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):
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 __lineToAtom(self, line):
"""put each coordinate line into atom class"""
ai = Atom()
tokens = line.strip().split()
ai.number = int(tokens[0])
ai.name = tokens[1]
ai.an = tokens[2]
ai.type1 = tokens[3]
ai.type2 = tokens[4]
ai.charge = float(tokens[5])
ai.x[0] = float(tokens[6])
ai.x[1] = float(tokens[7])
ai.x[2] = float(tokens[8])
ai.resn = int(tokens[9])
ai.resname = tokens[10]
ai.cg = int(tokens[11])
return ai
def __lineToAtom(self, line):
"""put each coordinate line into atom class"""
ai = Atom()
tokens = line.strip().split()
ai.number = int(tokens[0])
ai.name = tokens[1]
ai.an = tokens[2]
ai.type1 = tokens[3]
ai.type2 = tokens[4]
ai.charge = float(tokens[5])
ai.x[0] = float(tokens[6])
ai.x[1] = float(tokens[7])
ai.x[2] = float(tokens[8])
ai.resn = int(tokens[9])
ai.resname = tokens[10]
ai.cg = int(tokens[11])
return ai
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
