def test_update_name(self):
"Make sure we can update Name info."
filename = path + "/h_top_c_fcc_far_noname.xsd"
xsd = XsdFile(filename)
xsd.update_name()
for elem in xsd.tree.iter("SymmetrySystem"):
name = elem.attrib["Name"]
break
self.assertTrue("E:" in name)
self.assertTrue("F:" in name)
self.assertTrue("M:" in name)
self.assertTrue("P:" in name)
def test_update_name(self):
"Make sure we can update Name info."
filename = path + "/h_top_c_fcc_far_noname.xsd"
xsd = XsdFile(filename)
xsd.update_name()
for elem in xsd.tree.iter("SymmetrySystem"):
name = elem.attrib["Name"]
break
self.assertTrue("E:" in name)
self.assertTrue("F:" in name)
self.assertTrue("M:" in name)
self.assertTrue("P:" in name)
def test_bulk_construction(self):
" Test XsdFile construction for a bulk. "
filename = path + "/bulk.xsd"
xsd = XsdFile(filename)
# Check the default coordinate value for the Atom3d tag without XYZ.
ref_origin_coord = [0.0, 0.0, 0.0]
ret_origin_coord = xsd.data[0].tolist()
self.assertListEqual(ref_origin_coord, ret_origin_coord)
# Check atom info update in new xsd file.
temp_file = "{}/temp.xsd".format(path)
xsd.tofile(temp_file)
tree = ET.parse(temp_file)
for atom3d in tree.iter('Atom3d'):
break
self.assertEqual(atom3d.get('XYZ'), '0.0,0.0,0.0')
os.remove(temp_file)
def test_bulk_construction(self):
" Test XsdFile construction for a bulk. "
filename = path + "/bulk.xsd"
xsd = XsdFile(filename)
# Check the default coordinate value for the Atom3d tag without XYZ.
ref_origin_coord = [0.0, 0.0, 0.0]
ret_origin_coord = xsd.data[0].tolist()
self.assertListEqual(ref_origin_coord, ret_origin_coord)
# Check atom info update in new xsd file.
temp_file = "{}/temp.xsd".format(path)
xsd.tofile(temp_file)
tree = ET.parse(temp_file)
for atom3d in tree.iter('Atom3d'):
break
self.assertEqual(atom3d.get('XYZ'), '0.0,0.0,0.0')
os.remove(temp_file)
def test_get_name_info(self):
" Make sure we can get correct info from Name property. "
filename = path + "/h_top_c_fcc_far_noname.xsd"
xsd = XsdFile(filename)
self.assertEqual(xsd.force, 0.0)
self.assertEqual(xsd.energy, 0.0)
self.assertEqual(xsd.magnetism, 0.0)
self.assertTrue(hasattr(xsd, "path"))
def read_xsd():
# Get xsd file
for filename in os.listdir('.'):
name_list = filename.split('.')
if name_list[-1] == 'xsd':
xsdname = name_list[0]
xsd = XsdFile(filename)
break
content = 'XSD -->\n'
content += " The xsdfile is : \033[31;1;4m%s\033[0m \n" %filename
return content, xsd, xsdname
def test_construction_query(self):
" Test OutCar construction and query functions. "
filename = path + "/h_top_c_fcc_far.xsd"
xsd = XsdFile(filename)
# Check query functions.
self.assertEqual(xsd.filename, filename)
self.assertEqual(xsd.bases_const, 1.0)
ref_bases = [[4.31035158, -2.48858265, 0.], [0., 4.97716529, 0.],
[0., 0., 18.09575766]]
self.assertListEqual(xsd.bases.tolist(), ref_bases)
self.assertEqual(xsd.force, 0.048)
self.assertEqual(xsd.energy, -100.896)
self.assertEqual(xsd.magnetism, 8.25)
self.assertTrue(hasattr(xsd, "path"))
pos = pos[idx]
forces = forces[idx]
_logger.info("{:<15s}: {}".format("max force atom", outcar.last_max_atom))
_logger.info("{:<15s}: ({}, {}, {})".format("atom position", *pos))
_logger.info("{:<15s}: {}, {}, {}".format("forces", *forces))
_logger.info("{:<15s}: {}\n".format("total-force", outcar.last_max_force))
# Get fort.188 info.
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
_logger.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE"))
_logger.info("-"*30)
_logger.info("{:<10s}{:<10s}{:<15s}\n".format(*str2list(atom_info)))
# Create .xsd file.
if args.xsd:
status, output = subprocess.getstatusoutput('ls *.xsd | head -1')
if not output.endswith('.xsd'):
_logger.info("No .xsd file in current directory.")
sys.exit(1)
xsd = XsdFile(filename=output)
# modify atom color
xsd.modify_color(atom_number=outcar.last_max_atom)
jobname = output.split('.')[0]
filename = jobname + '-force.xsd'
xsd.tofile(filename=filename)
_logger.info(filename + " has been created.")
