def checkbalance(bot, update, args):
equation = "".join(args)
user = Chemistry(equation)
if user.check_equation():
# if equation is written right
balanced = user.printifBalanced()
if balanced == False:
# if something went wrong during the balance
bot.send_message(chat_id=update.message.chat_id,
text=chemistry.balance_error)
equation_example(bot, update)
else:
# if it went all right
bot.send_message(chat_id=update.message.chat_id, text=balanced)
else:
# if equation wasn't written right
bot.send_message(chat_id=update.message.chat_id,
text=chemistry.balance_error)
equation_example(bot, update)
def getElements(bot, update, args):
equation = "".join(args)
user = Chemistry(equation)
if user.check_equation():
# if equation is written right
elements = user.returnElements()
if elements == False:
# if something went wrong during the balance
bot.send_message(chat_id=update.message.chat_id,
text=chemistry.balance_error)
equation_example(bot, update)
else:
# if it went all right
bot.send_message(chat_id=update.message.chat_id, text=elements)
else:
# if equation wasn't written right
bot.send_message(chat_id=update.message.chat_id,
text=chemistry.balance_error)
equation_example(bot, update)
def __init__(self,
file_name_preq,
file_name_opt,
heteroatom_list,
epochs,
percents,
population_size=4,
code_mode='binary'):
self.population_size = population_size
self.code = Code(file_name_preq, file_name_opt, heteroatom_list,
code_mode)
self.epochs = epochs
self.percents = percents
self.percents = self.distribute()
self.population = self.code.generate_population(self.population_size)
self.current_epoch = 0
self.heteroatom_list = heteroatom_list
self.chemistry = Chemistry(self.population_size)
self._write_file()
self._write_head_lines()
def balance(bot, update, args):
equation = "".join(args)
user = Chemistry(equation)
if user.check_equation():
# if the equation is written right
balanced = user.balance()
if balanced == False:
# if something went wrong during the balance
bot.send_message(chat_id=update.message.chat_id,
text="Something"
" went wrong during the balance of the equation.")
equation_example(bot, update)
else:
# went all right
bot.send_message(chat_id=update.message.chat_id, text=balanced)
else:
# if the equation isn't written right
bot.send_message(chat_id=update.message.chat_id,
text="Something went "
"wrong during the balance of the equation.")
equation_example(bot, update)
import random from sys import argv from chemistry import Chemistry #random.seed(0) chemfile = 'data/world.chem' if len(argv) > 2: chemfile = argv[2] chem = Chemistry(open(chemfile).read()) quantities = [random.randint(0, 100) for i in chem.species] total_matter = sum(quantities) # iteration previous_quantities = [1] iterations = 0 print quantities while quantities != previous_quantities and iterations < 1000: previous_quantities = quantities quantities = chem.react(list(previous_quantities)) iterations += 1 print quantities print 'starting matter:', total_matter print 'end matter:', sum(quantities) print 'iterations:', iterations
if self.iterr < -1 :
n = self.n*(self.nspecies+1)
q[-1] = q[-5]
q[-2] = q[-6]
q[-3] = q[-7]
q[-4] = q[-8]
print "boundary"
def postprocess(self, q):
pass
if __name__ == "__main__":
#species = ['A', 'B', 'C', 'D']
species = ['A2', 'B2', 'C2', 'D2']#, 'B2', 'C10A10']
enthalpy = [0.0, 0.0, 1.5e6/2, 0.0]
S_minf = [300.0, 0.1, 0.1, 0.1, 0.7]#, 0.3, 0.5]
S_pinf = [900.0, 0.0, 0.0, 0.0, 1.0]#, 0.0, 0.0]
c = Chemistry(species, enthalpy)
# reaction = {'equation':'A = B', 'A': 1e9, 'b': 1.0, 'Ta':14000.0, 'Q': 1.5e6}
# c.add_reaction(reaction)
# reaction = {'equation':'D = C', 'A': 1e9, 'b': 1.0, 'Ta':14000.0, 'Q': 1.5e6}
# c.add_reaction(reaction)
# reaction = {'equation':'C = D', 'A': 1e9, 'b': 1.0, 'Ta':14000.0, 'Q': -1.5e6}
# c.add_reaction(reaction)
# reaction = {'equation':'B = A', 'A': 1e9, 'b': 1.0, 'Ta':14000.0, 'Q': -1.5e6}
# c.add_reaction(reaction)
#reaction = {'equation':'A2 = C2', 'A': 1e9, 'b': 1.0, 'Ta':14000.0}
#c.add_reaction(reaction)
import random
from sys import argv
from chemistry import Chemistry
#random.seed(0)
chemfile = 'data/world.chem'
if len(argv) > 2: chemfile = argv[2]
chem = Chemistry(open(chemfile).read())
quantities = [random.randint(0, 100) for i in chem.species]
total_matter = sum(quantities)
# iteration
previous_quantities = [1]
iterations = 0
print quantities
while quantities != previous_quantities and iterations < 1000:
previous_quantities = quantities
quantities = chem.react(list(previous_quantities))
iterations += 1
print quantities
print 'starting matter:', total_matter
print 'end matter:', sum(quantities)
print 'iterations:', iterations
class GenePopulation:
def __init__(self,
file_name_preq,
file_name_opt,
heteroatom_list,
epochs,
percents,
population_size=4,
code_mode='binary'):
self.population_size = population_size
