def create_incar(xsdname, args):
""""""
if os.path.exists('INCAR'):
return 'INCAR already exists, not changed.\n'
incar = InCar()
if args.task:
task = args.task
incar.quickgen(args.task)
else:
task = 'SC'
content = 'INCAR -->\n'
content += ' Task is %s\n' %task
if PY2:
pname_value_pairs = args.__dict__.iteritems()
else:
pname_value_pairs = args.__dict__.items()
for pname, value in pname_value_pairs :
if (value is not None):
if pname in incar.pnames:
incar.set(pname, value)
else:
if (pname in INCAR_PARAMETERS.keys()):
incar.add(pname, value)
content += " {} -> {}\n".format(pname, value)
#incar.set('SYSTEM', xsdname)
incar.tofile(verbos=False)
content += '\n'
return content
def test_parameter_set(self):
" Test existed parameter can be set correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
self.assertTrue(incar.ISIF, "2")
incar.set("ISIF", 3)
self.assertTrue(incar.ISIF, "3")
def test_parameter_set(self):
" Test existed parameter can be set correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
self.assertTrue(incar.ISIF, "2")
incar.set("ISIF", 3)
self.assertTrue(incar.ISIF, "3")
distance = np.linalg.norm(b)
# Create fort.188
content = '1\n3\n6\n4\n0.04\n%-5d%-5d%f\n0\n' % \
(atom_idxs[0]+1, atom_idxs[1]+1, distance)
with open('fort.188', 'w') as f:
f.write(content)
_logger.info("fort.188 has been created.")
_logger.info('-' * 20)
_logger.info("atom number: {:<5d}{:<5d}".format(
atom_idxs[0] + 1, atom_idxs[1] + 1))
_logger.info("atom name: {} {}".format(*atom_names))
_logger.info("distance: {:f}".format(distance))
_logger.info('-' * 20)
# Set IBRION = 1
incar.set('IBRION', 1)
_logger.info("{} -> {}".format("IBRION", "1"))
if PY2:
pname_value_pairs = args.__dict__.iteritems()
else:
pname_value_pairs = args.__dict__.items()
for pname, value in pname_value_pairs:
if (value is not None) and (pname in incar.pnames):
incar.set(pname, value)
_logger.info("{} -> {}".format(pname, value))
# Generate new INCAR file.
incar.tofile()
class InCarTest(unittest.TestCase):
def setUp(self):
# Create an InCar object.
self.incar = InCar("./testdata/INCAR")
def test_rdata(self):
" Test data line in INCAR can be read correctly. "
# Test integer parameter.
ref_line = "ISTART = 0 # 0 = new job, 1 = restart"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["ISTART"])
self.assertListEqual(datas, ["0"])
# Test string parameter.
ref_line = "PREC = Normal # [Low/Medium/High/Accurate/Normal]"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["PREC"])
self.assertListEqual(datas, ["Normal"])
# Test comment line.
ref_line = "! Electronic Structure"
result = self.incar.rdata(ref_line)
self.assertIsNone(result)
# Test multi-parameter line.
ref_line = "LHFCALC = .TRUE. ; HFSCREEN = 0.2 # HSE"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["LHFCALC", "HFSCREEN"])
self.assertListEqual(datas, [".TRUE.", "0.2"])
def test_load(self):
" Test all data in INCAR can be loaded. "
ref_pnames = ['SYSTEM', 'ISTART', 'ISPIN', 'PREC', 'ENCUT',
'NELM', 'NELMIN', 'ISMEAR', 'SIGMA', 'LREAL',
'EDIFFG', 'ALGO', 'ISIF', 'NSW', 'IBRION', 'POTIM',
'ISYM', 'NWRITE', 'LCHARG', 'LWAVE', 'NCORE']
ref_datas = ['per', '0', '2', 'Normal', '450', '400', '3',
'1', '0.1', 'A', '-0.05', 'Fast', '2', '900',
'1', '0.2', '0', '1', '.False.', '.False.', '4']
for pname, data in zip(ref_pnames, ref_datas):
self.assertEqual(getattr(self.incar, pname), data)
def test_parameter_set(self):
" Test existed parameter can be set correctly. "
self.assertTrue(self.incar.ISIF, "2")
self.incar.set("ISIF", 3)
self.assertTrue(self.incar.ISIF, "3")
def test_parameter_add(self):
" Test new parameter can be added correctly. "
self.assertFalse(hasattr(self.incar, "TEST_zjshao"))
self.incar.add("TEST_zjshao", "True")
self.assertTrue(self.incar.TEST_zjshao, "True")
def test_tofile(self):
" Test INCAR content can be write to file. "
# NEED IMPLEMENTATIN
pass
b = A*x
distance = np.linalg.norm(b)
# Create fort.188
content = '1\n3\n6\n4\n0.04\n%-5d%-5d%f\n0\n' % \
(atom_idxs[0]+1, atom_idxs[1]+1, distance)
with open('fort.188', 'w') as f:
f.write(content)
_logger.info("fort.188 has been created.")