force_info = outcar.atom_forces[max_num - 1, :]
pos = force_info[:3].tolist()
forces = force_info[3:].tolist()
logging.info("{:<15s}: {}".format("max force atom", max_num))
logging.info("{:<15s}: ({}, {}, {})".format("atom position", *pos))
logging.info("{:<15s}: {}, {}, {}".format("forces", *forces))
logging.info("{:<15s}: {}\n".format("total-force", np.linalg.norm(forces)))
# Get fort.188 info.
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
logging.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE"))
logging.info("-" * 30)
logging.info("{:<10s}{:<10s}{:<15s}\n".format(*str2list(atom_info)))
# Create .xsd file.
if args.xsd:
status, output = commands.getstatusoutput('ls *.xsd | head -1')
if not output.endswith('.xsd'):
logging.info("No .xsd file in current directory.")
sys.exit(1)
xsd = XsdFile(filename=output)
# modify atom color
xsd.modify_color(atom_number=max_num)
jobname = output.split('.')[0]
filename = jobname + '-force.xsd'
xsd.tofile(filename=filename)
print filename + " has been created."
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
potdir = r'/data/pot/vasp/potpaw_PBE2010/'
# delete old POTCAR
if os.path.exists('./POTCAR'):
os.remove('./POTCAR')
for elem in xsd.atoms:
# if os.path.exists(potdir + elem + '_new/'):
# potcar = potdir + elem + '_new/POTCAR'
if os.path.exists(potdir + elem):
potcar = potdir + elem + '/POTCAR'
else:
max_num = outcar.max_force_atom
force_info = outcar.atom_forces[max_num-1, :]
pos = force_info[: 3].tolist()
forces = force_info[3:].tolist()
print "\nmax force atom: %d" % max_num
print " atom position: (%f, %f, %f)" % tuple(pos)
print " forces: %f, %f, %f" % tuple(forces)
print " total-force: %f\n" % np.linalg.norm(forces)
# get fort.188 info
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
print "%10s%10s%15s" % ('Atom1', 'Atom2', 'DISTANCE')
print "-"*35
print "%10s%10s%15s\n" % tuple(str2list(atom_info))
# create .xsd file
if '--xsd' in sys.argv:
status, output = commands.getstatusoutput('ls *.xsd | head -1')
if not output.endswith('.xsd'):
print "No .xsd file in current directory."
sys.exit(1)
xsd = XsdFile(filename=output)
# modify atom color
xsd.modify_color(atom_number=max_num)
jobname = output.split('.')[0]
filename = jobname + '-force.xsd'
xsd.tofile(filename=filename)
print filename + " has been created."
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
potdir = r'/data/pot/vasp/potpaw_PBE2010/'
# delete old POTCAR
if os.path.exists('./POTCAR'):
os.remove('./POTCAR')
for elem in xsd.atom_types:
# if os.path.exists(potdir + elem + '_new/'):
# potcar = potdir + elem + '_new/POTCAR'
if os.path.exists(potdir + elem):
potcar = potdir + elem + '/POTCAR'
else:
_logger.info("{:<15s}: ({}, {}, {})".format("atom position",
*poses[i]))
_logger.info("{:<15s}: {}, {}, {}".format("forces", *forces[i]))
else:
_logger.info("Cannot get the max force in %s." % x)
_logger.info("Atoms not optimized >>> \n" + " " * 24 + "%s" %
([i + 1 for i in bad_ids]))
# Get fort.188 info.
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
_logger.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE"))
_logger.info("-" * 30)
_logger.info("{:<10s}{:<10s}{:<15s}\n".format(*str2list(atom_info)))
# Create .xsd file.
if args.xsd:
status, output = subprocess.getstatusoutput('ls *.xsd | head -1')
if not output.endswith('.xsd'):
_logger.info("No .xsd file in current directory.")
sys.exit(1)
xsd = XsdFile(filename=output)
# modify atom color
xsd.modify_color(atom_number=outcar.last_max_atom)
jobname = output.split('.')[0]
filename = jobname + '-force.xsd'
xsd.tofile(filename=filename)
_logger.info(filename + " has been created.")
parser = argparse.ArgumentParser()
parser.add_argument('-x', '--xsd', \
default='default.xsd', help='xsd File')
parser.add_argument('-g', '--gen', \
default='geo_in.gen', help='Gen Format File Name')
args = parser.parse_args()
# read xsd and get fixes
if args.xsd == 'default.xsd':
for fname in os.listdir('.'):
name_list = fname.split('.')
if name_list[-1] == 'xsd':
xsdname = name_list[0]
xsd = XsdFile(fname)
break
else:
xsd = XsdFile(args.xsd)
symbol_dict = {}
for i, symbol in enumerate(xsd.atom_types):
symbol_dict[symbol] = i + 1
symbols = []
for num, sym in zip(xsd.atom_numbers, xsd.atom_types):
symbols.extend([sym] * num)
content = (' {:<8d} {:<s}\n').format(xsd.natom, 'F')
content += ('{:>4s}' * len(xsd.atom_types) + '\n').format(*xsd.atom_types)
for i, (sym, coord) in enumerate(zip(symbols, xsd.data)):
