" 0.98 0.92 1.03 \n"
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myunstrained = MASTFile("files/POSCAR_unstrained")
myunstrained.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_strain()
my_strained = Poscar.from_file("%s/CONTCAR" % ingdir).structure
strained_compare = Poscar.from_file("files/POSCAR_strained").structure
self.assertEquals(my_strained, strained_compare)
self.assertFalse(os.path.isfile("%s/submitlist" % self.test_control))
def test_run_scale(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['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=kdict, structure=my_structure)
myri.run_scale()
my_scaled = Poscar.from_file("%s/CONTCAR" % ingdir).structure.get_sorted_structure()
scaled_compare = Poscar.from_file("files/POSCAR_scaled").structure.get_sorted_structure()
self.assertEquals(my_scaled, scaled_compare)
def test_ready_structure(self):
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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_pos = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
my_pos.write_file("writedir/single_label1/POSCAR")
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_pos.structure)
self.assertTrue(myrdi.ready_structure())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_structure())
def test_get_my_phonon_params(self):
ingdir="writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_phonon_settings']=dict()
kdict['mast_phonon_settings']['phonon_center_site']="0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius']="1"
kdict['mast_phonon_settings']['threshold']="0.075"
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
[mysite, myrad, mythresh] = mywi.get_my_phonon_params()
self.assertEqual(mysite,"0.33 0.25 0.0")
self.assertEqual(myrad,"1")
self.assertEqual(mythresh,"0.075")
def test_run_subfolders(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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
os.mkdir(subname)
shutil.copy("files/metadata_single","%s/metadata.txt" % subname)
mywr = ChopIngredient(name=subname, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_subfolders()
self.assertFalse(myri.checker.is_ready_to_run())
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
myri.checker.keywords['name'] = subname
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s/sub1\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/sub2\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/sub3\n" % ingdir)
self.assertEquals(mysubmit.data[3], "%s/sub4\n" % ingdir)
def test_give_saddle_structure(self):
ingdir = "%s/writedir/neb_labelinit-labelfin" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
kdict['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = dict()
myosz = dict()
mywav = dict()
mychg = dict()
for subdir in ['00', '01', '02', '03', '04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myosz[subdir] = MASTFile("files/OSZICAR_%s" % subdir)
myosz[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/OSZICAR" % subdir)
mychg[subdir] = MASTFile("files/CHGCAR")
mychg[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CHGCAR" %
subdir)
mywav[subdir] = MASTFile("files/WAVECAR")
mywav[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/WAVECAR" % subdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_saddle_structure("next_ingred") #should be OSZ3
saddle = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed['03'].data, saddle.data)
saddledir = myuci.get_saddle_dir()
self.assertEqual(saddledir, "03")
def test_write_phonon_single(self):
ingdir="writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_phonon_settings']=dict()
kdict['mast_phonon_settings']['phonon_center_site']="0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius']="1"
kdict['mast_phonon_settings']['threshold']="0.075"
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_phonon_single()
self.assertTrue(mywi.checker.is_ready_to_run())
compare_phon_single = MASTFile("files/phon_single_POSCAR")
phon_singlepos = MASTFile("%s/POSCAR" % ingdir)
self.assertEqual(phon_singlepos.data, compare_phon_single.data)
def test_get_parent_structures(self):
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
kdict['mast_neb_settings']['lines'] = neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_init = MASTFile("unsorted/parent_structure_labelinit")
#unsorted_init = MASTFile("unsorted/parent_structure_labelinit_scrambled")
unsorted_init.to_file("%s/parent_structure_labelinit" % ingdir)
unsorted_fin = MASTFile("unsorted/parent_structure_labelfin")
unsorted_fin.to_file("%s/parent_structure_labelfin" % ingdir)
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
[sinit, sfin] = mywi.get_parent_structures()
init_compare = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit").structure
fin_compare = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelfin").structure
