Introduction

To provide more flexibility and to reduce the number of configuration parameters, certain methods can be customized by users. For example to use custom grid refinement or to write custom output.

List of methods that can be modified

  !> User-defined refinement routine
  procedure(af_subr_ref), pointer :: user_refine => null()
 
  !> If defined, call this routine after setting initial conditions
  procedure(af_subr), pointer :: user_initial_conditions => null()
 
  !> If defined, call this routine after a new voltage pulse starts
  procedure(af_subr), pointer :: user_new_pulse_conditions => null()
 
  !> To set custom boundary conditions for the electric potential
  procedure(af_subr_bc), pointer :: user_potential_bc => null()
 
  !> To set a user-defined gas number density
  procedure(gas_dens_func), pointer :: user_gas_density => null()
 
  !> To set the field amplitude manually
  procedure(field_func), pointer :: user_field_amplitude => null()
 
  !> Generic procedure that is called every time step
  procedure(generic_subr), pointer :: user_generic_method => null()
 
  !> To write a custom log file
  procedure(log_subr), pointer :: user_write_log => null()
 
  !> To add entries to the log file
  procedure(log_vars), pointer :: user_log_variables => null()
 
  !> Custom level-set function to define an electrode
  procedure(mg_func_lsf), pointer :: user_lsf => null()
 
  !> Function to get boundary value for level set function
  procedure(mg_func_lsf), pointer :: user_lsf_bc => null()

How to set a custom method

In the m_user.f90 file, first add your custom routine. For example, it could be a method for initial conditions called my_init_cond. This method can then be activated in the user_initialize subroutine:

subroutine user_initialize(cfg, tree)
    type(CFG_t), intent(inout) :: cfg
    type(af_t), intent(inout) :: tree

    user_initial_conditions => my_init_cond
end subroutine user_initialize

Interfaces of the methods

For some of the interfaces, check out the Afivo documentation. The other interfaces are listed below.

     subroutine log_subr(tree, filename, out_cnt)
       import
       type(af_t), intent(in)      :: tree
       character(len=*), intent(in) :: filename
       integer, intent(in)          :: out_cnt
     end subroutine log_subr
 
     subroutine log_vars(tree, n_vars, var_names, var_values)
       import
       type(af_t), intent(in)                 :: tree
       integer, intent(out)                   :: n_vars
       character(len=name_len), intent(inout) :: var_names(user_max_log_vars)
       real(dp), intent(inout)                :: var_values(user_max_log_vars)
     end subroutine log_vars
 
     function gas_dens_func(box, IJK) result(dens)
       import
       type(box_t), intent(in) :: box
       integer, intent(in)     :: IJK
       real(dp)                :: dens
     end function gas_dens_func
 
     function field_func(tree, time) result(amplitude)
       import
       type(af_t), intent(in) :: tree
       real(dp), intent(in)   :: time
       real(dp)               :: amplitude
     end function field_func
 
     logical function bool_subr(tree, time)
       import
       type(af_t), intent(in) :: tree
       real(dp), intent(in)   :: time
     end function bool_subr
 
     subroutine generic_subr(tree, time)
       import
       type(af_t), intent(in) :: tree
       real(dp), intent(in)   :: time
     end subroutine generic_subr