def correct(self):
backup()
vi = VaspInput.from_directory(".")
potim = float(vi["INCAR"].get("POTIM", 0.5)) * 0.5
actions = [{"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}}]
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": ["POTIM"], "actions": actions}
def setup(self):
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError("{} structures found. Unable to continue."
.format(num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
vi = VaspInput.from_directory(".")
incar = vi["INCAR"]
#Only optimized NPAR for non-HF and non-RPA calculations.
if (not incar.get("LHFCALC")) and (not incar.get("LRPA")):
import multiprocessing
ncores = multiprocessing.cpu_count()
for npar in range(int(round(math.sqrt(ncores))), ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
vi = VaspInput.from_directory(".")
m = Modder([FileActions, DictActions])
modified = []
for a in self.settings_override:
if "dict" in a:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"],
vi[a["dict"]])
elif "filename" in a:
m.modify(a["action"], a["filename"])
for f in modified:
vi[f].write_file(f)
def correct(self):
backup(self.output_filename)
p = Poscar.from_file("POSCAR")
s = p.structure
trans = PerturbStructureTransformation(0.05)
new_s = trans.apply_transformation(s)
actions = [{"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict}]
m = Modder()
vi = VaspInput.from_directory(".")
for a in actions:
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
vi["POSCAR"].write_file("POSCAR")
return {"errors": ["Frozen job"], "actions": actions}
def correct(self):
backup(self.output_filename)
vi = VaspInput.from_directory(".")
m = reduce(operator.mul, vi["KPOINTS"].kpts[0])
m = max(int(round(m ** (1 / 3))), 1)
if vi["KPOINTS"].style.lower().startswith("m"):
m += m % 2
actions = [{"dict": "KPOINTS",
"action": {"_set": {"kpoints": [[m] * 3]}}}]
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": ["mesh_symmetry"], "actions": actions}
def test_strict_mode(self):
modder = Modder(actions=[FileActions])
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
self.assertRaises(ValueError, modder.modify, mod, d)
#In non-strict mode, unknown actions are ignored.
d = {"Hello": "World"}
modder = Modder(actions=[FileActions], strict=False)
modder.modify(mod, d)
self.assertEqual(d, {"Hello": "World"})
#File actions not supported
modder = Modder()
self.assertRaises(ValueError, modder.modify,
{'_file_create': {'content': 'Test data'}},
'test_file')
def correct(self):
backup()
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}},
{"dict": "INCAR",
"action": {"_set": {"ISTART": 1,
"ALGO": "Normal",
"NELMDL": 6,
"BMIX": 0.001,
"AMIX_MAG": 0.8,
"BMIX_MAG": 0.001}}}]
vi = VaspInput.from_directory(".")
m = Modder(actions=[DictActions, FileActions])
for a in actions:
if "dict" in a:
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
elif "file" in a:
m.modify(a["action"], a["file"])
vi["INCAR"].write_file("INCAR")
return {"errors": ["Unconverged"], "actions": actions}
def correct(self):
backup(self.output_filename)
actions = []
vi = VaspInput.from_directory(".")
if "tet" in self.errors or "dentet" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brmix" in self.errors or "zpotrf" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
if "subspacematrix" in self.errors or "rspher" in self.errors or \
"real_optlay" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
if "tetirr" in self.errors or "incorrect_shift" in self.errors:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
else:
with open("OUTCAR") as f:
for line in f:
if "NBANDS" in line:
try:
d = line.split("=")
nbands = int(d[-1].strip())
break
except (IndexError, ValueError):
pass
actions.append({"dict": "INCAR",
"action": {"_set": {"NBANDS": int(1.1 * nbands)}}})
if "triple_product" in self.errors:
s = vi["POSCAR"].structure
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
if "rot_matrix" in self.errors or "pricel" in self.errors:
s = vi["POSCAR"].structure
trans = PerturbStructureTransformation(0.05)
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brions" in self.errors:
potim = float(vi["INCAR"].get("POTIM", 0.5)) + 0.1
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": list(self.errors), "actions": actions}
def test_dict_modify(self):
modder = Modder()
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'Hello': 'Universe'})
mod = {'_unset': {'Hello': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World'})
mod = {'_push': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1]})
mod = {'_push': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2]})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 5})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 10})
mod = {'_rename': {'num': 'number'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 3}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3], 'number': 10})
mod = {'_add_to_set': {'number': 3}}
self.assertRaises(ValueError, modder.modify, mod, d)
mod = {'_pull': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [2, 3], 'number': 10})
mod = {'_pull_all': {'List': [2, 3]}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [], 'number': 10})
mod = {'_push_all': {'List': xrange(10)}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
'number': 10})
mod = {'_pop': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8],
'number': 10})
mod = {'_pop': {'List':-1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3, 4, 5, 6, 7, 8],
'number': 10})
d = {}
mod = {'_set': {'a->b->c': 100}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_set': {'a->b->d': 200}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 200}}})
mod = {'_set': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 300}}})
mod = {'_unset': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_push': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}, 'e': {'f': [300]}}})
mod = {'_push_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100},
'e': {'f': [300, 100, 200]}}})
mod = {'_inc': {'a->b->c': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [300, 100, 200]}}})
mod = {'_pull': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [100, 200]}}})
mod = {'_pull_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': []}}})
mod = {'_push_all': {'a->e->f': [101, 201, 301, 401]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [101, 201, 301, 401]}}})
mod = {'_pop': {'a->e->f': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [101, 201, 301]}}})
mod = {'_pop': {'a->e->f':-1}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [201, 301]}}})
def test_modify_object(self):
modder = Modder()
o = MyObject(1)
self.assertEqual(o.b["a"], 1)
mod_o = modder.modify_object({'_set': {'b->a': 20}}, o)
self.assertEqual(mod_o.b["a"], 20)
def test_file_modify(self):
modder = Modder(actions=[FileActions])
modder.modify({'_file_create': {'content': 'Test data'}}, 'test_file')
modder.modify({'_file_copy': {'dest': 'test_file_copy'}}, 'test_file')
modder.modify({'_file_copy': {'dest1': 'test_file_copy1',
'dest2': 'test_file_copy2'}},
'test_file')
modder.modify({'_file_move': {'dest': 'renamed_test_file'}},
'test_file')
modder.modify({'_file_delete': {'mode': "actual"}},
'renamed_test_file')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy1')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy2')