self.code = Code(file_name_preq, file_name_opt, heteroatom_list,
code_mode)
self.epochs = epochs
self.percents = percents
self.percents = self.distribute()
self.population = self.code.generate_population(self.population_size)
self.current_epoch = 0
self.heteroatom_list = heteroatom_list
self.chemistry = Chemistry(self.population_size)
self._write_file()
self._write_head_lines()
def _write_file(self):
os.makedirs('generations/generation{}'.format(self.current_epoch))
for i, v in enumerate(self.population):
self.code.generate_file(self.current_epoch, i, v)
time.sleep(0.1)
def _write_head_lines(self):
with open('log.txt', 'w') as f:
f.write('***********************************************\n')
f.write('Genetic Algorithm in search of optimal material\n')
f.write('***********************************************\n')
f.write('initial population size: {}, maximum epoch: {}\n'.format(
self.population_size, self.epochs))
f.write('***********************************************\n')
f.write('heteroatom_list: {}\n'.format(self.heteroatom_list))
f.write('***********************************************\n')
f.write(
'population distribution percent:\n fit: {}; switch: {}; mutate: {}; random: {}\n'
.format(self.percents[0], self.percents[1], self.percents[2],
self.percents[3]))
f.write('***********************************************\n')
time.sleep(0.1)
def _write_fitness(self, cal_results):
with open('log.txt', 'a') as f:
f.write('***********************************************\n')
f.writelines(['\n', 'epoch: {}\n'.format(self.current_epoch)])
for i, result in enumerate(cal_results):
f.write('No.{} individual {}, fitness {}\n'.format(
i, result[0], result[1]))
f.write('***********************************************\n')
time.sleep(0.1)
def cal_fitness(self, percent):
self.write_message('starting to cal fitness')
cal_results = self.chemistry.cal_fitness(self.current_epoch)
self._write_fitness(cal_results)
new_population = []
for i in range(int(percent), 0, -1):
idx = list(cal_results.items())[0]
new_population.append(self.population[idx])
self.population = new_population
def switch(self, percent):
self.write_message('starting to switch')
new_population_list = []
for i in range(int(percent)):
random_idx = np.random.randint(0, len(self.population), 2)
rand_point = np.random.randint(0, self.code.get_sequence_len(), 1)
new_individual = self.population[random_idx[0]]
new_individual[rand_point[0]:] = self.population[
random_idx[1]][rand_point[0]:]
new_population_list.append(new_individual)
self.population.extend(new_population_list)
def mutate(self, percent):
self.write_message('starting to mutate')
new_population_list = []
for i in range(int(percent)):
new_individual = self.population[np.random.randint(
0, len(self.population), 1)[0]]
mutate_idx = np.random.randint(0, self.code.get_sequence_len(), 1)
new_individual[mutate_idx[0]] = self.code.random_mutation(
new_individual[mutate_idx[0]])
new_population_list.append(new_individual)
self.population.extend(new_population_list)
def random(self, percent):
self.write_message('starting to random')
new_population = self.code.generate_population(int(percent))
self.population.extend(new_population)
def iterate(self):
while self.current_epoch <= self.epochs:
self.cal_fitness(self.percents[0])
self.switch(self.percents[1])
self.mutate(self.percents[2])
self.random(self.percents[3])
self.current_epoch += 1
self._write_file()
@staticmethod
def write_message(message):
with open('log.txt', 'a') as f:
f.write('***********************************************\n')
f.write(message + '\n')
time.sleep(0.1)
def distribute(self):
leftover = 0.0
distributed_total = []
for weight in self.percents:
weight = float(weight)
leftover, weighted_value = modf(weight * self.population_size +
leftover)
distributed_total.append(weighted_value)
distributed_total[-1] = round(distributed_total[-1] +
leftover) # mitigate round off errors
distributed_total[0], distributed_total[-1] = distributed_total[
-1], distributed_total[0]
return distributed_total
# generate unform mesh
uniform_grid = UniformGrid(N,PG_min,PG_max,PG_ref, T_ref, -z_ref, rho_ref)
print "mesh generated.","N =",N
"""
Diffusion object
"""
print "Diffusion solver setup..."
diffusion_solver = ExplicitDiffusion(K,uniform_grid)
"""
chemsitry object
"""
print "chemistry solver setup..."
chemistry_obj = Chemistry(mechanism_path,composition,uniform_grid,atol,rtol)
print "Number of species:", chemistry_obj.gas.n_species, "Number of reactions:",chemistry_obj.gas.n_reactions
print "The absolute error is", chemistry_obj.network.atol, "The relative error is", chemistry_obj.network.rtol
"""
time evolution
"""
print "Initialize the composition..."
if restart == 0:
# a new run, start from equilibrium abundances
y = chemistry_obj.equilibrate()
# write equilibrium values into files
np.savetxt('./output/y_equilibrium.txt',y)
t_0 = 0
else:
# restart
