void
TensorMechanicsPlasticModel::dhardPotential_dintnlV(const RankTwoTensor & stress,
                                                    Real intnl,
                                                    std::vector<Real> & dh_dintnl) const
{
  dh_dintnl.resize(numberSurfaces(), dhardPotential_dintnl(stress, intnl));
}
void
MultiPlasticityLinearSystem::calculateJacobian(const RankTwoTensor & stress, const std::vector<Real> & intnl, const std::vector<Real> & pm, const RankFourTensor & E_inv, const std::vector<bool> & active, const std::vector<bool> & deactivated_due_to_ld, std::vector<std::vector<Real> > & jac)
{
  // see comments at the start of .h file

  mooseAssert(intnl.size() == _num_models, "Size of intnl is " << intnl.size() << " which is incorrect in calculateJacobian");
  mooseAssert(pm.size() == _num_surfaces, "Size of pm is " << pm.size() << " which is incorrect in calculateJacobian");
  mooseAssert(active.size() == _num_surfaces, "Size of active is " << active.size() << " which is incorrect in calculateJacobian");
  mooseAssert(deactivated_due_to_ld.size() == _num_surfaces, "Size of deactivated_due_to_ld is " << deactivated_due_to_ld.size() << " which is incorrect in calculateJacobian");


  unsigned ind = 0;
  unsigned active_surface_ind = 0;


  std::vector<bool> active_surface(_num_surfaces); // active and not deactivated_due_to_ld
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
    active_surface[surface] = (active[surface] && !deactivated_due_to_ld[surface]);
  unsigned num_active_surface = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
    if (active_surface[surface])
      num_active_surface++;

  std::vector<bool> active_model(_num_models); // whether a model has surfaces that are active and not deactivated_due_to_ld
  for (unsigned model = 0 ; model < _num_models ; ++model)
    active_model[model] = anyActiveSurfaces(model, active_surface);

  unsigned num_active_model = 0;
  for (unsigned model = 0 ; model < _num_models ; ++model)
    if (active_model[model])
      num_active_model++;

  ind = 0;
  std::vector<unsigned int> active_model_index(_num_models);
  for (unsigned model = 0 ; model < _num_models ; ++model)
    if (active_model[model])
      active_model_index[model] = ind++;
    else
      active_model_index[model] = _num_models+1; // just a dummy, that will probably cause a crash if something goes wrong



  std::vector<RankTwoTensor> df_dstress;
  dyieldFunction_dstress(stress, intnl, active_surface, df_dstress);

  std::vector<Real> df_dintnl;
  dyieldFunction_dintnl(stress, intnl, active_surface, df_dintnl);

  std::vector<RankTwoTensor> r;
  flowPotential(stress, intnl, active, r);

  std::vector<RankFourTensor> dr_dstress;
  dflowPotential_dstress(stress, intnl, active, dr_dstress);

  std::vector<RankTwoTensor> dr_dintnl;
  dflowPotential_dintnl(stress, intnl, active, dr_dintnl);

  std::vector<Real> h;
  hardPotential(stress, intnl, active, h);

  std::vector<RankTwoTensor> dh_dstress;
  dhardPotential_dstress(stress, intnl, active, dh_dstress);

  std::vector<Real> dh_dintnl;
  dhardPotential_dintnl(stress, intnl, active, dh_dintnl);




  // d(epp)/dstress = sum_{active alpha} pm[alpha]*dr_dstress
  RankFourTensor depp_dstress;
  ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
    if (active[surface]) // includes deactivated_due_to_ld
      depp_dstress += pm[surface]*dr_dstress[ind++];
  depp_dstress += E_inv;

  // d(epp)/dpm_{active_surface_index} = r_{active_surface_index}
  std::vector<RankTwoTensor> depp_dpm;
  depp_dpm.resize(num_active_surface);
  ind = 0;
  active_surface_ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
  {
    if (active[surface])
    {
      if (active_surface[surface]) // do not include the deactived_due_to_ld, since their pm are not dofs in the NR
        depp_dpm[active_surface_ind++] = r[ind];
      ind++;
    }
  }

