def parser(self,):
""" parse poscar to system
@todo : handle coordinates acoording to Direct tag
"""
s = System()
scale = float(self.scale)
a = [scale*float(i) for i in self.a]
b = [scale*float(i) for i in self.b]
c = [scale*float(i) for i in self.c]
s.name = self.name
s.pbc = v2lattice(a, b, c)
s.geotag = "XTLGRF 200"
for i in range(len(self.atoms)):
if i == 0:
prev = 0
now = int(self.atoms[0])
else:
prev = now
now += int(self.atoms[i])
for j in range(prev, now):
atom = Atom()
atom.name = self.atomtypes[i]
x = float(self.coords[j][0])
y = float(self.coords[j][1])
z = float(self.coords[j][2])
atom.x[0] = a[0]*x + b[0]*y + c[0]*z
atom.x[1] = a[1]*x + b[1]*y + c[1]*z
atom.x[2] = a[2]*x + b[2]*y + c[2]*z
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.name = self.atomtypes[int(i[2]) - 1]
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
elif n == 5 or n == 8:
# n = 5 is a charge type, n = 8 is a charge type generated
# by restart2data
atom.name = self.atomtypes[int(i[1]) - 1]
atom.x[0] = float(i[3])
atom.x[1] = float(i[4])
atom.x[2] = float(i[5])
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.name = self.atomtypes[int(i[2]) - 1]
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
elif n == 6 or n == 9:
# n = 5 is a charge type, n = 8 is a charge type generated
# by restart2data
atom.name = self.atomtypes[int(i[1]) - 1]
atom.x[0] = float(i[3])
atom.x[1] = float(i[4])
atom.x[2] = float(i[5])
s.atoms.append(atom)
return s
def parser(self, ):
""" parse poscar to system
@todo : handle coordinates acoording to Direct tag
"""
s = System()
scale = float(self.scale)
a = [scale * float(i) for i in self.a]
b = [scale * float(i) for i in self.b]
c = [scale * float(i) for i in self.c]
s.name = self.name
s.pbc = v2lattice(a, b, c)
s.natoms = self.natoms
s.atomtypes = self.atomtypes
s.scaleFactor = self.scale
s.geotag = "XTLGRF 200"
for i in range(len(self.natoms)):
if i == 0:
prev = 0
now = int(self.natoms[0])
else:
prev = now
now += int(self.natoms[i])
for j in range(prev, now):
atom = Atom()
#print self.atomtypes, i
atom.name = self.atomtypes[i]
x = float(self.coords[j][0])
y = float(self.coords[j][1])
z = float(self.coords[j][2])
atom.xFrac = [x, y, z]
atom.x[0] = a[0] * x + b[0] * y + c[0] * z
atom.x[1] = a[1] * x + b[1] * y + c[1] * z
atom.x[2] = a[2] * x + b[2] * y + c[2] * z
if len(self.coords[j]) == 6 and self.sd == 1:
xr = self.coords[j][3]
yr = self.coords[j][4]
zr = self.coords[j][5]
if xr == "F":
atom.xr[0] = 1
if yr == "F":
atom.xr[1] = 1
if zr == "F":
atom.xr[2] = 1
if len(self.coords[j]) == 3:
atom.xr = [0, 0, 0]
s.atoms.append(atom)
return s
def parser(self,):
""" parse poscar to system
@todo : handle coordinates acoording to Direct tag
"""
s = System()
scale = float(self.scale)
a = [scale*float(i) for i in self.a]
b = [scale*float(i) for i in self.b]
c = [scale*float(i) for i in self.c]
s.name = self.name
s.pbc = v2lattice(a, b, c)
s.natoms = self.natoms
s.atomtypes = self.atomtypes
s.scaleFactor = self.scale
s.geotag = "XTLGRF 200"
for i in range(len(self.natoms)):
if i == 0:
prev = 0
now = int(self.natoms[0])
else:
prev = now
now += int(self.natoms[i])
for j in range(prev, now):
atom = Atom()
#print self.atomtypes, i
atom.name = self.atomtypes[i]
x = float(self.coords[j][0])
y = float(self.coords[j][1])
z = float(self.coords[j][2])
atom.xFrac = [x, y, z]
atom.x[0] = a[0]*x + b[0]*y + c[0]*z
atom.x[1] = a[1]*x + b[1]*y + c[1]*z
atom.x[2] = a[2]*x + b[2]*y + c[2]*z
if len(self.coords[j]) == 6 and self.sd == 1:
xr = self.coords[j][3]
