class System():
def __init__(self, setting):
self.setting = setting
self.elsProps = [] # elements properties
self.setting['nAt'] = [] # number of atoms per specie
self.px = self.setting['period'][0]
self.py = self.setting['period'][1]
self.pz = self.setting['period'][2]
self.a0 = self.setting['a']
self.box =[[0, self.px*self.a0],\
[0,self.py*self.a0],\
[0,self.pz*self.a0]]
self.setElsProps()
self.setCrystal()
if self.setting['positions'] == 'rnd':
self.setRandomStructure()
self.setNumbers()
self.bulk.set_atomic_numbers(self.numbers)
def setNumbers(self):
self.numbers = []
for e in self.t1_:
self.numbers.append( self.elsProps[e - 1]['number'])
def setElsProps(self):
for e in self.setting['elements']:
a = ase.Atom(e)
mass = a.mass / _Nav
number = a.number
form = pt.formula(a.symbol)
e_ = form.structure[0][1]
crys = e_.crystal_structure['symmetry']
a_ = e_.crystal_structure['a']
self.elsProps.append({'ase':a, 'mass': mass, 'structure': crys,
'a':a_ , 'number':number})
def setCrystal(self):
crys = self.setting['structure']
if crys == 'rnd':
print 'rnd implemented'
self.genRandomPositions()
d = 1.104 # N2 bondlength
formula = 'Cu'+str(len(self.pos))
cell =[(self.px*self.a0,0,0),(0,self.py*self.a0,0),(0,0,self.pz*self.a0)]
self.bulk = ase.Atoms(formula, self.pos, pbc=True, cell=cell)
if crys == 'fcc':
print 'fcc implemented'
from ase.lattice.cubic import FaceCenteredCubic
self.bulk = FaceCenteredCubic(directions=[[1,0,0], [0,1,0], [0,0,1]],
size=(self.px,self.py,self.pz), symbol='Cu',
pbc=(1,1,1), latticeconstant=self.a0)
if crys == 'bcc':
print 'bcc implemented'
from ase.lattice.cubic import BodyCenteredCubic
self.bulk = BodyCenteredCubic(directions=[[1,0,0], [0,1,0], [0,0,1]],
size=(self.px,self.py,self.pz), symbol='Cu',
pbc=(1,1,1), latticeconstant=self.a0)
if self.setting['structure'] == 'hcp':
print 'hcp no implemented'
sys.exit(0)
self.setting['nAtoms'] = self.bulk.get_number_of_atoms()
self.calcAtoms2()
self.genStructure()
self.pos = self.bulk.get_positions()
def update (self):
cell = self.bulk.get_cell()
self.box =[[0, cell[0][0]],[0, cell[1][1]],[0, cell[2][2]]]
self.pos = self.bulk.get_positions()
def genStructure(self):
self.t1_ = []
for i,e in enumerate(self.setting['nAt']):
[self.t1_.append(i+1) for j in range(e)]
def setRandomStructure(self):
x = [int(random.random()*len(self.t1_)) for i in range(len(self.t1_))]
for i in range(len(x) - 1):
t1 = self.t1_[x[i]]
t2 = self.t1_[x[i+1]]
self.t1_[x[i]] = t2
self.t1_[x[i+1]] = t1
return self.pos, self.t1_, self.box
def genRandomPositions(self):
Lx = self.box[0][1]
Ly = self.box[1][1]
Lz = self.box[2][1]
self.pos =[]
for i in range(self.setting['nAtoms']):
x = random.random() * Lx
y = random.random() * Ly
z = random.random() * Lz
self.pos.append([x,y,z])
def getAtoms(self):
return self.elsProps
def Interaction (self):
if self.setting['pot'] == 'lj':
ljp = ljParameters.LjParameters()
str_ = ljp.lammpsInteraction(self.elsProps)
if self.setting['pot'] == 'zhou':
gz = zhou.calcPotentials(self.setting['elements'])
gz.createPot()
str_ = gz.lammpsZhouEam()
return str_
def calcAtoms2(self):
nAt = []
sum_ = 0
sumpc = 0.0000001
len_elements = len(self.setting['elements'])
len_pca = len(self.setting['pca'])
print 'calcAtom2', len_pca, len_elements
if len_elements != len_pca + 1:
print 'error len'
sys.exit(0)
for p in self.setting['pca']:
sumpc +=p
if sumpc >= 100 or sumpc <= 0:
print 'error pc'
sys.exit(0)
sumpc = 0
for i in range(len(self.setting['elements']) - 1):
p = self.setting['pca'][i]
sumpc +=p
t = int(p * self.setting['nAtoms'] / 100.0)
sum_ +=t
nAt.append(t)
nAt.append(self.setting['nAtoms'] - sum_)
self.setting['nAtoms'] = 0
for e in nAt:
self.setting['nAtoms'] +=e
print 'pca', self.setting['pca']
self.setting['nAt'] = nAt
def getMasess(self):
str_ =''
i = 1
for e in self.elsProps:
str_ += 'mass ' + str(i) + ' ' +str(e['mass']) + '\n'
i+=1
return str_
