Re: Regarding creating more number of dimer using raspberry model

[Jean-Noël Grad]

Dear Chandra,

It is hard to tell, because your python script is interpreted as a 
markup language by most email processors and gets rendered in a way that 
is hard to read and copy-paste in a python terminal. It would be easier 
for the community to help if the script was attached as a text file.

From what I understand, your for loop seems to add a particle with id=0 
twice, which is not possible in ESPResSo. You can omit the argument id 
when calling system.part.add(), in which case ESPResSo automatically 
assigns a monotonically increasing id. This is the preferred way of 
creating particles, because the id is usually not a relevant piece of 
information for the user, and it can be retrieved easily from the system 
in the rare cases where it is relevant.

Hope this helps,
JN

On 12/10/20 2:58 PM, chandra shekhar maurya wrote:
> 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 ---> 23system.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
> *
> *
> *Your help will be highly appreciated.
> *
> *
> *
> *Thanks & Regards*
> Chandra Shekhar Maurya
> Mechanical Eng. Dept.
> Indian Institute of Technology Patna
> Contact No:9793572837