_logger.info('-'*20)
_logger.info("atom number: {:<5d}{:<5d}".format(atom_idxs[0]+1, atom_idxs[1]+1))
_logger.info("atom name: {} {}".format(*atom_names))
_logger.info("distance: {:f}".format(distance))
_logger.info('-'*20)
# Set IBRION = 1
incar.set('IBRION', 1)
_logger.info("{} -> {}".format("IBRION", "1"))
if PY2:
pname_value_pairs = args.__dict__.iteritems()
else:
pname_value_pairs = args.__dict__.items()
for pname, value in pname_value_pairs :
if (value is not None) and (pname in incar.pnames):
incar.set(pname, value)
_logger.info("{} -> {}".format(pname, value))
# Generate new INCAR file.
incar.tofile()
atom_idxs.append(idx)
atom_names.append(atom_name)
# if constrained get distance and create fort.188
if atom_idxs:
if len(atom_idxs) > 2:
raise ValueError("More than two atoms end with '_c'")
pt1, pt2 = [xsd.data[idx, :] for idx in atom_idxs]
# use Ax=b convert to cartisan coordinate
diff = pt1 - pt2
A = np.matrix(xsd.bases.T)
x = np.matrix(diff).T
b = A*x
distance = np.linalg.norm(b)
# create fort.188
content = '1\n3\n6\n4\n0.04\n%-5d%-5d%f\n0\n' % \
(atom_idxs[0]+1, atom_idxs[1]+1, distance)
with open('fort.188', 'w') as f:
f.write(content)
print "fort.188 has been created."
print '-'*20
print "atom number: %-5d%-5d" % (atom_idxs[0]+1, atom_idxs[1]+1)
print "atom name: %s %s" % tuple(atom_names)
print "distance: %f" % distance
print '-'*20
# set IBRION = 1
incar = InCar()
incar.set('IBRION', 1)
incar.tofile()
print "IBRION is set to 1."
kpoints = []
for base in xtd.bases:
l = np.dot(base, base)**0.5
kpt = int(20/l) + 1
kpoints.append(str(kpt))
else:
kpoints = [i.strip() for i in args.kpoints.split(",")]
_logger.info("Set k-point -> {} {} {}".format(*kpoints))
kpt_str = " ".join(kpoints)
kpt_content = "mesh auto\n0\nG\n" + kpt_str + "\n0 0 0\n"
with open("KPOINTS", "w") as f:
f.write(kpt_content)
# Modify INCAR parameters.
incar = InCar()
incar.set("IBRION", 3)
incar.set("POTIM", 0)
neb_parameters = [("IOPT", 1),
("ICHAIN", 0),
("LCLIMB", ".TRUE."),
("SPRING", -5),
("IMAGES", n_images)]
for pname, value in neb_parameters:
incar.add(pname, value)
_logger.info("{} -> {}".format(pname, value))
incar.tofile()
# Modify qsub script.
jobname = xtdname.split('.')[0]
with open('vasp.script', 'r') as f:
content_list = f.readlines()
kpoints = []
for base in xtd.bases:
l = np.dot(base, base)**0.5
kpt = int(20 / l) + 1
kpoints.append(str(kpt))
else:
kpoints = [i.strip() for i in args.kpoints.split(",")]
_logger.info("Set k-point -> {} {} {}".format(*kpoints))
kpt_str = " ".join(kpoints)
kpt_content = "mesh auto\n0\nG\n" + kpt_str + "\n0 0 0\n"
with open("KPOINTS", "w") as f:
f.write(kpt_content)
# Modify INCAR parameters.
incar = InCar()
incar.set("IBRION", 3)
incar.set("POTIM", 0)
neb_parameters = [("IOPT", 1), ("ICHAIN", 0), ("LCLIMB", ".TRUE."),
("SPRING", -5), ("IMAGES", n_images)]
for pname, value in neb_parameters:
incar.add(pname, value)
_logger.info("{} -> {}".format(pname, value))
incar.tofile()