  // d(epp)/dintnl_{active_model_index} = sum(pm[asdf]*dr_dintnl[fdsa])
  std::vector<RankTwoTensor> depp_dintnl;
  depp_dintnl.assign(num_active_model, RankTwoTensor());
  ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
  {
    if (active[surface])
    {
      unsigned int model_num = modelNumber(surface);
      if (active_model[model_num]) // only include models with surfaces which are still active after deactivated_due_to_ld
        depp_dintnl[active_model_index[model_num]] += pm[surface]*dr_dintnl[ind];
      ind++;
    }
  }


  // df_dstress has been calculated above
  // df_dpm is always zero
  // df_dintnl has been calculated above, but only the active_surface+active_model stuff needs to be included in Jacobian: see below

  std::vector<RankTwoTensor> dic_dstress;
  dic_dstress.assign(num_active_model, RankTwoTensor());
  ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
  {
    if (active[surface])
    {
      unsigned int model_num = modelNumber(surface);
      if (active_model[model_num]) // only include ic for models with active_surface (ie, if model only contains deactivated_due_to_ld don't include it)
        dic_dstress[active_model_index[model_num]] += pm[surface]*dh_dstress[ind];
      ind++;
    }
  }


  std::vector<std::vector<Real> > dic_dpm;
  dic_dpm.resize(num_active_model);
  ind = 0;
  active_surface_ind = 0;
  for (unsigned model = 0 ; model < num_active_model ; ++model)
    dic_dpm[model].assign(num_active_surface, 0);
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
  {
    if (active[surface])
    {
      if (active_surface[surface]) // only take derivs wrt active-but-not-deactivated_due_to_ld pm
      {
        unsigned int model_num = modelNumber(surface);
        // if (active_model[model_num]) // do not need this check as if the surface has active_surface, the model must be deemed active!
          dic_dpm[active_model_index[model_num]][active_surface_ind] = h[ind];
        active_surface_ind++;
      }
      ind++;
    }
  }


  std::vector<std::vector<Real> > dic_dintnl;
  dic_dintnl.resize(num_active_model);
  for (unsigned model = 0 ; model < num_active_model ; ++model)
  {
    dic_dintnl[model].assign(num_active_model, 0);
    dic_dintnl[model][model] = 1; // deriv wrt internal parameter
  }
  ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
  {
    if (active[surface])
    {
      unsigned int model_num = modelNumber(surface);
      if (active_model[model_num]) // only the models that contain surfaces that are still active after deactivation_due_to_ld
        dic_dintnl[active_model_index[model_num]][active_model_index[model_num]] += pm[surface]*dh_dintnl[ind];
      ind++;
    }
  }



  unsigned int dim = 3;
  unsigned int system_size = 6 + num_active_surface + num_active_model; // "6" comes from symmeterizing epp
  jac.resize(system_size);
  for (unsigned i = 0 ; i < system_size ; ++i)
    jac[i].assign(system_size, 0);

  unsigned int row_num = 0;
  unsigned int col_num = 0;
  for (unsigned i = 0 ; i < dim ; ++i)
    for (unsigned j = 0 ; j <= i ; ++j)
    {
      for (unsigned k = 0 ; k < dim ; ++k)
        for (unsigned l = 0 ; l <= k ; ++l)
          jac[col_num][row_num++] = depp_dstress(i, j, k, l) + (k != l ? depp_dstress(i, j, l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
      for (unsigned surface = 0 ; surface < num_active_surface ; ++surface)
        jac[col_num][row_num++] = depp_dpm[surface](i, j);
      for (unsigned a = 0 ; a < num_active_model ; ++a)
        jac[col_num][row_num++] = depp_dintnl[a](i, j);
      row_num = 0;
      col_num++;
    }

