def test_rdata(self):
" Test data line in INCAR can be read correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
# Test integer parameter.
ref_line = "ISTART = 0 # 0 = new job, 1 = restart"
pnames, datas = 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 = incar.rdata(ref_line)
self.assertListEqual(pnames, ["PREC"])
self.assertListEqual(datas, ["Normal"])
# Test comment line.
ref_line = "! Electronic Structure"
result = incar.rdata(ref_line)
self.assertIsNone(result)
# Test multi-parameter line.
ref_line = "LHFCALC = .TRUE. ; HFSCREEN = 0.2 # HSE"
pnames, datas = incar.rdata(ref_line)
self.assertListEqual(pnames, ["LHFCALC", "HFSCREEN"])
self.assertListEqual(datas, [".TRUE.", "0.2"])
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_add(self):
" Test new parameter can be added correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
self.assertFalse(hasattr(incar, "TEST_zjshao"))
incar.add("TEST_zjshao", "True")
self.assertTrue(incar.TEST_zjshao, "True")
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")
def test_parameter_add(self):
" Test new parameter can be added correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
self.assertFalse(hasattr(incar, "TEST_zjshao"))
incar.add("TEST_zjshao", "True")
self.assertTrue(incar.TEST_zjshao, "True")
def test_ne(self):
" Test __ne__() function."
# Two equal INCAR.
filename1 = path + "/INCAR"
filename2 = path + "/INCAR2"
incar1 = InCar(filename1)
incar2 = InCar(filename1)
self.assertFalse(incar1 != incar2)
# Different INCAR.
incar1 = InCar(filename1)
incar2 = InCar(filename2)
self.assertTrue(incar1 != incar2)
def test_parameter_del(self):
" Make sure we can remove parameters correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
# Check before deletion.
self.assertTrue(hasattr(incar, "ISIF"))
self.assertTrue("ISIF" in incar.pnames)
pname, value = incar.pop("ISIF")
# Check after deletion.
self.assertEqual(pname, "ISIF")
self.assertEqual(value, "2")
self.assertFalse(hasattr(incar, "ISIF"))
self.assertFalse("ISIF" in incar.pnames)
def test_parameter_del(self):
" Make sure we can remove parameters correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
# Check before deletion.
self.assertTrue(hasattr(incar, "ISIF"))
self.assertTrue("ISIF" in incar.pnames)
pname, value = incar.pop("ISIF")
# Check after deletion.
self.assertEqual(pname, "ISIF")
self.assertEqual(value, "2")
self.assertFalse(hasattr(incar, "ISIF"))
self.assertFalse("ISIF" in incar.pnames)
def test_compare(self):
" Make sure we can compare two InCar objects correctly. "
# Two equal INCAR.
filename1 = path + "/INCAR"
filename2 = path + "/INCAR2"
incar1 = InCar(filename1)
incar2 = InCar(filename1)
a_dict, b_dict = incar1.compare(incar2)
self.assertDictEqual(a_dict, {})
self.assertDictEqual(b_dict, {})
# Different INCAR.
incar1 = InCar(filename1)
incar2 = InCar(filename2)
a_dict, b_dict = incar1.compare(incar2)
self.assertDictEqual(a_dict, {'ISMEAR': '1', 'LREAL': 'A'})
self.assertDictEqual(b_dict, {'ISMEAR': '2', 'LREAL': ''})
def test_rdata(self):
" Test data line in INCAR can be read correctly. "
filename = path + "/INCAR"
incar = InCar(filename)
# Test integer parameter.
ref_line = "ISTART = 0 # 0 = new job, 1 = restart"
pnames, datas = 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 = incar.rdata(ref_line)
self.assertListEqual(pnames, ["PREC"])
self.assertListEqual(datas, ["Normal"])
# Test comment line.
ref_line = "! Electronic Structure"
result = incar.rdata(ref_line)
self.assertIsNone(result)
# Test multi-parameter line.
ref_line = "LHFCALC = .TRUE. ; HFSCREEN = 0.2 # HSE"
pnames, datas = incar.rdata(ref_line)
self.assertListEqual(pnames, ["LHFCALC", "HFSCREEN"])
self.assertListEqual(datas, [".TRUE.", "0.2"])
def test_compare(self):
" Make sure we can compare two InCar objects correctly. "
# Two equal INCAR.
filename1 = path + "/INCAR"
filename2 = path + "/INCAR2"
incar1 = InCar(filename1)
incar2 = InCar(filename1)
a_dict, b_dict = incar1.compare(incar2)
self.assertDictEqual(a_dict, {})
self.assertDictEqual(b_dict, {})
# Different INCAR.
incar1 = InCar(filename1)
incar2 = InCar(filename2)
a_dict, b_dict = incar1.compare(incar2)
self.assertDictEqual(a_dict, {'ISMEAR': '1', 'LREAL': 'A'})
self.assertDictEqual(b_dict, {'ISMEAR': '2', 'LREAL': ''})
def test_load(self):
" Test all data in INCAR can be loaded. "
filename = path + "/INCAR"
incar = InCar(filename)
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(incar, pname), data)
_logger = logging.getLogger("vaspy.script")
# Set arguments parser.
parser = argparse.ArgumentParser()
parser.add_argument("--xsd",
help="create MaterStudio .xsd file",
action="store_true")
args = parser.parse_args()
outcar = OutCar()
poses, forces = outcar.forces(-1)
poscar = PosCar()
tfs = poscar.tf
incar = InCar()
#print(incar.paras)
EDIFFG = incar.get_pvalue('EDIFFG')
#EDIFFG = 0.05
bad_ids = []
max_idx = [-1, -1, -1]
max_force = [0., 0., 0.]
