def lengths(self):
"""
Lengths of axes of supercell.
晶格基向量长度。
"""
with open(self.filename, "r") as f:
for line in f:
line = line.strip()
if line.startswith("PBC "):
line_list = str2list(line)
return [float(l) for l in line_list[1: 4]]
return None
def angles(self):
"""
Angels of axes of supercell in Degrees.
晶格基向量夹角(角度)。
"""
with open(self.filename, "r") as f:
for line in f:
line = line.strip()
if line.startswith("PBC "):
line_list = str2list(line)
return [float(l) for l in line_list[4: 7]]
return None
def lengths(self):
"""
Lengths of axes of supercell.
晶格基向量长度。
"""
with open(self.filename, "r") as f:
for line in f:
line = line.strip()
if line.startswith("PBC "):
line_list = str2list(line)
return [float(l) for l in line_list[1:4]]
return None
def angles(self):
"""
Angels of axes of supercell in Degrees.
晶格基向量夹角(角度)。
"""
with open(self.filename, "r") as f:
for line in f:
line = line.strip()
if line.startswith("PBC "):
line_list = str2list(line)
return [float(l) for l in line_list[4:7]]
return None
def elements(self):
"""
Element name of all atom in lattice.
晶格中的所有元素种类名称。
"""
with open(self.filename, "r") as f:
collecting = False
elements = []
for line in f:
line = line.strip()
if not collecting and line.startswith("PBC "):
collecting = True
elif collecting and line.startswith("end"):
collecting = False
return elements
# Collect coordinates data.
elif collecting:
line_list = str2list(line)
element = line_list[0]
elements.append(element)
def elements(self):
"""
Element name of all atom in lattice.
晶格中的所有元素种类名称。
"""
with open(self.filename, "r") as f:
collecting = False
elements = []
for line in f:
line = line.strip()
if not collecting and line.startswith("PBC "):
collecting = True
elif collecting and line.startswith("end"):
collecting = False
return elements
# Collect coordinates data.
elif collecting:
line_list = str2list(line)
element = line_list[0]
elements.append(element)
def coords_iterator(self):
"""
Return generator for Cartisan coordinates in arc file iteration.
返回每个轨迹的所有原子的笛卡尔坐标
"""
with open(self.filename, "r") as f:
collecting = False
coords = []
for line in f:
line = line.strip()
if not collecting and line.startswith("PBC "): # NOTE: Use "PBC " to tell "PBC=" apart
collecting = True
elif collecting and line.startswith("end"):
collecting = False
yield np.array(coords)
coords = []
# Collect coordinates data.
elif collecting:
line_list = str2list(line)
coord = [float(c) for c in line_list[1: 4]]
coords.append(coord)
def coords_iterator(self):
"""
Return generator for Cartisan coordinates in arc file iteration.
返回每个轨迹的所有原子的笛卡尔坐标
"""
with open(self.filename, "r") as f:
collecting = False
coords = []
for line in f:
line = line.strip()
if not collecting and line.startswith("PBC "): # NOTE: Use "PBC " to tell "PBC=" apart
collecting = True
elif collecting and line.startswith("end"):
collecting = False
yield np.array(coords)
coords = []
# Collect coordinates data.
elif collecting:
line_list = str2list(line)
coord = [float(c) for c in line_list[1: 4]]
coords.append(coord)
idx = outcar.last_max_atom - 1
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."
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."
a = XyzFile(filename=filename)
b = PosCar(filename='POSCAR')
#create new dir
if not os.path.exists('./continue'):
os.mkdir('./continue')
if os.path.isfile('./fort.188'):
fail = os.system("cp INCAR POTCAR KPOINTS fort.188 vasp.script ./continue")
else:
fail = os.system("cp INCAR POTCAR KPOINTS vasp.script ./continue")
if not fail:
#new fort.188
#change distance of 2 atoms
with open('./continue/fort.188', 'r') as f:
content_list = f.readlines()
m, n, distance = str2list(content_list[5]) # atom number and distance
x = a.data[int(m)-1, :] # atom coordinates
y = a.data[int(n)-1, :]
z = x - y
#get new distance
new_distance = np.dot(z, z)**0.5
newline = "%-5s%-5s%-10.6f\n" % (m, n, new_distance)
content_list[5] = newline
content_str = ''.join(content_list)
#write new fort.188
with open('./continue/fort.188', 'w') as f:
f.write(content_str)
else:
raise ContinueError('Failed to create continue dir.')
#add new POSCAR
a = XyzFile(filename=filename)
b = PosCar(filename='POSCAR')
#create new dir
if not os.path.exists('./continue'):
os.mkdir('./continue')
if os.path.isfile('./fort.188'):
fail = os.system("cp INCAR POTCAR KPOINTS fort.188 vasp.script ./continue")
else:
fail = os.system("cp INCAR POTCAR KPOINTS vasp.script ./continue")
if not fail:
#new fort.188
#change distance of 2 atoms
with open('./continue/fort.188', 'r') as f:
content_list = f.readlines()
m, n, distance = str2list(content_list[5]) # atom number and distance
x = a.data[int(m) - 1, :] # atom coordinates
y = a.data[int(n) - 1, :]
z = x - y
#get new distance
new_distance = np.dot(z, z)**0.5
newline = "%-5s%-5s%-10.6f\n" % (m, n, new_distance)
content_list[5] = newline
content_str = ''.join(content_list)
#write new fort.188
with open('./continue/fort.188', 'w') as f:
f.write(content_str)
else:
raise ContinueError('Failed to create continue dir.')
#add new POSCAR
# lattice basis
info['bases'] = []
for i in range(3):
vector = line2list(f.readline())
info['bases'].append(vector)
info_nline = 7
info = {}
with open(filename, 'r') as f:
system = f.readline().strip()
__read_info(info)
# atom info
info['atom_types'] = str2list(f.readline())
info['atoms_num'] = str2list(f.readline())
info['atom_numbers'] = [int(i) for i in info['atoms_num']]
info['natom'] = sum(info['atom_numbers'])
info['atom_names'] = []
for n, atom in zip(info['atoms_num'], info['atom_types']):
info['atom_names'].extend([atom] * int(n))
while True:
try:
content = ''
flush = f.readline().strip()
if flush == system:
__read_info(info) # update info
# skip atom info
f.readline()
