In [20]:

    

%matplotlib notebook
import numpy as np
import matplotlib.pyplot as plt
import particlesim.api
import particlesim.helpers_for_tests
from mpl_toolkits.mplot3d import Axes3D


    

In [21]:

    

def create_system_conf_with_na_and_cl(num_na, num_cl, box_size = 6):
    particles = particlesim.helpers_for_tests.create_positions(box_size=box_size,number_of_particles=num_na+num_cl)
    na = {'sigma':1.21496,'epsilon':0.0469,'charge':1}
    cl = {'sigma':2.02234, 'epsilon':0.15,'charge':-1.0}
    return particlesim.api.SystemConfiguration(xyz=particles, 
                                                      sigmas=([na['sigma']]*num_na)+([cl['sigma']]*num_cl),
                                                      epsilons=[na['epsilon']]*num_na+[cl['epsilon']]*num_cl,
                                                      charges=[na['charge']]*num_na+[cl['charge']]*num_cl,
                                                      box_size=6)


    

In [22]:

    

def periodic_distance(part1,part2,box_size):
    return np.linalg.norm(0.5 * box_size- (part1 - part2 + 0.5 * box_size) % box_size)


    

In [23]:

    

num_na_glob=20
num_cl_glob=20
box_size_glob = 6
system_conf = create_system_conf_with_na_and_cl(num_na=num_na_glob,num_cl=num_cl_glob, box_size = box_size_glob)
sampler = particlesim.api.Sampler(system_configuration=system_conf)


    

In [24]:

    

%%time
traj1,potential = sampler.metropolis(iteration_number=1000,beta=100)


    

    




CPU times: user 2min 5s, sys: 99.9 ms, total: 2min 5s
Wall time: 2min 5s

In [25]:

    

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
rang_of_samples = -1

ax.scatter(traj1[rang_of_samples:,:num_na_glob,0], traj1[rang_of_samples:,:num_na_glob,1], traj1[rang_of_samples:,:num_na_glob,2],c='r')

ax.scatter(traj1[rang_of_samples:,num_na_glob:,0], traj1[rang_of_samples:,num_na_glob:,1], traj1[rang_of_samples:,num_na_glob:,2],c='b')

ax.set_xlim([0,box_size_glob])
ax.set_ylim([0,box_size_glob])
ax.set_zlim([0,box_size_glob])


    

    















    












    
Out[25]:





(0, 6)

In [27]:

    

%%time
system_conf._total_potential.longrange_energy(positions=system_conf.xyz)


    

    




CPU times: user 63.5 ms, sys: 24 µs, total: 63.5 ms
Wall time: 54 ms






    
Out[27]:





-5.7492553084106497

In [28]:

    

%%time
system_conf._total_potential.shortrange_energy(positions=system_conf.xyz)


    

    




CPU times: user 103 ms, sys: 4 ms, total: 107 ms
Wall time: 107 ms






    
Out[28]:





6376956.151901708

In [29]:

    

num_part = 100
num_na_glob=num_part//2
num_cl_glob=num_part//2
box_size_glob = 6
system_conf_test = create_system_conf_with_na_and_cl(num_na=num_na_glob,num_cl=num_cl_glob, box_size = box_size_glob)


    

In [30]:

    

%%time
for i in range(num_part):
    system_conf_test._total_potential.shortrange.nlist.get_particles_within_radius(i)


    

    




CPU times: user 543 ms, sys: 14 µs, total: 543 ms
Wall time: 538 ms

In [31]:

    

%%time
system_conf_test._total_potential.shortrange_energy(positions=system_conf_test.xyz)


    

    




CPU times: user 569 ms, sys: 4 ms, total: 573 ms
Wall time: 570 ms






    
Out[31]:





180247098.67432696

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