#print sinit
#print init_compare
#print sfin
#print fin_compare
self.assertEqual(sinit.sites, init_compare.sites)
self.assertEqual(sinit.lattice, init_compare.lattice)
self.assertEqual(sfin.sites, fin_compare.sites)
self.assertEqual(sfin.lattice, fin_compare.lattice)
def test_give_neb_structures_to_neb(self):
ingdir="%s/writedir/neb_labelinit-labelfin" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed=dict()
for subdir in ['00','01','02','03','04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_neb_structures_to_neb("next_ingred")
for subdir in ['01','02','03']:
givenstr = MASTFile("%s/writedir/next_ingred/parent_structure_labelinit-labelfin_%s" % (testdir,subdir))
self.assertEqual(myrelaxed[subdir].data, givenstr.data)
def test_run_strain(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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_strain'] = " 0.98 0.92 1.03 \n"
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myunstrained = MASTFile("files/POSCAR_unstrained")
myunstrained.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_strain()
my_strained = Poscar.from_file("%s/CONTCAR" % ingdir).structure
strained_compare = Poscar.from_file("files/POSCAR_strained").structure
self.assertEquals(my_strained, strained_compare)
self.assertFalse(os.path.isfile("%s/submitlist" % self.test_control))
def test_write_singlerun_automesh(self):
ingdir = "writedir/single_label1"
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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_kpoint_density'] = '1000'
mypos = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
mypos.write_file("writedir/single_label1/POSCAR")
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=mypos.structure)
mywi.write_singlerun_automesh()
mykpts = pymatgen.io.vaspio.Kpoints.from_file(
"writedir/single_label1/KPOINTS")
self.assertEqual(mykpts.as_dict()['kpoints'][0], [6, 6, 6])
#print mykpts
self.assertTrue(mywi.checker.is_ready_to_run())
def test_run_neb_subfolders(self):
#raise SkipTest
ingdir="%s/writedir/neb_labelinit-labelfin_stat" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['lines']=neblines
kdict['mast_neb_settings']['images']=3
str_00 = MASTFile("files/POSCAR_00")
str_00.to_file("%s/parent_structure_labelinit" % ingdir)
str_04 = MASTFile("files/POSCAR_04")
str_04.to_file("%s/parent_structure_labelfin" % ingdir)
str_01 = MASTFile("files/POSCAR_01")
str_01.to_file("%s/parent_structure_labelinit-labelfin_01" % ingdir)
str_02 = MASTFile("files/POSCAR_02")
str_02.to_file("%s/parent_structure_labelinit-labelfin_02" % ingdir)
str_03 = MASTFile("files/POSCAR_03")
str_03.to_file("%s/parent_structure_labelinit-labelfin_03" % ingdir)
en_00 = MASTFile("files/OSZICAR_00")
en_00.to_file("%s/parent_energy_labelinit" % ingdir)
en_04 = MASTFile("files/OSZICAR_04")
en_04.to_file("%s/parent_energy_labelfin" % ingdir)
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
mywr.write_neb_subfolders()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_neb_subfolders()
mysubmit = MASTFile("%s/submitlist" % self.test_control)
myri.checker.keywords['name'] = "%s/00" % ingdir
self.assertFalse(myri.checker.is_ready_to_run()) #do not run endpoints again
myri.checker.keywords['name'] = "%s/01" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/02" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/03" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/04" % ingdir
self.assertFalse(myri.checker.is_ready_to_run()) #do not run endpoints again
self.assertEquals(mysubmit.data[0], "%s/01\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/02\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/03\n" % ingdir)
def test_run_subfolders(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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
for subfolder in ['sub1', 'sub2', 'sub3', 'sub4']:
subname = "%s/%s" % (ingdir, subfolder)
os.mkdir(subname)
shutil.copy("files/metadata_single", "%s/metadata.txt" % subname)
mywr = ChopIngredient(name=subname,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_subfolders()
self.assertFalse(myri.checker.is_ready_to_run())
for subfolder in ['sub1', 'sub2', 'sub3', 'sub4']:
subname = "%s/%s" % (ingdir, subfolder)
myri.checker.keywords['name'] = subname
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s/sub1\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/sub2\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/sub3\n" % ingdir)
self.assertEquals(mysubmit.data[3], "%s/sub4\n" % ingdir)
def test_run_singlerun(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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)
def test_complete_singlerun(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.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myoutcar = MASTFile("files/OUTCAR_completed")