yr = self.coords[j][4]
zr = self.coords[j][5]
if xr == "F":
atom.xr[0] = 1
if yr == "F":
atom.xr[1] = 1
if zr == "F":
atom.xr[2] = 1
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s
def gen_scan(s, args):
start = 0.7
end = 1.3
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
if os.path.exists('../pbs'):
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
def gen_scan(s, args):
start = 0.8
end = 1.2
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
def parser(self,):
""" parse dump file into System
"""
s = System()
s.name = self.name
# transform a, b, c to [xx, xy, yz]
# [yx, yy, yz] and [zx, zy, zz]
# caution! A hard coded code for specified dump file
a = []
# some dump file only have xl and xh. Normalize to three terms
if len(self.a) == 2:
self.a.append(0.0)
if len(self.b) == 2:
self.b.append(0.0)
if len(self.c) == 2:
self.c.append(0.0)
#a.append(float(self.a[1]) - float(self.a[0]))
#@ref: http://lammps.sandia.gov/doc/Section_howto.html#howto_12
xlo = float(self.a[0]) - min(0.0, float(self.a[2]), float(self.b[2]),\
float(self.a[2]) + float(self.c[2]))
xhi = float(self.a[1]) - max(0.0, float(self.a[2]), float(self.b[2]),\
float(self.a[2]) + float(self.c[2]))
a.append(xhi - xlo)
a.append(0.0)
a.append(0.0)
#print a
b = []
b.append(float(self.a[2]))
ylo = float(self.b[0]) - min(0.0, float(self.c[2]))
yhi = float(self.b[1]) - max(0.0, float(self.c[2]))
b.append(yhi - ylo)
b.append(0.0)
#print b
c = []
c.append(float(self.b[2]))
c.append(float(self.c[2]))
c.append(float(self.c[1]) - float(self.c[0]))
s.pbc = v2lattice(a, b, c)
#print c
# begin to parse atoms
flag = 0
if os.path.exists("inp"):
flag = 1
n2a = self.parseInp()
counter = 0
for i in self.coords:
atom = Atom()
if flag:
atom.name = n2a[int(i[1])]
else:
atom.name = i[1]
"""
atom.x[0] = float(i[3])
atom.x[1] = float(i[4])
atom.x[2] = float(i[5])
"""
atom.an = counter + 1
atom.x[0] = float(i[2])
atom.x[1] = float(i[3])
atom.x[2] = float(i[4])
s.atoms.append(atom)
counter += 1
return s
def parser(self, ):
""" parse dump file into System
"""
s = System()
s.name = self.name
# transform a, b, c to [xx, xy, yz]
# [yx, yy, yz] and [zx, zy, zz]
# caution! A hard coded code for specified dump file
a = []
# some dump file only have xl and xh. Normalize to three terms
if len(self.a) == 2:
self.a.append(0.0)
if len(self.b) == 2:
self.b.append(0.0)
if len(self.c) == 2:
self.c.append(0.0)
#a.append(float(self.a[1]) - float(self.a[0]))
#@ref: http://lammps.sandia.gov/doc/Section_howto.html#howto_12
xlo = float(self.a[0]) - min(0.0, float(self.a[2]), float(self.b[2]),\
float(self.a[2]) + float(self.c[2]))
xhi = float(self.a[1]) - max(0.0, float(self.a[2]), float(self.b[2]),\
float(self.a[2]) + float(self.c[2]))
a.append(xhi - xlo)
a.append(0.0)
a.append(0.0)
#print a
b = []
b.append(float(self.a[2]))
ylo = float(self.b[0]) - min(0.0, float(self.c[2]))
yhi = float(self.b[1]) - max(0.0, float(self.c[2]))
b.append(yhi - ylo)
b.append(0.0)
#print b
c = []
c.append(float(self.b[2]))
c.append(float(self.c[2]))
c.append(float(self.c[1]) - float(self.c[0]))
s.pbc = v2lattice(a, b, c)
#print c
# begin to parse atoms
flag = 0
if os.path.exists("inp"):
flag = 1
n2a = self.parseInp()
counter = 0
for i in self.coords:
atom = Atom()
if flag:
atom.name = n2a[int(i[1])]
else:
atom.name = i[1]
"""
atom.x[0] = float(i[3])
atom.x[1] = float(i[4])
atom.x[2] = float(i[5])
"""
atom.an = counter + 1
atom.x[0] = float(i[2])
atom.x[1] = float(i[3])
atom.x[2] = float(i[4])
s.atoms.append(atom)
counter += 1
return s
