Я хочу прочитать данные из двух разных файлов. В моем коде у меня есть два полимерных объекта, и я хочу прочитать их начальные координаты из файла CSV. На данный момент я могу прочитать только один файл. Может кто-нибудь подсказать, как я могу это сделать за секунду?
Вот полный код и метод, использованный для чтения первого файла.
#Define an object called 'monomer' which consists of a position (list with 3 entries)
class monomer:
def __init__(self, pos):
# assign the given position to the 'pos' attribute
self.pos = pos
#self.m = np.loadtxt('traj_T_4.csv')
@classmethod
def from_file(cls, filename):
instances = []
with open(filename, 'r') as file:
for line in file:
pos = str(map(float, line.split(',')))
instances.append(cls(pos))
return instances
def LJ(self, other):
# Define the LJ interaction between one and another monomer
# Calculate the distance between position of one and the other monomer
rij =self.distance(other)
sig_by_r6 = np.power(sigma**2 / rij, 6)
sig_by_r12 = np.power(sigma**2 / rij, 12)
return 4*epsilon*(sig_by_r12 - sig_by_r6)
def FENE(self, other):
rij =self.distance(other)
fene = (-0.5 * K * np.power(R,2) * np.log(1 - ((np.sqrt(rij) - r0) / R)**2))
if not np.isfinite(fene): # Make sure, that NaN (or - infinity) values (because of the log) are never passed to the energy calculation, as the programme behaves uncontrollably then
return float("inf") # Rather return infinity, since this will always fail the energy comparison
else:
return fene
def distance(self, other):
return np.linalg.norm(list(np.array(self.pos) - np.array(other.pos)))
def shift(self, vector):
# Move a monomer by 'vector'
self.pos += vector
# Define an object called 'polymer', which is a chain (list) of monomer objects
class polymer:
def __init__(self, base, N):
self.chain = []
# append each monomer to the polymer's chain
# base (list of 2) represents the initial x and y value of all monomers
for i in range(N):
self.chain.append( monomer([base[0], base[1], i*0.7]) )
def FENE_Energy(self):
# Define polymer FENE energy as sum of FENE interactions between bonded monomers
fene = 0.0
for i in range(N-1):
fene += self.chain[i].FENE(self.chain[i+1])
return fene
def LJ_Energy(self):
LJ = 0.0
for i in range(N):
for j in range(N):
if np.absolute(i-j) > 1:
if self.chain[i].distance(self.chain[j]) < rcutoff: # LJ only for non-bonded monomers, i.e. distance is greater than 1
LJ += self.chain[i].LJ(self.chain[j])
return LJ/2.
def Energy(self):
return self.LJ_Energy() + self.FENE_Energy()
def move(self): # Method returns a 'polymer' object, which is either the same as put in or a shifted one
backup = copy.deepcopy(self) # "backup = self" does not work as expected, as 'backup' becomes a mere synonym of 'self', but not an independent (immutable) object, as intended
monomer_index = np.random.randint(low=1, high=N) # choose a random monomer but 0, since it is grafted
direction = np.random.rand(3) - [0.5, 0.5, 0.5] # random vector consists of movement between [-0.5, -0.5, -0.5] and [0.5, 0.5, 0.5]
self.chain[monomer_index].shift(direction)
if self.chain[monomer_index].pos[2] < 0.0:
return backup
rnd = np.random.rand(1)
deltaE = self.Energy() - backup.Energy()
if np.exp(-(1/k_B*T)*deltaE) < rnd:
return backup
else:
return self # return the shifted polymer
if __name__ == "__main__":
list_of_monomers = monomer.from_file('monomer.csv')
list_of_monomers = monomer.from_file('monomer1.csv')
K = 40.0
R = 0.3
r0 = 0.7
sigma = r0/2**6
rcutoff = 2.5*sigma
epsilon = 1.0
max_delta = 0.21 # -sigma/10 to sigma/10
N = 20
k_B = 1
T = 4.0
shifts = 100
# Declare two variables to be 'polymers'
pol1 = polymer([-r0/2, 0.0], N)
pol2 = polymer([ r0/2, 0.0], N)