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.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()
if self.name:
s.name = self.name
else:
s.name = "pdbjob"
if self.pbc:
s.pbc = [float(i) for i in self.pbc]
for i in self.coords:
a = Atom()
# note need to confirm with the standary pdb format
a.name = i[12:17].strip()
a.x[0] = float(i[27:39])
a.x[1] = float(i[39:47])
a.x[2] = float(i[47:55])
s.atoms.append(a)
# only storage the first half of the bond matrix
for i in self.connect:
tokens = i.strip().split()
a1 = int(tokens[1])
for j in [int(k) for k in tokens[2:]]:
a2 = j
if a2 > a1:
s.connect.append([a1, a2])
return s
def parser(self, ):
s = System()
if self.name:
s.name = self.name
else:
s.name = "pdbjob"
if self.pbc:
s.pbc = [float(i) for i in self.pbc]
for i in self.coords:
a = Atom()
# note need to confirm with the standary pdb format
a.name = i[12:17].strip()
a.x[0] = float(i[27:38])
a.x[1] = float(i[38:46])
a.x[2] = float(i[46:55])
s.atoms.append(a)
# only storage the first half of the bond matrix
for i in self.connect:
tokens = i.strip().split()
a1 = int(tokens[1])
for j in [int(k) for k in tokens[2:]]:
a2 = j
if a2 > a1:
s.connect.append([a1, a2])
return s
def parser(self,):
s = System()
if self.pbc:
s.pbc = [float(i) for i in self.pbc.split()[1:7]]
for i in self.coords:
a = Atom()
a.name = i[:6].strip()
a.x[0] = float(i[6:20])
a.x[1] = float(i[20:35])
a.x[2] = float(i[35:50])
s.atoms.append(a)
return s
def parser(self, ):
s = System()
if self.pbc:
s.pbc = [float(i) for i in self.pbc.split()[1:7]]
for i in self.coords:
a = Atom()
a.name = i[:6].strip()
a.x[0] = float(i[6:20])
a.x[1] = float(i[20:35])
a.x[2] = float(i[35:50])
s.atoms.append(a)
return s
def parser(self, ):
""" parse geo file into System
"""
s = System()
s.name = self.name
s.pbc = [float(i) for i in self.pbc]
s.geotag = self.type
for i in self.coords:
a = Atom()
a.name = i[13:16]
a.x[0] = float(i[31:41])
a.x[1] = float(i[41:51])
a.x[2] = float(i[51:61])
s.atoms.append(a)
return s
def parser(self,):
""" parse geo file into System
"""
s = System()
s.name = self.name
s.pbc = [float(i) for i in self.pbc]
s.geotag = self.type
for i in self.coords:
a = Atom()
a.name= i[13:16]
a.x[0] = float(i[31:41])
a.x[1] = float(i[41:51])
a.x[2] = float(i[51:61])
s.atoms.append(a)
return s
def parser(self, ):
s = System()
if self.name:
s.name = self.name
else:
s.name = "xyzjob"
for i in self.coords:
tokens = i.strip().split()
a = Atom()
a.name = tokens[0]
a.x[0] = float(tokens[1])
a.x[1] = float(tokens[2])
a.x[2] = float(tokens[3])
s.atoms.append(a)
return s
def parser(self,):
s = System()
if self.name:
s.name = self.name
else:
s.name = "xyzjob"
for i in self.coords:
tokens = i.strip().split()
a = Atom()
a.name = tokens[0]
a.x[0] = float(tokens[1])
a.x[1] = float(tokens[2])
a.x[2] = float(tokens[3])
s.atoms.append(a)
return s
def parser(self,):
s = System()
s.name = self.name
s.methods = self.__parse_keyword()
s.spin = self.spin
s.charge = self.charge
for i in self.redundant:
s.redundant.append(i.strip().split())
for i in self.atoms:
a = Atom()
a.name = ELEMENT[int(i[1])]
a.x[0] = float(i[3])
a.x[1] = float(i[4])
a.x[2] = float(i[5])
s.atoms.append(a)
return s
def parser(self,):
""" parse cfg to system
"""
s = System()
s.pbc = v2lattice(a, b, c)
s.natoms = self.natoms
for i in range(s.natoms):
atom = Atom()
atom.name = self.coords[i][1][0]
x = float(self.coords[i][2][0])
y = float(self.coords[i][2][1])
z = float(self.coords[i][2][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)
def parser(self, ):
s = System()
for i in self.atoms:
a = Atom()
a.name = i[0]
a.x[0] = float(i[1].strip("#"))
a.x[1] = float(i[2].strip("#"))
a.x[2] = float(i[3].strip("#"))
s.atoms.append(a)
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 __init__(self, filename):
self.name = filename
"""@ivar: input file name
@type: char
"""
self.remarks = []
"""@ivar: remarks (lines starts with '#')
@type: list
"""
self.pbc = []
"""@ivar: pbc info
@type: list
"""
self.sys = System()
"""@ivar: system
def parser(self, ):
s = System()
s.options = self.options
s.methods = self.methods
for i in self.redundant:
s.redundant.append(i.strip().split())
s.connect = self.connect
s.spin = self.spin
s.charge = self.charge
s.name = self.title.strip()
for i in self.atoms:
a = Atom()
a.name = i[0]
a.x[0] = float(i[1])
a.x[1] = float(i[2])
a.x[2] = float(i[3])
s.atoms.append(a)
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.options = self.options
s.methods = self.methods
for i in self.redundant:
s.redundant.append(i.strip().split())
s.connect = self.connect
s.spin = self.spin
s.charge = self.charge
s.name = self.title.strip()
for i in self.atoms:
a = Atom()
a.name = i[0]
a.x[0] = float(i[1])
a.x[1] = float(i[2])
a.x[2] = float(i[3])
s.atoms.append(a)
return s
def parser(self, ):
s = System()
s.name = self.name
s.methods = self.__parse_keyword()
s.spin = self.spin
s.charge = self.charge
for i in self.redundant:
s.redundant.append(i.strip().split())
for i in self.atoms:
a = Atom()
a.name = ELEMENT[int(i[1])]
a.x[0] = float(i[3])
a.x[1] = float(i[4])
a.x[2] = float(i[5])
s.atoms.append(a)
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 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