Dear users,
I am creating a dimer and applying for a loop for creating two dimer, but I am getting an error. It may be because of id. But I am unable to fix this problem. Can anyone help me?
The error is:
Exception Traceback (most recent call last)
<ipython-input-5-1e08fe5a06b8> in <module>
21 print(system.box_l)
22 # Place the central particle
---> 23 system.part.add(id=0, pos=colPos, type=0, q=q_col, fix=(1, 1, 1),
24 rotation=(1, 1, 1)) # Create central particle
25 print('done')
particle_data.pyx in espressomd.particle_data.ParticleList.add()
particle_data.pyx in espressomd.particle_data.ParticleList._place_new_particle()
Exception: Particle 0 already exists.
The program is:
system.thermostat.set_langevin(kT=0.00001, gamma=40., seed=42)
print("# Creating raspberry")
center = system.box_l / 2
colPos = center
# Charge of the colloid
q_col = -40
# Number of particles making up the raspberry (surface particles + the central particle).
#n_col_part = int(4 * np.pi * np.power(radius_col, 2) + 1)
n_col_part = int(1 + 1)
for j in range(2):
center = np.random.randn(3)
print(center)
center = system.box_l/2 + center/np.linalg.norm(center)*system.box_l/2
colPos = center
print(center)
print(system.box_l)
# Place the central particle
system.part.add(id=0, pos=colPos, type=0, q=q_col, fix=(1, 1, 1),
rotation=(1, 1, 1)) # Create central particle
print('done')
# Create surface beads uniformly distributed over the surface of the central particle
for i in range(1, n_col_part):
colSurfPos = np.random.randn(2)
colSurfPos = colSurfPos / np.linalg.norm(colSurfPos) * radius_col
print(colPos)
colSurfPos = np.append(colSurfPos,0)
print(colSurfPos)
colSurfPos = colSurfPos + colPos
print(colSurfPos)
system.part.add(id=i, pos=colSurfPos, type=1)
system.part[i].add_bond((col_center_surface_bond, 0))
print("# Number of colloid beads = {}".format(n_col_part))
system.force_cap = 1000
system.time_step = eq_tstep
print("Relaxation of the raspberry surface particles")
for i in range(n_cycle):
system.integrator.run(integ_steps)
# Restore time step
system.time_step = time_step
print("# Creating raspberry")
center = system.box_l / 2
colPos = center
# Charge of the colloid
q_col = -40
# Number of particles making up the raspberry (surface particles + the central particle).
#n_col_part = int(4 * np.pi * np.power(radius_col, 2) + 1)
n_col_part = int(1 + 1)
for j in range(2):
center = np.random.randn(3)
print(center)
center = system.box_l/2 + center/np.linalg.norm(center)*system.box_l/2
colPos = center
print(center)
print(system.box_l)
# Place the central particle
system.part.add(id=0, pos=colPos, type=0, q=q_col, fix=(1, 1, 1),
rotation=(1, 1, 1)) # Create central particle
print('done')
# Create surface beads uniformly distributed over the surface of the central particle
for i in range(1, n_col_part):
colSurfPos = np.random.randn(2)
colSurfPos = colSurfPos / np.linalg.norm(colSurfPos) * radius_col
print(colPos)
colSurfPos = np.append(colSurfPos,0)
print(colSurfPos)
colSurfPos = colSurfPos + colPos
print(colSurfPos)
system.part.add(id=i, pos=colSurfPos, type=1)
system.part[i].add_bond((col_center_surface_bond, 0))
print("# Number of colloid beads = {}".format(n_col_part))
system.force_cap = 1000
system.time_step = eq_tstep
print("Relaxation of the raspberry surface particles")
for i in range(n_cycle):
system.integrator.run(integ_steps)
# Restore time step
system.time_step = time_step
Your help will be highly appreciated.
Thanks & Regards
Chandra Shekhar Maurya
Mechanical Eng. Dept.
Indian Institute of Technology Patna
Contact No:9793572837