  ind = 0;
  for (unsigned surface = 0 ; surface < _num_surfaces ; ++surface)
    if (active_surface[surface])
    {
      for (unsigned k = 0 ; k < dim ; ++k)
        for (unsigned l = 0 ; l <= k ; ++l)
        jac[col_num][row_num++] = df_dstress[ind](k, l) + (k != l ? df_dstress[ind](l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
      for (unsigned beta = 0 ; beta < num_active_surface ; ++beta)
        jac[col_num][row_num++] = 0; // df_dpm
      for (unsigned model = 0 ; model < _num_models ; ++model)
        if (active_model[model]) // only use df_dintnl for models in active_model
        {
          if (modelNumber(surface) == model)
            jac[col_num][row_num++] = df_dintnl[ind];
          else
            jac[col_num][row_num++] = 0;
        }
      ind++;
      row_num = 0;
      col_num++;
    }

  for (unsigned a = 0 ; a < num_active_model ; ++a)
  {
    for (unsigned k = 0 ; k < dim ; ++k)
      for (unsigned l = 0 ; l <= k ; ++l)
        jac[col_num][row_num++] = dic_dstress[a](k, l) + (k != l ? dic_dstress[a](l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
    for (unsigned alpha = 0 ; alpha < num_active_surface ; ++alpha)
      jac[col_num][row_num++] = dic_dpm[a][alpha];
    for (unsigned b = 0 ; b < num_active_model ; ++b)
      jac[col_num][row_num++] = dic_dintnl[a][b];
    row_num = 0;
    col_num++;
  }

  mooseAssert(col_num == system_size, "Incorrect filling of cols in Jacobian");
}
void
FiniteStrainPlasticBase::calculateJacobian(const RankTwoTensor & stress, const std::vector<Real> & intnl, const std::vector<Real> & pm, const RankFourTensor & E_inv, std::vector<std::vector<Real> > & jac)
{
  // construct quantities used in the Newton-Raphson linear system
  // These should have been defined by the derived classes, if
  // they are different from the default functions given elsewhere
  // in this class
  std::vector<RankTwoTensor> df_dstress;
  dyieldFunction_dstress(stress, intnl, df_dstress);

  std::vector<std::vector<Real> > df_dintnl;
  dyieldFunction_dintnl(stress, intnl, df_dintnl);

  std::vector<RankTwoTensor> r;
  flowPotential(stress, intnl, r);

  std::vector<RankFourTensor> dr_dstress;
  dflowPotential_dstress(stress, intnl, dr_dstress);

  std::vector<std::vector<RankTwoTensor> > dr_dintnl;
  dflowPotential_dintnl(stress, intnl, dr_dintnl);

  std::vector<std::vector<Real> > h;
  hardPotential(stress, intnl, h);

  std::vector<std::vector<RankTwoTensor> > dh_dstress;
  dhardPotential_dstress(stress, intnl, dh_dstress);

  std::vector<std::vector<std::vector<Real> > > dh_dintnl;
  dhardPotential_dintnl(stress, intnl, dh_dintnl);


  // construct matrix entries
  // In the following
  // epp = pm*r - E_inv*(trial_stress - stress) = pm*r - delta_dp
  // f = yield function
  // ic = intnl - intnl_old + pm*h

  RankFourTensor depp_dstress;
  for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
    depp_dstress += pm[alpha]*dr_dstress[alpha];
  depp_dstress += E_inv;

  std::vector<RankTwoTensor> depp_dpm;
  depp_dpm.resize(numberOfYieldFunctions());
  for (unsigned alpha = 0; alpha < numberOfYieldFunctions() ; ++alpha)
    depp_dpm[alpha] = r[alpha];

  std::vector<RankTwoTensor> depp_dintnl;
  depp_dintnl.assign(numberOfInternalParameters(), RankTwoTensor());
  for (unsigned a = 0; a < numberOfInternalParameters() ; ++a)
    for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
      depp_dintnl[a] += pm[alpha]*dr_dintnl[alpha][a];