for i, (pos, force, tf) in enumerate(zip(poses, forces, tfs)):
for j, (c, f) in enumerate(zip(tf, force)):
if c == 'T':
if np.fabs(f) >= max_force[j]:
max_idx[j] = i
max_force[j] = np.fabs(f)
if np.fabs(f) > np.fabs(float(EDIFFG)):
if i not in bad_ids:
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
def setUp(self):
# Create an InCar object.
self.incar = InCar("./testdata/INCAR")
def setUp(self):
# Create an InCar object.
self.incar = InCar("./testdata/INCAR")
# Copy INCAR vasp.script
subprocess.getstatusoutput('cp $HOME/example/INCAR $HOME/example/vasp.script ./')
# Set argument parser.
parser = argparse.ArgumentParser()
# Add optional argument.
parser.add_argument("-k", "--kpoints", help="set k-points")
parser.add_argument("--nnode", help="node number used for the job")
parser.add_argument("--ncpu", help="cpu number on each node")
parser.add_argument("-q", "--queue", help="pbs queue type")
# Add all possible arguments in INCAR file.
if os.path.exists("INCAR"):
incar = InCar()
parameters = incar.pnames
for parameter in parameters:
help_info = "Set '{}' in INCAR".format(parameter)
parser.add_argument("--{}".format(parameter), help=help_info)
args = parser.parse_args()
# Create POSCAR
status, output = subprocess.getstatusoutput('ls *.xsd | head -1')
xsd = XsdFile(filename=output)
poscar_content = xsd.get_poscar_content(bases_const=1.0)
with open('POSCAR', 'w') as f:
f.write(poscar_content)
# Create POTCAR
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."
import logging
from vaspy.incar import InCar
SHELL_COMMAND = "find ./ -name 'INCAR'"
if "__main__" == __name__:
# Check command validity.
status, output = commands.getstatusoutput(SHELL_COMMAND)
if status:
raise SystemExit("Invalid shell commands - '{}'".format(SHELL_COMMAND))
# Get InCar objects.
incar_paths = (incar_path.strip() for incar_path in output.split('\n'))
incars = [InCar(incar_path) for incar_path in incar_paths]
# Get all possible arguments.
set_list = [set(incar.pnames()) for incar in incars]
possible_args = set.intersection(*set_list)
# Set arguments for this script.
parser = argparse.ArgumentParser()
for arg in possible_args:
arg_str = "--{}".format(arg)
parser.add_argument(arg_str, help="set {} INCAR parameter".format(arg))
args_space = parser.parse_args()
# Change parameters for all incars.
for pname, value in args_space.__dict__.iteritems():
if value is None:
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
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.")
return output
if "__main__" == __name__:
# Set argument parser.
parser = argparse.ArgumentParser()
# Add optional arguments.
parser.add_argument("-k", "--kpoints", help="set k-points")
parser.add_argument("--nnode", help="node number used for the job")
parser.add_argument("--ncpu", help="cpu number on each node")
parser.add_argument("-q", "--queue", help="pbs queue type")
# Add all possible arguments in INCAR file.
if os.path.exists("INCAR"):
incar = InCar()
parameters = incar.pnames
for parameter in parameters:
help_info = "Set '{}' in INCAR".format(parameter)
parser.add_argument("--{}".format(parameter), help=help_info)
args = parser.parse_args()
# Create XtdFile & ArcFile objects.
arcname = _exec_command("ls *.arc | head -1")
xtdname = _exec_command("ls *.xtd | head -1")
xtd = XtdFile(filename=xtdname, arcname=arcname)
# Create images.
for idx, dir_coords in enumerate(xtd.coords_iterator):
# Create images dir.
if "__main__" == __name__:
# Set argument parser.
parser = argparse.ArgumentParser()
# Add optional arguments.
parser.add_argument("-k", "--kpoints", help="set k-points")
parser.add_argument("--nnode", help="node number used for the job")
parser.add_argument("--ncpu", help="cpu number on each node")
parser.add_argument("-q", "--queue", help="pbs queue type")
# Add all possible arguments in INCAR file.
if os.path.exists("INCAR"):
incar = InCar()
parameters = incar.pnames
for parameter in parameters:
help_info = "Set '{}' in INCAR".format(parameter)
parser.add_argument("--{}".format(parameter), help=help_info)
args = parser.parse_args()
# Create XtdFile & ArcFile objects.
arcname = _exec_command("ls *.arc | head -1")
xtdname = _exec_command("ls *.xtd | head -1")
xtd = XtdFile(filename=xtdname, arcname=arcname)
# Create images.
for idx, dir_coords in enumerate(xtd.coords_iterator):
# Create images dir.
# Copy INCAR vasp.script
subprocess.getstatusoutput(
'cp $HOME/example/INCAR $HOME/example/vasp.script ./')
# Set argument parser.
parser = argparse.ArgumentParser()
# Add optional argument.
parser.add_argument("-k", "--kpoints", help="set k-points")
parser.add_argument("--nnode", help="node number used for the job")
parser.add_argument("--ncpu", help="cpu number on each node")
parser.add_argument("-q", "--queue", help="pbs queue type")
# Add all possible arguments in INCAR file.
if os.path.exists("INCAR"):
incar = InCar()
parameters = incar.pnames
for parameter in parameters:
help_info = "Set '{}' in INCAR".format(parameter)
parser.add_argument("--{}".format(parameter), help=help_info)
args = parser.parse_args()
# Create POSCAR
status, output = subprocess.getstatusoutput('ls *.xsd | head -1')
xsd = XsdFile(filename=output)
poscar_content = xsd.get_poscar_content(bases_const=1.0)
with open('POSCAR', 'w') as f:
f.write(poscar_content)
# Create POTCAR
import logging
import os
from vaspy import PY2
from vaspy.incar import InCar
if PY2:
import commands as subprocess
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:
