class Model(object):
""" xyz model file class
functions:
write_our_xyz(outfile)
write_cif(outfile)
generate_neighbors(cutoff)
get_atoms_in_cutoff(atom,cutoff)
nearest_neigh(atom)
save_vp_dict(vp_dict) """
def __init__(self, *args, **kwargs):
""" sets:
self.comment
self.lx
self.ly
self.lz
self.atoms
self.natoms
self.atomtypes
Extra routines can set:
self.coord_numbers """
super(Model,self).__init__()
if(len(args) == 1):
modelfile = args[0]
if modelfile[-4:] == '.xyz':
self.read_xyz(modelfile)
elif modelfile[-4:] == '.dat':
self.read_dat(modelfile)
else:
raise Exception("Unknown input model type!")
elif(len(args) == 5):
self.comment = args[0]
self.lx = args[1]
self.ly = args[2]
self.lz = args[3]
self.atoms = args[4]
self.natoms = len(args[4])
else:
raise Exception("Unknown input parameters to Model()!")
self.hutch = Hutch(self)
self.atomtypes = {}
for atom in self.atoms:
self.atomtypes[atom.z] = self.atomtypes.get(atom.z, 0) + 1
def read_xyz(self,modelfile):
with open(modelfile) as f:
content = f.readlines()
self.comment = content.pop(0) # Comment line
if('-1' in content[-1] and '.' not in content[-1]): # '-1' line
content.pop(-1)
self.lx,self.ly,self.lz = tuple([float(x) for x in content.pop(0).strip().split()])
self.natoms = len(content)
content = [x.strip().split() for x in content]
for i in range(0,len(content)):
for j in range(0,len(content[i])):
try:
content[i][j] = int(content[i][j])
except:
try:
content[i][j] = float(content[i][j])
except:
pass
self.atoms = []
for i,atom in enumerate(content):
self.atoms.append(Atom(i,atom[0],atom[1],atom[2],atom[3]))
if type(self.atoms[i].z) == type('hi'):
self.atoms[i].z = znum2sym.sym2z(self.atoms[i].z)
def read_dat(self,modelfile):
with open(modelfile) as f:
content = f.readlines()
self.comment = content.pop(0) # Comment line
content = [x for x in content if not x.startswith('#')]
for line in content:
if('atoms' in line): self.natoms = int(line.split()[0])
if('xlo' in line and 'xhi' in line):
self.lx = abs(float(line.split()[0])) + abs(float(line.split()[1]))
if('ylo' in line and 'yhi' in line):
self.ly = abs(float(line.split()[0])) + abs(float(line.split()[1]))
if('zlo' in line and 'zhi' in line):
self.lz = abs(float(line.split()[0])) + abs(float(line.split()[1]))
if('atom types' in line): nelems = int(line.split()[0])
if('Masses' in line): mflag = content.index(line) + 1
if('Atoms' in line): aflag = content.index(line) + 1
try:
mflag
except NameError:
raise Exception("ERROR! You need to define the masses in the .dat file.")
atomtypes = {}
while(nelems > 0):
if(len(content[mflag].split()) == 2):
atomtypes[int(content[mflag].split()[0])] = masses.get_znum(float(content[mflag].split()[1]))
nelems -= 1
mflag += 1
self.atoms = []
natoms = self.natoms
while(natoms > 0):
sline = content[aflag].split()
if(len(sline) >= 5):
# We found an atom
id = int(sline[0])
type = int(sline[1])
x = float(sline[2])
y = float(sline[3])
z = float(sline[4])
znum = atomtypes[type]
# Add it to the model
self.atoms.append(Atom(id,znum,x,y,z))
natoms -= 1
aflag += 1
def write_dat(self,outfile=None):
if outfile is None:
of = sys.stdout
else:
of = open(outfile,'w')
of.write(self.comment+'\n')
of.write('{0} atoms\n\n'.format(self.natoms))
of.write('{0} atom types\n\n'.format(len(self.atomtypes)))
of.write('{0} {1} xlo xhi\n'.format(-self.lx/2,self.lx/2))
of.write('{0} {1} ylo yhi\n'.format(-self.ly/2,self.ly/2))
of.write('{0} {1} zlo zhi\n\n'.format(-self.lz/2,self.lz/2))
of.write('Masses\n\n')
atomtypes = list(self.atomtypes)
atomtypes.sort()
atomtypes.reverse()
for i,z in enumerate(atomtypes):
of.write('{0} {1}\n'.format(i+1,round(masses.get_mass(z),2)))
of.write('\n')
of.write('Atoms\n\n')
for i,atom in enumerate(self.atoms):
of.write('{0} {1} {2} {3} {4}\n'.format(atom.id+1, atomtypes.index(atom.z)+1, atom.coord[0], atom.coord[1], atom.coord[2]))
def write_our_xyz(self,outfile=None):
if outfile is None:
of = sys.stdout
else:
of = open(outfile,'w')
of.write(self.comment.strip()+'\n')
of.write("{0} {1} {2}\n".format(self.lx, self.lx, self.lz))
for atom in self.atoms:
of.write(atom.ourxyz()+'\n')
of.write('-1')
of.close()
def write_real_xyz(self,outfile=None):
if outfile is None:
of = sys.stdout
else:
of = open(outfile,'w')
of.write(str(self.natoms)+'\n')
of.write("{0} {1} {2} {3}\n".format(self.comment.strip(),self.lx, self.lx, self.lz))
for i,atom in enumerate(self.atoms):
of.write(atom.realxyz()+'\n')
def write_cif(self,outfile=None):
if outfile is None:
of = sys.stdout
else:
of = open(outfile,'w')
of.write('_pd_phase_name\t'+self.comment+'\n')
of.write('_cell_length_a '+str(self.lx)+'\n')
of.write('_cell_length_b '+str(self.ly)+'\n')
of.write('_cell_length_c '+str(self.lz)+'\n')
of.write('_cell_angle_alpha 90\n_cell_angle_beta 90\n_cell_angle_gamma 90\n')
of.write('_symmetry_space_group_name_H-M \'P 1\'\n_symmetry_Int_Tables_number 1\n\n')
of.write('loop_\n_symmetry_equiv_pos_as_xyz\n \'x, y, z\'\n\n')
of.write('loop_\n _atom_site_label\n _atom_site_occupancy\n _atom_site_fract_x\n _atom_site_fract_y\n _atom_site_fract_z\n _atom_site_adp_type\n _atom_site_B_iso_or_equiv\n _atom_site_type_symbol\n')
atomtypes = {}
for atom in self.atoms:
atomtypes[atom.z] = atomtypes.get(atom.z, 0) + 1
of.write(' '+znum2sym.z2sym(atom.z)+str(atomtypes[atom.z])+'\t1.0\t'+str(atom.coord[0]/self.lx+0.5)+'\t'+str(atom.coord[1]/self.ly+0.5)+'\t'+str(atom.coord[2]/self.lz+0.5)+'\tBiso\t1.000000\t'+znum2sym.z2sym(atom.z)+'\n')
of.write('\n')
of.close()
def add_atom(self,atom):
self.atoms.append(atom)
self.hutch.add_atom(atom)
self.natoms += 1
def generate_neighbors(self,cutoff):
for atom in self.atoms:
atom.neighs = self.get_atoms_in_cutoff(atom,cutoff)
atom.cn = len(atom.neighs)
def check_neighbors(self):
for atom in self.atoms:
for n in atom.neighs:
if atom not in n.neighs:
print("You're neighbors are screwed up! Atom IDs are {0}, {1}.".format(atom.id,n.id))
print("Neighbors of: {0}".format(atom))
print(atom.neighs)
print("Neighbors of: {0}".format(n))
print(n.neighs)
print("Dist = {0}".format(self.dist(atom,n)))
print("Dist = {0}".format(self.dist(n,atom)))
def generate_coord_numbers(self):
""" atom.neighs must be defined first for all atoms """
