def binding_energy():
print('Binding Energy -------------')
d = np.linspace(5, 25, 5).tolist()
data = {}
means = []
errors = []
time_data = []
for i in d:
variable_finals = []
for _ in range(3):
number_of_seconds = 1 # i.e. 1 hour = 3600 seconds
model = Master(dimension=1000,
binding_energy=int(i),
time_unit=10e-3,
number_of_receptors=2,
receptor_length=100,
number_of_nanoparticles=1,
nanoparticle_radius=50,
number_of_ligands=2,
ligand_length=7,
binding_distance=4,
receptor_radius=3,
ligand_radius=3,
cell_diffusion_coef=1)
model.create_receptors() # 100 nm for receptor
model.create_nanoparticles_and_ligands(
) # 1-2 nm for ligand # 95 particles
print(
f'{model.dimension/1000} μm\u00b3 system, {model.binding_energy} binding energy, {model.number_of_nanoparticles} Nanoparticles,\n'
f'{model.nanoparticle_radius} nm Nanoparticle Radius, {model.number_of_ligands} Ligands, Ligand length {model.ligand_length} nm,\n'
f'{model.number_of_receptors} Receptors, {model.receptor_length} nm Receptor length, {model.binding_distance} Binding distance'
)
model.run(steps=number_of_seconds) # 3600 for 1 hour
print(f'The surface coverage is {model.surface_coverage}')
variable_finals.append(model.surface_coverage)
time_data.append(np.array(model.coverage))
mean_time = np.mean(time_data, axis=0)
error_time = np.std(time_data, axis=0)
data[f'{model.binding_energy} KT binding energy '] = np.array(
[list(range(0, model.time + 1)), mean_time, error_time])
mean_coverage = np.mean(np.array(variable_finals))
print(f'The mean surface coverage is {mean_coverage}')
errors.append(np.std(np.array(variable_finals)))
means.append(np.mean(np.array(variable_finals)))
plt.xlabel('Time (milliseconds)')
plt.ylabel('Surface Coverage')
for key, value in data.items():
plt.plot(value[0], value[1], label=key)
plt.fill_between(value[0],
value[1] - value[2],
value[1] + value[2],
alpha=0.2)
plt.legend()
plt.show()
second_variable_plot('Binding energy (kt)', 'Surface Coverage', d, means,
errors)
import sys
import os
import shutil
sys.path.append('src')
from Master import Master
if os.path.exists('Testing/Master'):
shutil.rmtree('Testing/Master')
m = Master(name = 'Server01', debug=True, destination_folder='Testing/Master', expected_connections=2)
m.setServer(host='localhost', port=8080)
m.setDelimeter(':::')
m.run()
if __name__ == '__main__':
if len(sys.argv) != 2:
print("ERROR: Expected 1 argument")
sys.exit()
mode = sys.argv[1]
permitted_modes = ['word_count', 'inverted_index']
if mode not in permitted_modes:
print("ERROR: Given mode not supported")
print("Permitted Modes:")
print(permitted_modes)
sys.exit()
f = open('config.json', 'r')
config = json.loads(f.read())
config = config[mode]
network_config = get_network_config(config['network_config'])
input_data = config['input_data']
mapper_count = config['n_mappers']
reducer_count = config['n_reducers']
output_data = config['output_data']
map_fn = get_map_method(config['map_fn'])
reduce_fn = get_reduce_method(config['reduce_fn'])
master = Master(network_config, [], mapper_count, reducer_count, map_fn, reduce_fn, input_data, output_data)
master.run()
