issue #70 - correction calculation with soil

[baugetfa]

The first 4 commits (9d42bc3, 5c0fdb2, 0bb808d, e87dd27) are also on branch psi_equivalent and PR #69.

I probably created the branch psi_equivalent from the solver_wrapper branch

[baugetfa]

The solute-water solver is limited at this stage to uniform external condition. This is not a bug or an error because in the function the external potential or pressure are set explicitly uniform. Here again this because they were developed for uniform conditions. This easy to change.

[baugetfa]

Still in the Flux class the case where invert_model = False , never used, should, if I well understood, distributes the flux according to the Jv given. But the code below do in fact calculate nothing else than psi_in. And for me it is not correct because psi_e and psi_base are input by definition then the potential inside the root are fixed by the boundary conditions and Jv. If we distribute the flux something must adapt and it is not the case, and it can not unless K and/or k. I am for deleting this case.

  if not(invert_model) : # distribute a given output into the root system

      #print 'entering Jv distribution'

      for v in traversal.pre_order2(g, v_base):
      #compute psi according to Millman theorem, then compute radial flux
          parent = g.parent(v)
          brothers = g.children_iter(parent)
          children = g.children(v) # prefer list because used twice

          Keq_brothers = sum( Keq[cid] for cid in brothers)
          Keq_children = sum( Keq[cid] for cid in children)

          if parent is None:
              assert v == v_base
              psi_out[v] = psi_base
              J_out[v] = Jv
          else:
              psi_out[v] = psi_in[parent]
              J_out[v] = (J_out[parent] - j[parent]) / ( 1.0 + Keq_brothers / Keq[v]  ) # only if no_soil

          if not self.HAS_SOIL:
              psi_in[v] = (K[v] * psi_out[v] + psi_e * (k[v] + Keq_children)) / (k[v] + K[v] + Keq_children)
              j[v] = (psi_e - psi_in[v]) * k[v]
          else:
              # psi_in[v] = (K[v] * psi_out[v] + psi_e[v] * (k[v] + Keq_children)) / (k[v] + K[v] + Keq_children)
              KeqPeq = sum( Peq[cid]*Keq[cid] for cid in children )
              psi_in[v] = (K[v] * psi_out[v] + psi_e[v] * k[v] + KeqPeq) / (k[v] + K[v] + Keq_children)
              j[v] = (psi_e[v] - psi_in[v]) * k[v]

[baugetfa]

I closed it because I replaced it by PR #72. There were some commits from different branches and PR.