self.coord_numbers = {}
# Form will be:
# {'Cu-Al': 4.5}, etc.
for typea in self.atomtypes:
self.coord_numbers[znum2sym.z2sym(typea)] = 0
for typeb in self.atomtypes:
self.coord_numbers[znum2sym.z2sym(typea)+'-'+znum2sym.z2sym(typeb)] = 0
for atom in self.atoms:
for n in atom.neighs:
self.coord_numbers[znum2sym.z2sym(atom.z)] += 1
self.coord_numbers[znum2sym.z2sym(atom.z)+'-'+znum2sym.z2sym(n.z)] += 1
self.bonds = self.coord_numbers.copy()
for key in self.coord_numbers:
elem = znum2sym.sym2z(key.split('-')[0])
self.coord_numbers[key] /= float(self.atomtypes[elem])
def get_atoms(self):
return self.atoms
def get_natoms(self):
return self.natoms
def get_box_size(self):
return (self.lx,self.ly,self.lz)
def get_atoms_in_cutoff(self,atom,cutoff):
x_start = atom.coord[0] - cutoff
y_start = atom.coord[1] - cutoff
z_start = atom.coord[2] - cutoff
x_end = atom.coord[0] + cutoff
y_end = atom.coord[1] + cutoff
z_end = atom.coord[2] + cutoff
if(x_start < -self.lx/2.0): x_start = x_start + self.lx #PBC
if(y_start < -self.ly/2.0): y_start = y_start + self.ly #PBC
if(z_start < -self.lz/2.0): z_start = z_start + self.lz #PBC
if(x_end > self.lx/2.0): x_end = x_end - self.lx #PBC
if(y_end > self.ly/2.0): y_end = y_end - self.ly #PBC
if(z_end > self.lz/2.0): z_end = z_end - self.lz #PBC
atom_s = Atom(0,0,x_start,y_start,z_start)
hutch_s = self.hutch.hutch_position(atom_s)
i_start = hutch_s[0]
j_start = hutch_s[1]
k_start = hutch_s[2]
atom_e = Atom(0,0,x_end,y_end,z_end)
hutch_e = self.hutch.hutch_position(atom_e)
i_end = hutch_e[0]
j_end = hutch_e[1]
k_end = hutch_e[2]
list = []
for i in range(0,self.hutch.nhutchs):
if(i_start <= i_end):
if(i < i_start or i > i_end): continue
else:
if(i < i_start and i > i_end): continue
for j in range(0,self.hutch.nhutchs):
if(j_start <= j_end):
if(j < j_start or j > j_end): continue
else:
if(j < j_start and j > j_end): continue
for k in range(0,self.hutch.nhutchs):
if(k_start <= k_end):
if(k < k_start or k > k_end): continue
else:
if(k < k_start and k > k_end): continue
list = list + self.hutch.get_atoms_in_hutch((i,j,k))
list.remove(atom)
list = [atomi for atomi in list if self.dist(atom,atomi) <= cutoff]
return list
def dist(self,atom1,atom2):
x = (atom1.coord[0] - atom2.coord[0])
y = (atom1.coord[1] - atom2.coord[1])
z = (atom1.coord[2] - atom2.coord[2])
while(x > self.lx/2): x = self.lx - x
while(y > self.ly/2): y = self.ly - y
while(z > self.lz/2): z = self.lz - z
while(x < -self.lx/2): x = self.lx + x
while(y < -self.ly/2): y = self.ly + y
while(z < -self.lz/2): z = self.lz + z
x2 = x**2
y2 = y**2
z2 = z**2
return math.sqrt(x2+y2+z2)
def get_all_dists(self):
dists = []
for atomi in self.atoms:
for atomj in self.atoms[self.atoms.index(atomi)+1:]:
dists.append([atomi,atomj,self.dist(atomi,atomj)])
return dists
def nearest_neigh(self,atom):
""" returns an atoms nearest neighbor """
hutch = self.hutch.hutch_position(atom)
atoms = self.hutch.get_atoms_in_hutch(hutch)[:]
if atom in atoms: atoms.remove(atom)
# This generation isn't perfect but it will work
rots = [(1,0,0),(0,1,0),(0,0,1)]
i = 0
while len(atoms) == 0:
hutch = ((hutch[0]+rots[i][0])%self.hutch.nhutchs,(hutch[1]+rots[i][1])%self.hutch.nhutchs,(hutch[2]+rots[i][2])%self.hutch.nhutchs)
i = (i+1) % 3
atoms = self.hutch.get_atoms_in_hutch(hutch)
if atom in atoms: atoms.remove(atom)
start = atoms[0]
atoms = self.get_atoms_in_cutoff(atom,self.dist(atom,start))
d = float("inf")
for atomi in atoms:
dt = self.dist(atom,atomi)
if dt < d:
d = dt
a = atomi
return a
def save_vp_dict(self,vp_dict):
self.vp_dict = vp_dict
def composition(self):
d = {}
for key in self.atomtypes:
d[znum2sym.z2sym(key)] = self.atomtypes[key]/float(self.natoms)
return d
def print_bond_stats(self):
comp = self.composition()
nbonds = 0.0
for key in self.bonds:
if '-' not in key:
nbonds += self.bonds[key]
bond_stats = self.bonds.copy()
for key in bond_stats.keys():
if '-' in key:
del bond_stats[key]
else:
#bond_stats[key] /= nbonds/comp[znum2sym.sym2z(key)]
bond_stats[key] *= 1.0/(nbonds*comp[key])
print('Bond statistics:')
pprint(self.bonds)
print('Ratio of actual/expected bonds:')
pprint(bond_stats)
def atom_coords(self):
coords = []
for atom in self.atoms:
coords.append(atom.coord)
return coords
def nn_vor(self):
coords = self.atom_coords()
vor = Voronoi(coords)
print(vor.vertices)
print(vor.regions)
voronoi_plot_2d(vor)
plt.show()