myoutcar.to_file("%s/OUTCAR" % ingdir)
myoszicar = MASTFile("files/OSZICAR_completed")
myoszicar.to_file("%s/OSZICAR" % ingdir)
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
self.assertTrue(myrdi.complete_singlerun())
os.remove("%s/OUTCAR" % ingdir)
self.assertFalse(myrdi.complete_singlerun())
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)
def test_write_neb_subfolders(self):
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
parent_01 = MASTFile(
"statfiles/parent_structure_labelinit-labelfin_01")
parent_01.to_file(ingdir + "/parent_structure_labelinit-labelfin_01")
parent_02 = MASTFile(
"statfiles/parent_structure_labelinit-labelfin_02")
parent_02.to_file(ingdir + "/parent_structure_labelinit-labelfin_02")
parent_03 = MASTFile(
"statfiles/parent_structure_labelinit-labelfin_03")
parent_03.to_file(ingdir + "/parent_structure_labelinit-labelfin_03")
parent_init = MASTFile("statfiles/parent_structure_labelinit")
parent_init.to_file(ingdir + "/parent_structure_labelinit")
parent_fin = MASTFile("statfiles/parent_structure_labelfin")
parent_fin.to_file(ingdir + "/parent_structure_labelfin")
peinit = MASTFile("statfiles/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("statfiles/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
kdict['mast_neb_settings']['lines'] = neblines
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_neb_subfolders()
self.assertFalse(os.path.isfile("%s/00/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/01/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/02/submit.sh" % ingdir))
self.assertTrue(os.path.isfile("%s/03/submit.sh" % ingdir))
self.assertFalse(os.path.isfile("%s/04/submit.sh" % ingdir))
oszinit = MASTFile("%s/00/OSZICAR" % ingdir)
oszfin = MASTFile("%s/04/OSZICAR" % ingdir)
pos00 = MASTFile("%s/00/POSCAR" % ingdir)
pos01 = MASTFile("%s/01/POSCAR" % ingdir)
pos02 = MASTFile("%s/02/POSCAR" % ingdir)
pos03 = MASTFile("%s/03/POSCAR" % ingdir)
pos04 = MASTFile("%s/04/POSCAR" % ingdir)
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfin.data, pefin.data)
self.assertEqual(pos01.data, parent_01.data)
self.assertEqual(pos02.data, parent_02.data)
self.assertEqual(pos03.data, parent_03.data)
self.assertEqual(pos00.data, parent_init.data)
self.assertEqual(pos04.data, parent_fin.data)
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))
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)
def test_complete_neb_subfolders(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.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myoutcar = MASTFile("files/OUTCAR_completed")
myoszicar = MASTFile("files/OSZICAR_completed")
for subdir in ['00', '01', '02', '03', '04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00', '04']:
mywr.write_singlerun()
mywr.write_submit_script()
myoutcar.to_file("%s/OUTCAR" % subname)
myoszicar.to_file("%s/OSZICAR" % subname)
myci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myci.complete_neb_subfolders())
os.remove("%s/03/OUTCAR" % ingdir)
self.assertFalse(myci.complete_neb_subfolders())
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))
def test_run_neb_subfolders(self):
#raise SkipTest
ingdir = "%s/writedir/neb_labelinit-labelfin_stat" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['lines'] = neblines
kdict['mast_neb_settings']['images'] = 3
str_00 = MASTFile("files/POSCAR_00")
str_00.to_file("%s/parent_structure_labelinit" % ingdir)
str_04 = MASTFile("files/POSCAR_04")
str_04.to_file("%s/parent_structure_labelfin" % ingdir)
str_01 = MASTFile("files/POSCAR_01")
str_01.to_file("%s/parent_structure_labelinit-labelfin_01" % ingdir)
str_02 = MASTFile("files/POSCAR_02")
str_02.to_file("%s/parent_structure_labelinit-labelfin_02" % ingdir)
str_03 = MASTFile("files/POSCAR_03")
str_03.to_file("%s/parent_structure_labelinit-labelfin_03" % ingdir)
en_00 = MASTFile("files/OSZICAR_00")
en_00.to_file("%s/parent_energy_labelinit" % ingdir)
en_04 = MASTFile("files/OSZICAR_04")
en_04.to_file("%s/parent_energy_labelfin" % ingdir)
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_neb_subfolders()
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_neb_subfolders()
mysubmit = MASTFile("%s/submitlist" % self.test_control)
myri.checker.keywords['name'] = "%s/00" % ingdir
self.assertFalse(
myri.checker.is_ready_to_run()) #do not run endpoints again
myri.checker.keywords['name'] = "%s/01" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/02" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/03" % ingdir
self.assertTrue(myri.checker.is_ready_to_run())
myri.checker.keywords['name'] = "%s/04" % ingdir
self.assertFalse(
myri.checker.is_ready_to_run()) #do not run endpoints again
self.assertEquals(mysubmit.data[0], "%s/01\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/02\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/03\n" % ingdir)