# Modify qsub script.
jobname = xtdname.split('.')[0]
with open('vasp.script', 'r') as f:
content_list = f.readlines()
# Change job name.
content_list[1] = '#PBS -N ' + jobname + '\n'
atom_names.append(atom_name)
# If constrained get distance and create fort.188
if atom_idxs:
if len(atom_idxs) > 2:
raise ValueError("More than two atoms end with '_c'")
pt1, pt2 = [xsd.data[idx, :] for idx in atom_idxs]
# Use Ax=b convert to cartisan coordinate
diff = pt1 - pt2
A = np.matrix(xsd.bases.T)
x = np.matrix(diff).T
b = A * x
distance = np.linalg.norm(b)
# Create fort.188
content = '1\n3\n6\n4\n0.04\n%-5d%-5d%f\n0\n' % \
(atom_idxs[0]+1, atom_idxs[1]+1, distance)
with open('fort.188', 'w') as f:
f.write(content)
logging.info("fort.188 has been created.")
logging.info('-' * 20)
logging.info("atom number: {:<5d}{:<5d}".format(
atom_idxs[0] + 1, atom_idxs[1] + 1))
logging.info("atom name: {} {}".format(*atom_names))
logging.info("distance: {:f}".format(distance))
logging.info('-' * 20)
# Set IBRION = 1
incar = InCar()
incar.set('IBRION', 1)
incar.tofile()
logging.info("IBRION is set to 1.")
class InCarTest(unittest.TestCase):
def setUp(self):
# Create an InCar object.
self.incar = InCar("./testdata/INCAR")
def test_rdata(self):
" Test data line in INCAR can be read correctly. "
# Test integer parameter.
ref_line = "ISTART = 0 # 0 = new job, 1 = restart"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["ISTART"])
self.assertListEqual(datas, ["0"])
# Test string parameter.
ref_line = "PREC = Normal # [Low/Medium/High/Accurate/Normal]"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["PREC"])
self.assertListEqual(datas, ["Normal"])
# Test comment line.
ref_line = "! Electronic Structure"
result = self.incar.rdata(ref_line)
self.assertIsNone(result)
# Test multi-parameter line.
ref_line = "LHFCALC = .TRUE. ; HFSCREEN = 0.2 # HSE"
pnames, datas = self.incar.rdata(ref_line)
self.assertListEqual(pnames, ["LHFCALC", "HFSCREEN"])
self.assertListEqual(datas, [".TRUE.", "0.2"])
def test_load(self):
" Test all data in INCAR can be loaded. "
ref_pnames = [
'SYSTEM', 'ISTART', 'ISPIN', 'PREC', 'ENCUT', 'NELM', 'NELMIN',
'ISMEAR', 'SIGMA', 'LREAL', 'EDIFFG', 'ALGO', 'ISIF', 'NSW',
'IBRION', 'POTIM', 'ISYM', 'NWRITE', 'LCHARG', 'LWAVE', 'NCORE'
]
ref_datas = [
'per', '0', '2', 'Normal', '450', '400', '3', '1', '0.1', 'A',
'-0.05', 'Fast', '2', '900', '1', '0.2', '0', '1', '.False.',
'.False.', '4'
]
for pname, data in zip(ref_pnames, ref_datas):
self.assertEqual(getattr(self.incar, pname), data)
def test_parameter_set(self):
" Test existed parameter can be set correctly. "
self.assertTrue(self.incar.ISIF, "2")
self.incar.set("ISIF", 3)
self.assertTrue(self.incar.ISIF, "3")
def test_parameter_add(self):
" Test new parameter can be added correctly. "
self.assertFalse(hasattr(self.incar, "TEST_zjshao"))
self.incar.add("TEST_zjshao", "True")
self.assertTrue(self.incar.TEST_zjshao, "True")
def test_tofile(self):
" Test INCAR content can be write to file. "
# NEED IMPLEMENTATIN
pass
else:
import subprocess
_logger = logging.getLogger("vaspy.script")
if "__main__" == __name__:
incar = InCar()
# Move files.
cmd = "cp ../KPOINTS ./"
status, output = subprocess.getstatusoutput(cmd)
if status:
raise ValueError(output)
_logger.info(cmd)
# Change INCAR parameters.
parameters = [("IBRION", 5), ("POTIM", 0.05), ("ISIF", 0), ("NFREE", 2)]
for pname, value in parameters:
if hasattr(incar, pname):
incar.set(pname, value)
else:
incar.add(pname, value)
_logger.info("{} --> {}".format(pname, value))
incar.pop("NCORE")
_logger.info("Remove Paramter NCORE")
incar.tofile()
