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