  // df_dstress has been calculated above
  // df_dpm is always zero
  // df_dintnl has been calculated above

  std::vector<RankTwoTensor> dic_dstress;
  dic_dstress.assign(numberOfInternalParameters(), RankTwoTensor());
  for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
    for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
      dic_dstress[a] += pm[alpha]*dh_dstress[a][alpha];

  std::vector<std::vector<Real> > dic_dpm;
  dic_dpm.resize(numberOfInternalParameters());
  for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
  {
    dic_dpm[a].resize(numberOfYieldFunctions());
    for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
      dic_dpm[a][alpha] = h[a][alpha];
  }

  std::vector<std::vector<Real> > dic_dintnl;
  dic_dintnl.resize(numberOfInternalParameters());
  for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
  {
    dic_dintnl[a].assign(numberOfInternalParameters(), 0);
    for (unsigned b = 0 ; b < numberOfInternalParameters() ; ++b)
      for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
        dic_dintnl[a][b] += pm[alpha]*dh_dintnl[a][alpha][b];
    dic_dintnl[a][a] += 1;
  }


  /**
   * now construct the Jacobian
   * It is:
   * ( depp_dstress depp_dpm depp_dintnl )
   * (  df_dstress       0      df_dintnl   )
   * ( dic_dstress    dic_dpm   dic_dintnl  )
   * For the "epp" terms, only the i>=j components are kept in the RHS, so only these terms are kept here too
   */

  unsigned int dim = 3;
  unsigned int system_size = 6 + numberOfYieldFunctions() + numberOfInternalParameters(); // "6" comes from symmeterizing epp
  jac.resize(system_size);
  for (unsigned i = 0 ; i < system_size ; ++i)
    jac[i].resize(system_size);

  unsigned int row_num = 0;
  unsigned int col_num = 0;
  for (unsigned i = 0 ; i < dim ; ++i)
    for (unsigned j = 0 ; j <= i ; ++j)
    {
      for (unsigned k = 0 ; k < dim ; ++k)
        for (unsigned l = 0 ; l <= k ; ++l)
          jac[col_num][row_num++] = depp_dstress(i, j, k, l) + (k != l ? depp_dstress(i, j, l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
      for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
        jac[col_num][row_num++] = depp_dpm[alpha](i, j);
      for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
        jac[col_num][row_num++] = depp_dintnl[a](i, j);
      row_num = 0;
      col_num++;
    }

  for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
  {
    for (unsigned k = 0 ; k < dim ; ++k)
      for (unsigned l = 0 ; l <= k ; ++l)
        jac[col_num][row_num++] = df_dstress[alpha](k, l) + (k != l ? df_dstress[alpha](l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
    for (unsigned beta = 0 ; beta < numberOfYieldFunctions() ; ++beta)
      jac[col_num][row_num++] = 0;
    for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
      jac[col_num][row_num++] = df_dintnl[alpha][a];
    row_num = 0;
    col_num++;
  }

  for (unsigned a = 0 ; a < numberOfInternalParameters() ; ++a)
  {
    for (unsigned k = 0 ; k < dim ; ++k)
      for (unsigned l = 0 ; l <= k ; ++l)
        jac[col_num][row_num++] = dic_dstress[a](k, l) + (k != l ? dic_dstress[a](l, k) : 0); // extra part is needed because i assume dstress(i, j) = dstress(j, i)
    for (unsigned alpha = 0 ; alpha < numberOfYieldFunctions() ; ++alpha)
      jac[col_num][row_num++] = dic_dpm[a][alpha];
    for (unsigned b = 0 ; b < numberOfInternalParameters() ; ++b)
      jac[col_num][row_num++] = dic_dintnl[a][b];
    row_num = 0;
    col_num++;
  }
}