How to add pores into a given network and assign them with different diameters?

[Camelot18]

Dear Prof. Gostick,

I want to add new pores into the created pore network to label them as "hydrate", assign them diameters, and put them in specific positions before exporting the data. However, the openpnm.topotools.extend(network, coords=[], conns=[], labels=[], **kwargs) I used didn't work for adding new geometry size of hydrate(pores). Could you please help with this?

for i in range(np.size(x)):
    op.topotools.extend(network = net, coords=[(x[i],y[i],z[i])], labels=['hydrate'])
   
for j in net.filter_by_label(pores=net['pore.all'], labels='pore.hydrate'):
    net['pore.diameter'][j] = r_h3[1]*net['pore.diameter'][j-2954]

The returned length of net['pore.diameter'] is still 2954. How can I build the new pore network(the initial network + new pores) in this case?

Many thanks in advance!
Peter

[jgostick]

I'm not totally sure what your doing in the second loop, but the first one looks ok to me. So you're saying that net.Np is 2954 both before AND after running that first loop? Not that you could try to just add all the x,y,z coords at once. I think
op.topotools.extend(network = net, coords=np.vstack((x, y, z)), labels=['hydrate']) should work (or use np.hstack, depending on the shape of x, y and z).

[Camelot18]

Sorry for the late reply.
The first loop will double the length of net['pore'](the initial size is 2954 and now turns to 5908), while the length of net['pore.hydrate'] is also 5908 but the first 2954 elements are 'false'. The second loop attempts to add geometry to the net['pore.hydrate'] but doesn't work. The idea is to creat the same number of spheres within the pores with customsized diameters and random positions, but I need to label them as 'hydrate'.

Besides, when I tried to use op.io.STL.export_data(network=net, filename='imported_pn_hfs'), it returned with "local variable 'csg' referenced before assignment". How to fix this?

Thanks again!